1. General topics
  3. mdp Options
  5. md.mdp

normal md.mdp

  • kayanizd
  • kayanizd's Avatar Topic Author
  • Offline
  • Fresh Boarder
More
11 years 5 months ago #1232 by kayanizd
md.mdp was created by kayanizd
Hi,
I work on a two chain protein( A: 21 a.a., B: 30 a.a.), two chains link with two disulfide bonds. I did all steps of coarse-grain running which is for protein in water and set steps for 3 micro-second, but when I checked the pressure it was "-8 bar" in 3 micro-second while I had set it as 1 bar, so I want ask you what should I do to equilibrate the pressure as 1 bar.
"the temperature 298k"
"the pressure 1bar"
the mdp that I used was,
================================================

tcoupl = Berendsen

tc-grps = system
tau_t = 1.0
ref_t = 298
Pcoupl = berendsen
Pcoupltype = isotropic
tau_p = 1.0
compressibility = 3e-4
ref_p = 1.0

gen_vel = no
gen_temp = 298
gen_seed = 473529

Yours Sincerely
Zahra Kayani

Please Log in or Create an account to join the conversation.

More
11 years 5 months ago #1233 by xavier
Replied by xavier on topic md.mdp
It is not clear what could be wrong! Did you visually checked the simulation? Any water freezing?

kayanizd wrote: Hi,
I work on a two chain protein( A: 21 a.a., B: 30 a.a.), two chains link with two disulfide bonds. I did all steps of coarse-grain running which is for protein in water and set steps for 3 micro-second, but when I checked the pressure it was "-8 bar" in 3 micro-second while I had set it as 1 bar, so I want ask you what should I do to equilibrate the pressure as 1 bar.

"the temperature 298k"
"the pressure 1bar"
the mdp that I used was,
================================================

tcoupl = Berendsen

tc-grps = system
tau_t = 1.0
ref_t = 298
Pcoupl = berendsen
Pcoupltype = isotropic
tau_p = 1.0
compressibility = 3e-4
ref_p = 1.0

gen_vel = no
gen_temp = 298
gen_seed = 473529

Yours Sincerely
Zahra Kayani

Please Log in or Create an account to join the conversation.

  • kayanizd
  • kayanizd's Avatar Topic Author
  • Offline
  • Fresh Boarder
More
11 years 5 months ago #1241 by kayanizd
Replied by kayanizd on topic md.mdp
Hi‏,‏
No, I did not check, But I only with this command check the pressure‏.‏
‏>> ‏g_energy -f traj.xtc -s topol.tpr -o pressure.xvg
and then it was -8 bar‎‏.‏

Yours Sincerely
Zahra Kayani

Please Log in or Create an account to join the conversation.

  • kayanizd
  • kayanizd's Avatar Topic Author
  • Offline
  • Fresh Boarder
More
11 years 5 months ago #1242 by kayanizd
Replied by kayanizd on topic md.mdp
Hi‏,‏
No, I did not check, But I only with this command check the pressure‏.‏
‏>> ‏g_energy -f traj.xtc -s topol.tpr -o pressure.xvg
and then it was -8 bar‎‏.‏

Yours Sincerely
Zahra Kayani

Please Log in or Create an account to join the conversation.

More
11 years 5 months ago #1248 by djurre
Replied by djurre on topic md.mdp
Even though Xavier's post did sound like a question, he was actually SUGGESTING that you should CHECK visually for freezing of water.

Please Log in or Create an account to join the conversation.

More
10 years 7 months ago #1962 by nivedita
Replied by nivedita on topic md.mdp
Hi all,
I want to run cg simulation in gromacs 4.5.5 using martini V2.1. It is not membranous one.my steps are as follows
1../martinize.py -f protein.pdb -x cg.pdb -o system.top -dssp /usr/local/dssp-2.0.4-linux-i386 -p backbone -pf 5000 -cys 1
it create Protein.itp, cg.pdb and system.top files. after that i open Protein.itp and did some modification like before constraint i wrote #ifdef EM then i copy paste constraint and repalce residue name by force contant value and [constraints] by [bonds]
#ifdef EM
[ constraints ]
23 24 1 0.26500 ; VAL
31 32 1 0.26500 ; VAL...............
[ bonds ]
;stiff bonds
23 24 1 0.26500 ; 5000
31 32 1 0.26500 ; 5000........
#elsif
#endif
[ angles ]
; Backbone angles
1 3 5 2 127 25 ; GLN(C)-MET(C)-PRO(C)....
2.editconf -f cg.pdb -o box.gro -c -d 1.2 -bt cubic -bf bfact.dat -atom
3. grompp -f em.mdp -c box.gro -p system.top -o em.tpr
my em.mdp file is
Define = -DEM
integrator = steep
dt = 0.02
nsteps = 500

nstlog = 1000
nstenergy = 500
nstxtcout = 500

nstlist = 10
ns_type = grid
pbc = xyz
periodic_molecules = no
rlist = 1.4

coulombtype = Shift
rcoulomb_switch = 0.0
rcoulomb = 1.2
epsilon_r = 15
epsilon_rf = 1
vdw_type = Shift
rvdw_switch = 0.9
rvdw = 1.2

tcoupl = no
tc-grps = system
tau_t = 1.0
ref_t = 308
Pcoupl = no
Pcoupltype = isotropic
tau_p = 3.0
compressibility = 3e-4
ref_p = 1.0

then it was showing following error:
Generated 0 of the 780 non-bonded parameter combinations
Program grompp, VERSION 4.5.5
Source code file: /build/buildd/gromacs-4.5.5/src/kernel/toppush.c, line: 1631

Fatal error:
Incorrect number of parameters - found 1, expected 2 or 4 for Bond.

