Dear All,
According to
"http://www.gromacs.org/Documentation/How-tos/Extending_Simulations" , the
commands for extending MD are:
tpbconv -s previous.tpr -extend timetoextendby -o next.tpr
mdrun -s next.tpr -cpi previous.cpt
But if you read
"http://www.gromacs.org/Documentation/File_Formats/Checkpoint_File";, it suggest
for extension of MD, state.cpt should be used. But if we use state.cpt for
extension, in
"
tpbconv -s previous.tpr -extend timetoextendby -o next.tpr
mdrun -s next.tpr -cpi previous.cpt
"
the "previous" in previous.tpr in tpbconv will be conflicting with "previous"
in previous.cpt in mdrun.
In addition in command
"
trjconv -s md_0_1.tpr -f md_0_1.xtc -o md_0_1_noPBC.xtc -pbc mol -ur compact
"
can we change md_0_1.xtc to traj.xtc?
I am looking forward to getting a clarification from you.
Cheers,
Acoot
________________________________
From: Mark Abraham <[email protected]>
To: Discussion list for GROMACS users <[email protected]>
Sent: Wednesday, 4 April 2012 6:56 PM
Subject: Re: [gmx-users] the -extend function of the tpbconv command
On 4/04/2012 6:24 PM, Acoot Brett wrote:
Hi Justin and All,
>
>The on-line document on "Extending Simulations" writes,
>
>"You might want to use the -append option of mdrun to append the new output to
>the old files. Note that this will only work when the old output files have
>not been modified by the user. Appending is the default behavior as of version
>4.5."
>
>We can see "Appending is the default behavior as of version 4.5", and what I
>use is version 4.5. Thus for mdrun, even without mention "-append " appending
>should be automatically done.
>
>In addition, after the old output files were created, I only use the "trjconv"
>to process them, and I did not modify them.
Any change is enough to prevent appending. mdrun computed a checksum
when it wrote them, saved the checksums in the checkpoint file, and
demands that newly-computed ones match when attempting to append
later. Use only the original trajectory files when attempting to
append.
Mark
>Thus the reason why the extended part output files were not automatically
>appended to my original old outputfiles according to what I have done (tpbconv
>-s previous.tpr -extend timetoextendby -o next.tpr mdrun -s next.tpr
>-cpi previous.cpt) is still unclear.
>
>Will you please give an explaination?
>
>Cheers,
>
>Acoot
>
>
>From: Justin A. Lemkul <[email protected]>
>To: Acoot Brett <[email protected]>; Discussion list for GROMACS users
><[email protected]>
>Sent: Wednesday, 4 April 2012 10:36 AM
>Subject: Re: [gmx-users] the -extend function of the tpbconv command
>
>
>
>Acoot Brett wrote:
>> Dear All,
>> I have completed a 1ns production MD. Then I
intended to extend it for another 1 ns.
>> I use command
>> "tpbconv -s previous.tpr -extend
timetoextendby -o next.tpr
>> mdrun -s next.tpr -cpi previous.cpt"
>> I think the results will be automatically
attended to previous md_0_1.tpr and
md_0_1_noPBC.xtc.
>>
>
>Only if you then run mdrun -append and the files
are appended. tpbconv doesn't do any of this for
you, it just creates a new run input file capable
of running a longer simulation. The fact that you
have a file called "md_0_1_noPBC.xtc" seems like
you've manipulated it in some way, so you
shouldn't (and likely can't) append to it. You
should append to your original files.
>
>> Then I use "g_rms -s md_0_1.tpr -f
md_0_1_noPBC.xtc -o rmsd.xvg -tu ns" to get the
rmsd.xvg file. Then I use "xmgrace -nxy
potential.xvg" to display it. However I find for
the curve the x-axis is from 0 ns to 1 ns, not
from 0 ns to 2 ns.
>>
>
>If you haven't run a new simulation, you'll only
have the data that already exists.
>
>> The definition of "-extend" of the command
"tpbconv" is "Extend runtime by this amount (ps)".
Thus the commands I used are correct.
>>
>
>You haven't shown us your actual tpbconv command,
so there's no way to verify that. In any case,
tpbconv doesn't actually extend the simulation,
mdrun does.
>
>> Will you please tell me how to process for
the extension MD so that the curve of the rmsd.xvg
(and all the other xvg files) will have x-axis
from the 0 to the 2 ns (2 ns is the total MD time,
including the 1 ns extended part)?
>>
>
>There are two steps here:
>
>http://www.gromacs.org/Documentation/How-tos/Extending_Simulations#Version_4
>
>You need to do both.
>
>-Justin
>
>-- ========================================
>
>Justin A. Lemkul
>Ph.D. Candidate
>ICTAS Doctoral Scholar
>MILES-IGERT Trainee
>Department of Biochemistry
>Virginia Tech
>Blacksburg, VA
>jalemkul[at]vt.edu | (540) 231-9080
>http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
>========================================
>
>
>
>
>
>
>
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