- Posts: 23
number of frames in the resulting XTC file
- Boccardo
-
Topic Author
- Visitor
7 years 2 months ago #7117
by Boccardo
number of frames in the resulting XTC file was created by Boccardo
Hi all,
I'm trying to figure out how to save N frames in the xtc mdp output file.
These are the parameters I used in order to simulate 100ns.
dt = 0.020
nsteps = 5000000
nstxout = 0
nstvout = 0
nstfout = 0
nstlog = 1000
nstenergy = 1000
energygrps =
nstcalcenergy = 100
nstxout-compressed = 10000
compressed-x-precision = 100
compressed-x-grps =
With these parameters I'm saving a frame every 10000 steps, isn't it? So I have 5000000 steps and I'm expecting 500 frames.
So why my overall xtc trajctory is made of only 52 frames?
Is there someone can help me in order to understand where I made a mistake?
Thank you in advance,
Silvia
I'm trying to figure out how to save N frames in the xtc mdp output file.
These are the parameters I used in order to simulate 100ns.
dt = 0.020
nsteps = 5000000
nstxout = 0
nstvout = 0
nstfout = 0
nstlog = 1000
nstenergy = 1000
energygrps =
nstcalcenergy = 100
nstxout-compressed = 10000
compressed-x-precision = 100
compressed-x-grps =
With these parameters I'm saving a frame every 10000 steps, isn't it? So I have 5000000 steps and I'm expecting 500 frames.
So why my overall xtc trajctory is made of only 52 frames?
Is there someone can help me in order to understand where I made a mistake?
Thank you in advance,
Silvia
Please Log in or Create an account to join the conversation.
- jbarnoud
-
- Offline
- Admin
Less
More
7 years 2 months ago #7119
by jbarnoud
Replied by jbarnoud on topic number of frames in the resulting XTC file
Hi Silvia,
Indeed, you should get 500 frames in your XTC file (501 with the initial frame). Did your simulation finished? It could be that your simulation ended prematurely. Are you sure these are actually the options you used? They should be summarized in the log file, you can also check them by using "gmx dump" on the TPR file.
Regards,
Jonathan
Indeed, you should get 500 frames in your XTC file (501 with the initial frame). Did your simulation finished? It could be that your simulation ended prematurely. Are you sure these are actually the options you used? They should be summarized in the log file, you can also check them by using "gmx dump" on the TPR file.
Regards,
Jonathan
Please Log in or Create an account to join the conversation.
- Boccardo
-
Topic Author
- Visitor
7 years 2 months ago #7122
by Boccardo
Replied by Boccardo on topic number of frames in the resulting XTC file
Hi Jonathan,
thank you for your quick reply!
Yes, I'm sure that the simulation ended properly since the mdrun reach the final step 5000000. I'm also sure about the options, I post here the relative part of the log file.
integrator = md
tinit = 0
dt = 0.02
nsteps = 5000000
init-step = 0
simulation-part = 1
comm-mode = Linear
nstcomm = 100
bd-fric = 0
ld-seed = 1118318013
emtol = 10
emstep = 0.01
niter = 20
fcstep = 0
nstcgsteep = 1000
nbfgscorr = 10
rtpi = 0.05
nstxout = 0
nstvout = 0
nstfout = 0
nstlog = 1000
nstcalcenergy = 100
nstenergy = 1000
nstxout-compressed = 10000
compressed-x-precision = 100
I really do not understand why I get 52 frames instead of 500.
Thank you again.
Silvia
thank you for your quick reply!
Yes, I'm sure that the simulation ended properly since the mdrun reach the final step 5000000. I'm also sure about the options, I post here the relative part of the log file.
integrator = md
tinit = 0
dt = 0.02
nsteps = 5000000
init-step = 0
simulation-part = 1
comm-mode = Linear
nstcomm = 100
bd-fric = 0
ld-seed = 1118318013
emtol = 10
emstep = 0.01
niter = 20
fcstep = 0
nstcgsteep = 1000
nbfgscorr = 10
rtpi = 0.05
nstxout = 0
nstvout = 0
nstfout = 0
nstlog = 1000
nstcalcenergy = 100
nstenergy = 1000
nstxout-compressed = 10000
compressed-x-precision = 100
I really do not understand why I get 52 frames instead of 500.
Thank you again.
Silvia
Please Log in or Create an account to join the conversation.
- jbarnoud
-
- Offline
- Admin
Less
More
- Posts: 23
7 years 2 months ago #7123
by jbarnoud
Replied by jbarnoud on topic number of frames in the resulting XTC file
Maybe you can try running "gmx check" on your trajectory.
Please Log in or Create an account to join the conversation.
Time to create page: 0.099 seconds