Question: in vacume minimization how i give bond constraint?
Is that anything wrong in my steps or parameter?

thanks in Advance,

Please Log in or Create an account to join the conversation.

More
10 years 7 months ago - 10 years 7 months ago #1968 by djurre
Replied by djurre on topic md.mdp
Constraints are defined the same in any simulation. Your mdp parameters seem reasonable for a vacuum minimization. I do see two mistakes in your itp:

[ bonds ]
;stiff bonds
23 24 1 0.26500 ; 5000


You have the semicolon between the length and the forceconstant. And:

#elsif


should be in between the bonds and constraints sections (and might be misspelled?).
Last edit: 10 years 7 months ago by djurre.

Please Log in or Create an account to join the conversation.

More
10 years 7 months ago #1973 by nivedita
Replied by nivedita on topic md.mdp
Hi djurre,
actually when i run this command:./martinize.py -f protein.pdb -x cg.pdb -o system.top -dssp /usr/local/dssp-2.0.4-linux-i386 -p backbone -pf 5000 -cys 1 after that, i modified Protein.itp file as i told you i copy paste constraint and replace the residue by FC like
#ifdef EM
[ constraints ]
23 24 1 0.26500 ; VAL
31 32 1 0.26500 ; VAL and so on
[ bonds ]
;stiff bonds
23 24 1 0.26500 ; 5000
31 32 1 0.26500 ; 5000 and so on
#elsif
#endif
this above change i did in .itp file but after running vacume minimization it was showing following error:
Generated 0 of the 780 non-bonded parameter combinations Program grompp, VERSION 4.5.5
Source code file: /build/buildd/gromacs-4.5.5/src/kernel/toppush.c, line: 1631
Fatal error:
Incorrect number of parameters - found 1, expected 2 or 4 for Bond.

my question is, By default .itp file showing different bonds constraint for backbone as well as side chains, extended side chain etc. By default force constant =1000 is it ok or i have to specify force constant using -pf and do some modification ?
how i do constraint (stiff bond) vacuum minimization?

Thanks in Advance

Please Log in or Create an account to join the conversation.

More
10 years 7 months ago #2025 by djurre
Replied by djurre on topic md.mdp
I'm not sure if I understand your question. The error is due to the semi-colons you have on every line in the bonds section. You don't have a force constant of 1000kJ/mol anywhere (I only see 5000). A bond of 5000kJ/mol is not really stiff, I would say it is intermediate.

Please Log in or Create an account to join the conversation.

More
10 years 7 months ago #2068 by nivedita
Replied by nivedita on topic md.mdp
Hi djurre,
Thanks for the reply. You are right, the error is due to semicolon but i have one doubt,how you define that the given constraint is intermediate. how i choose correct force constraint for my protein? and one more doubt i have , in .mdp file it is written that "during energy minimization the constrainst should be replaced by stiff bonds what does it means?
is it constraints= all-bonds or something else?

thanks in Advance

Please Log in or Create an account to join the conversation.

More
10 years 6 months ago #2103 by jaakko
Replied by jaakko on topic md.mdp
Hi nivedita,

nivedita wrote: how you define that the given constraint is intermediate.

First off, those are bonds not constraints. Bonds have different strengths, constraints are always just that, the md code tries to satisfy them exactly. (In theory there is a very high corresponding bond force constant but that's beside the point here.) What Djurre was pointing out is that you can try even one order of magnitude higher force constants if required.

nivedita wrote: how i choose correct force constraint for my protein?

You're using them just for energy minimzation, trial and error should work.

nivedita wrote: one more doubt i have , in .mdp file it is written that "during energy minimization the constrainst should be replaced by stiff bonds what does it means?
is it constraints= all-bonds or something else?

Something else. Ideally using an itp file with every constraint replaced with a bond of say 50000 kJ/mol should work better in energy minimization. You are already doing this but the #elseif is in a wrong place as Djurre pointed out.

Please Log in or Create an account to join the conversation.

More
7 years 5 months ago #6277 by MOURI
Replied by MOURI on topic md.mdp
Hi Sir,

I would like to run steered molecular dynamics (SMD) in my protein complex system to find out the PMF without using umbrella sampling.

In the tutorial of umbrella sampling: after equilibration, the steps are: (a) Generating Configurations: pull code are used, configurations files are generated, (b) umbrella sampling.

I am confused about the pull code: pull_coord1_type = umbrella. Will I use "pull_coord1_type= constant-force" in the mdp file?

After getting the cofigurations file, how will I find the PMF without using umbrella sampling?

Thanks in advance for the help.


Best Regards
Mouri

Please Log in or Create an account to join the conversation.

More
7 years 5 months ago #6290 by peterkroon
Replied by peterkroon on topic md.mdp
Why do you not want to use US? It is generally far more accurate than getting the PMF from a direct pulling simulation.

Reconsider using Umbrella Sampling.

If you really insist, I would (I think) still use the "umbrella" option. This puts a harmonic force between the two groups you're pulling. I'm not sure how to convert this to a PMF though (you probably need to integrate the force exerted by the pull code). You should consult the Gromacs userlist.

Peter

Please Log in or Create an account to join the conversation.

  1. General topics
  3. mdp Options
  5. md.mdp
Time to create page: 0.120 seconds