AMBER Archive (2009)
Subject: Re: [AMBER] trajout problem
From: Daniel Roe (droe_at_nist.gov)
Date: Tue Dec 01 2009 - 06:34:34 CST
The way to generate your restart file with ptraj should just be:
trajin md_2_complex.mdcrd 4243 4243
trajout complex.rst restart
Since you have specified that this is a periodic system (ntb > 0) the
box information has to be in the restart file. Also, you shouldn't need
the append flag - you could potentially be writing the same coordinates
over and over to the same file. A quick way to make sure the restart
file you have generated is viable is to try and visualize it using VMD
or whatever your favorite program is.
Also, I noticed that in your input file you have ntx = 7 and irest = 1.
This specifies that you want to use the velocities specified in the
restart file. Since you are using a restart generated with ptraj, the
velocities of all of your atoms 0.0, meaning your system is essentially
going to start at 0 K. This may cause problems with your simulation. I
recommend if you're going to use a restart from ptraj you set irest to 0
and set the 'ig' option (seed for random # generator). This will give
the atoms in your system velocities consistent with your specified
Anna Reymer wrote:
> Thanks a lot Carlos for your quick response.
> Well, I do have periodic box. I tried 'nobox' option just to see whether it will produce something else. Initially I was not using 'nobox', however the rst file produced then and gave no output with sander as well.
> The input file is the following:
> GCGAATTGCG + Ru_phen2_dppz: 1ns MD
> imin = 0, irest = 1, ntx = 7,
> ntb = 2, pres0 = 1.0, ntp = 1,
> taup = 2.0,
> cut = 10, ntr = 0,
> ntc = 2, ntf = 2,
> tempi = 300.0, temp0 = 300.0,
> ntt = 3, gamma_ln = 1.0,
> nstlim = 500000, dt = 0.002,
> ntpr = 100, ntwx = 100, ntwr = 1000
> And yes, I am using the same topology file and the same mdin file as I used to generate the previous trajectories.
> Thanks again for help.
> From: amber-bounces_at_ambermd.org [amber-bounces_at_ambermd.org] On Behalf Of Carlos Simmerling [carlos.simmerling_at_gmail.com]
> Sent: Monday, November 30, 2009 1:09 PM
> To: AMBER Mailing List
> Subject: Re: [AMBER] trajout problem
> the second half is velocities, and since there are none in the trajectory
> file, ptraj just adds zeros. this should not cause sander to get stuck
> though, just means the velocities are zero.
> it's hard to know what's wrong with the little information you have given.
> is the system periodic? I assume no, since you say "nobox". what is your
> input file? are you using the same setup as the one used to generate the
> trajectory file? (meaning same prmtop, same mdin file)
> On Mon, Nov 30, 2009 at 7:03 AM, Anna Reymer <reymer_at_chalmers.se> wrote:
>> Dear All,
>> I have the following problem.
>> When I try to run MD where I use my complex.rst as an input coordinates
>> file and Sander produces no output files, neither trajectory file, nor
>> restart file and the out file is just empty.
>> I have tested the input and topology files and they are fine, and the
>> problem seems to be in the restart file.
>> I produce the restart file from a trajectory file, using ptraj script:
>> trajin md_2_complex.mdcrd 4243 4243
>> trajout complex.rst restart nobox append
>> I guess the problem is in initial rst file, which, for some strange reason,
>> contains just columns of zeroes in the second half.
>> Has anybody any advice? Thanks in advance.
>> Anna Reymer, PhD student
>> Physical Chemistry,
>> Department of Chemical and Biological Engineering
>> Chalmers University of Technology
>> Kemivägen 10
>> SE-412 96 Gothenburg
>> Phone: +46-(0)31-7722815
>> AMBER mailing list
> AMBER mailing list
> AMBER mailing list
Daniel R. Roe, Ph.D.
National Institute of Standards and Technology
100 Bureau Drive, Stop 8443
Gaithersburg, MD 20899-8443
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