AMBER Archive (2009)

Subject: RE: [AMBER] trajout problem

From: Anna Reymer (reymer_at_chalmers.se)
Date: Tue Dec 01 2009 - 07:23:22 CST

Dear all,
Thanks a lot for your help Daniel and Carlos!
The solution to my problem was to change the input file, the new input file is:

polyA-polyT 10-mer + Ru_phen2_dppz: 1ns MD
 &cntrl
  imin = 0, irest = 0, 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, ig= -1,
  nstlim = 500000, dt = 0.002,
  ntpr = 100, ntwx = 100, ntwr = 1000
 /

The problem was in irest flag, which was set up to 1meaning that the velocities should be read from the rst file.
However, trajout produces rst files with zero velocities, and that is why one should invoke random generator with the ig option. (Thanks ones more Daniel)
 
Best regards,
Anna

________________________________________
From: amber-bounces_at_ambermd.org [amber-bounces_at_ambermd.org] On Behalf Of Daniel Roe [droe_at_nist.gov]
Sent: Tuesday, December 01, 2009 1:34 PM
To: AMBER Mailing List
Subject: Re: [AMBER] trajout problem

Hi Anna,

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
initial temperature.

Good luck!

-Dan

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
> &cntrl
> 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.
>
> /Anna
> ________________________________________
> 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.
>>
>> Regards,
>> Anna
>>
>> -----------
>> Anna Reymer, PhD student
>> Physical Chemistry,
>> Department of Chemical and Biological Engineering
>> Chalmers University of Technology
>> Kemivägen 10
>> SE-412 96 Gothenburg
>> Sweden
>>
>> Phone: +46-(0)31-7722815
>> _______________________________________________
>> AMBER mailing list
>> AMBER_at_ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>>
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--
Daniel R. Roe, Ph.D.
Research Chemist
National Institute of Standards and Technology
100 Bureau Drive, Stop 8443
Gaithersburg, MD 20899-8443
(301) 975-8741

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