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normal simulation blow up in the protein in water simulation

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11 years 3 months ago - 11 years 3 months ago #1355 by junfeng
simulation blow up in the protein in water simulation was created by junfeng
I am following the protein in water tutorial. After I solvated ubiquitin in water, I carried out minimization and position restraint simulation with the given em.mdp and md.mdp file. But during minimization, the water went scattered (I can see some empty space using vmd). position restraint simulation crash because of failure of LINCS constraint which indicates the system blows up.
The solvated ubiquitin in water looks fine. But the minimized pdb has empty spaces in water. There must be some errors but I could not figure out what went wrong.
Additional Qs:
How to use stiff bond for minimization? I do not know what it corresponds to in mdp file.
Do I need to add ions to the system to make it neutral for martini simulation?

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11 years 3 months ago #1359 by djurre
Replied by djurre on topic simulation blow up in the protein in water simulation
Scattering water: Hard to say what is happening, but could it be the the order of molecules in the top and gro/pdb file is different? And does the water in the solvated structure look normal, eg no areas where the density of the water is higher then else where?

Stiff bonds for minimization: Do you mean replacing constraints by stiff bonds during minimization? In my experience that is not really needed in most situations.

Adding ions: Neutralizing your systems doesn't hurt.

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11 years 3 months ago #1363 by junfeng
Replied by junfeng on topic simulation blow up in the protein in water simulation
I checked the gro file, protein first then water.
In the top file:
#include "martini_v2.1.itp"
#include "Protein_A.itp"

[ system ]
; name
Martini system from 1UBQ.pdb

[ molecules ]
; name number
Protein_A 1
W 890

As I said the solvated structure looks normal, Ubiquitin is at the center of box surrounded by W. the water density looks even everywhere. I pasted the gro file so maybe people can find sth wrong there.
I am able to run protein alone in vacumm without error for 500000 steps. I am able to run water box alone without error for 116100 steps. But when I run protein in water, something went wrong within a few thousand steps.
I noted in mdp file of protein simulation, I cannot put Protein_A as energygrps. I got error messages when "grompp". Why?
How can I add ions to solvated box? Can you give me an example of gromacs command?
Here is the gro file of protein in water:

Warning: Spoiler! [ Click to expand ]

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11 years 3 months ago #1367 by djurre
Replied by djurre on topic simulation blow up in the protein in water simulation
The gro and top files look fine, so there is probably something wrong with your mdp options (or the Protein_A.itp). Did you change anything compare to the tutorial files?
You can't use Protein_A as a group, because it is not one of the groups grompp recognizes by default. Just 'Protein' should work.

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11 years 3 months ago #1370 by junfeng
Replied by junfeng on topic simulation blow up in the protein in water simulation
Here are some of the observations:
1. If I do minimization too long(I know we do not have to, but it is a testcase), lets say 5000 steps, I can see water becomes scattered in the box and create vacumm space. Why? I am just curious to know.
2. I only get mdrun error when applying position restraint. I just put "define = -DPOSRES" as one line in the mdp file:

define = -DPOSRES

integrator = md
tinit = 0.0
dt = 0.02
nsteps = 5000
....

Error messages are:
Program mdrun, VERSION 4.5.5
Source code file: /tmp/build/gromacs-4.5.5/src/mdlib/domdec.c, line: 3266

Software inconsistency error:
Inconsistent DD boundary staggering limits!
For more information and tips for troubleshooting, please check the GROMACS
website at www.gromacs.org/Documentation/Errors

The Protein_A.itp file has those lines defining position restraints:
#ifdef POSRES
#ifndef POSRES_FC
#define POSRES_FC 1000.00
#endif
[ position_restraints ]
1 1 POSRES_FC POSRES_FC POSRES_FC
3 1 POSRES_FC POSRES_FC POSRES_FC
5 1 POSRES_FC POSRES_FC POSRES_FC
....


Anything I am doing wrong? When I remove the line, mdrun runs fine.

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