AMBER Archive (2009)

Subject: Re: [AMBER] creating a restart file from md.out

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Tue Feb 03 2009 - 07:36:44 CST

why did you do the
>n-dodecane.rest
??
this sends the ptrajout output to that file, overwriting the restart
file that you make in the trajout command.
send the ptraj output to a different fil;e, and make sure to read the
ptraj output carefully, noting any errors or warnings and make sure
that the output from ptraj looks like what you expect from the
commands that you gave. ptraj is very good about telling you what it
thinks you asked it to do.

On Tue, Feb 3, 2009 at 8:22 AM, oguz gurbulak <gurbulakoguz_at_gmail.com> wrote:
> I created a ptraj input file as you said and run the script writing:
> ptraj n-dodecane.prmtop < ptraj.in > n-dodecane.rest , but I couldn't get
> the n-dodecane.rest file. Could you help me about it ?
>
> Thanks in advance.
>
> ptraj.in
>
> trajin n-dodecane.equ.mdcrd 726000 726000
> trajout n-dodecane.rest restart
>
> 2009/2/3 Carlos Simmerling <carlos.simmerling_at_gmail.com>
>
>> the mdout file does not have coordinate information. that is in the mdcrd
>> file.
>> if you wrote to the mdcrd file at this step (if depends on your
>> setting of ntwx), then
>> you can use ptraj trajin/trajout to extract that frame to a restart file.
>>
>> let's say you want to extract frame 726 (your nstep is 726000 and
>> perhaps you set ntwx to 1000)
>> then you can do this inside a ptraj script
>>
>> trajin mdout 726000 726000
>> trajout filename restart
>>
>> along with all of the other things needed for running ptraj, this is
>> just part but I assume you've already learned ptraj)
>>
>>
>>
>> On Tue, Feb 3, 2009 at 5:44 AM, oguz gurbulak <gurbulakoguz_at_gmail.com>
>> wrote:
>> > Dear All,
>> >
>> > I want to extract the output informations for NSTEP = 726000 in target
>> > Density =0.7636 , create a restart file for input and start a md from
>> this
>> > point with little time steps. Is
>> > it possible to do this in Amber ? If so, what should I do to do this
>> > operation ?
>> >
>> >
>> >
>> > NSTEP = 726000 TIME(PS) = 1452.000 TEMP(K) = 271.69 PRESS =
>> > 350.4
>> > Etot = 3756.1288 EKtot = 2374.7495 EPtot =
>> > 1381.3794
>> > BOND = 346.1359 ANGLE = 1656.2278 DIHED =
>> > 677.9015
>> > 1-4 NB = 456.8660 1-4 EEL = 384.6550 VDWAALS =
>> > -1729.3428
>> > EELEC = -411.0640 EHBOND = 0.0000 RESTRAINT =
>> > 0.0000
>> > EKCMT = 73.3705 VIRIAL = -206.8362 VOLUME =
>> > 37038.6242
>> > Density =
>> > 0.7636
>> > Ewald error estimate: 0.4255E-04
>> > _______________________________________________
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>> > AMBER_at_ambermd.org
>> > http://lists.ambermd.org/mailman/listinfo/amber
>> >
>>
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