[gmx-users] mdp file

He, Yang yang.he at mavs.uta.edu
Fri Nov 7 15:31:16 CET 2008

Hi Mark,

This is what I got when I use the command gmxcheck:

Checking file traj.trr
trn version: GMX_trn_file (single precision)
Reading frame       0 time    0.000
# Atoms  34
Last frame          1 time    0.100

Item        #frames Timestep (ps)
Step             2    0.1
Time             2    0.1
Lambda           2    0.1
Coords           2    0.1
Velocities       2    0.1
Forces           0
Box              2    0.1

Also, I have tried to increase  the value of nsteps to 10000, but no change happened still just the static figure.

I really got stuck about that.

Hope to get your further suggestions,

Thank you .


From: gmx-users-bounces at gromacs.org [gmx-users-bounces at gromacs.org] On Behalf Of Mark Abraham [Mark.Abraham at anu.edu.au]
Sent: Thursday, November 06, 2008 3:52 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] mdp file

He, Yang wrote:
> Hi all users,
> When I use the command "mdrun -tablep table.xvg " to run my model in gromacs,  it always shows that:
> starting mdrun 'DNA in water'
> 10000 steps,     20.0 ps.

This is orders of magnitude too short to expect a large conformational
change to happen. Think nanoseconds at least. Depending on the number of
base pairs, think much more than that. You should be aware of how long
this might take, since you've read some literature about MD on DNA, right?

> Warning: 1-4 interaction between 11 and 19 at distance 1.437 which is larger than the 1-4 table size 1.000 nm
> These are ignored for the rest of the simulation
> This usually means your system is exploding,
> if not, you should increase table-extension in your mdp file

Don't ignore warnings unless you know what they mean and it's OK. See

> And no more information . Furthermore, I use the command ngmx to look at the trajectory , I found that  only when I set the value of nsteps by 10,  will there be little animation about my DNA two strands' disassociation . While I try to reduce the value of dt , nstdisreout , nstorireout and nstdihreout , it also did not work and I can not see any disassociation of DNA strands  using the command "ngmx".

Probably, you only wrote one frame before it crashed. Does the log file
look like it terminated normally after 10000 steps? Use gmxcheck to see
how many frames you have in the trajectory file.

> Also, what I got confused is that when I set the value of nsteps larger than 10, there is just static figure about DNA model.  This is my part of mdp file

1) You need the simulation not to crash
2) You need to simulate for long enough (nsteps) to see a change
3) You need to write output (nstxout or nstxtcout) sufficiently often to
keep yourself happy.

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