[gmx-users] Follow up (How to define pull-init for two pull groups) How to concatenate pullx.xvg files
Rini Gupta
rinisgupta at gmail.com
Thu Feb 20 00:08:38 CET 2014
Dear gmx-users,
Thanks for the nice suggestion.
-noappend option in mdrun works fine and
I have successfully extended the simulation of each of the umbrella
sampling windows (Total 44 windows with spacing of 0.1 nm) up to 25ns in
steps of 5ns.
So, now I have 5 sets of .tpr, .xvg files corresponding to each umbrella
sampling window for 25 ns simulation.
Now, in order to get PMF following tutorial, I ran g_wham command as:
g_wham_mpi_d -it tpr-files.dat -if pullf-files.dat -sym -o profilejsym.xvg
-hist histojsym.xvg -unit kJ
I have prepared the list of .tpr files, pullf.xvg and pullx.xvg file
corresponding to last run ( i.e 20 ns to 25 ns ) for each of the umbrella
sampling.
How can I concatenate .tpr , pullf.xvg and pullx.xvg for full 25ns
length of simulation run. Is there some gromacs tool like trjcat for
joining .xvg files?
I have searched across mailing list but did not get any satisfactory answer
of this question except the use of -b and -e option in g-wham command.
However, considering only last frames of each of the umbrella window , I
got PMF which have some broken points especially near centre of the lipid
bilayer.
Can anyone please tell is this an artefact of poor sampling or real nature
of the system.
The other output histo.xvg, shows sufficient overlap between each of the
umbrella sampling windows, but it looks noisy.
Here, I have used the default value of number of bins in histogram i.e.
200. Is this correct?
Please find attached here with profile.xvg and histo.xvg
Please suggest me if this is right or I should further extend these
simulation in order to get better convergence.
Best Regards,
Rini
>
>
>
> On 1/17/14, 8:06 PM, Rini Gupta wrote:
>
>> Dear gmx-users,
>>
>> Thanks for the reply.
>>
>> That means if I will use the frames generated by script
>> (setup-umbrella.py)
>> it will not generate a sufficient overlap between adjacent
>> windows for this system?
>>
>
> What I'm saying is that I know the scripts, input files, etc. work as
> advertised for the system in the tutorial. They may or may not work for
> any other system you may create. That's up to you do evaluate.
>
>
> So, In order to extract starting window structures for umbrella sampling
>> of
>> my system I prepared a list of frames at a distance of 0.1 nm
>> including frames where distance between reference group and pull group is
>> decreasing in steps of 0.1 nm and then increasing by same amount.
>> Please let me know if this is right.
>>
>>
> Whether or not something is "right" depends on whether or not it works.
> In the case of umbrella sampling, that means the sampling overlap is
> adequate. Again, that is for you to judge.
>
>
> Then, in order to equilibrate each of these initial configuration, I use
>> the following .mdp settings (as given by tutorial)
>>
>>
>> ; Pull code
>>> pull = umbrella
>>> pull_geometry = position ;
>>> pull_dim = N N Y
>>> pull_start = yes ; define initial COM distance > 0
>>> pull_ngroups = 2
>>> pull_group0 = cbilayer ; center of carbon's of bilayer
>>> pull_group1 = phosup ; phosphate atom of 16th PEPC in top
>>> pull_pbcatom1 = 0
>>> pull_vec1 = 0.0 0.0 -1.0
>>> pull_init1 = 0 0 0
>>> pull_rate1 = 0 ; no pulling
>>> pull_k1 = 1000 ; kJ mol^-1 nm^-2
>>> pull_group2 = phoslow ; phosphate atom of 56th PEPC in bottom
>>> pull_pbcatom2 = 0
>>> pull_vec2 = 0.0 0.0 1.0
>>> pull_init2 = 0 0 0
>>> pull_rate2 = 0 ; no pulling
>>> pull_k2 = 1000 ; kJ mol^-1 nm^-2
>>> pull_nstxout = 100 ; every 2 ps
>>> pull_nstfout = 100 ; every 2 ps
>>>
>>>
>>> After equilibration of 4 ns, if I want to extend these runs for longer
>> time using tpbconv:
>>
>> # tpbconv_mpi_d -f npt0.trr -s npt0.tpr -e npt0.edr -n index.ndx -extend
>> 2000 -o npt0.tpr
>> # mdrun_mpi_d -s npt0.tpr -cpi npt0.cpt -deffnm ${MDRUN_RUN_NAME}
>>
>> ------------------------------------------------------------
>> ----------------------------------------------------------
>> Program tpbconv_mpi_d, VERSION 4.6.2
>> Source code file: /home/roman/gromacs-4.6.2/src/gmxlib/index.c, line:
>> 1192
>>
>> Fatal error:
>> Cannot read from input
>> and
>> Program mdrun_mpi_d, VERSION 4.6.2
>> Source code file: /home/roman/gromacs-4.6.2/src/gmxlib/checkpoint.c,
>> line:
>> 2118
>>
>> Fatal error:
>> Can't read 34580 bytes of 'npt0.xvg' to compute checksum. The file has
>> been
>> replaced or its contents have been modified. Cannot do appending because
>> of
>> this condition.
>> ------------------------------------------------------------
>> ------------------------------------------------------------
>> ----------------------------
>> Please let me what is wrong here, I did not modify any file after 4 ns and
>> I have been successfully extending normal simulation runs (without pull
>> code) using these settings.
>> So, I guess here problem is related to
>> generation of *.xvg file.
>> How to supply this file to tpbconv? I have searched on mailing list but
>> didn't get any satisfactory answer for extending equilibration or even
>> production runs (which generate pullf.xvg and pullx.xvg files)
>> for these umbrella sampling simulations.
>>
>>
> I seem to recall appending to .xvg files is broken. Just use the
> -noappend option of mdrun.
>
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>
> ==================================================
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