Dear Justin,<div><br></div><div>I have set 1.5 dodecahedron. i centered the complex in box.</div><div>complex.gro,
complexsol.gro and complex_sol_ions.gro seems inside in box. I m using
VMD for visualization. i have rotated it in 3D</div>
<div>while when after EM step, i visualize em.gro then half complex
seems outside the box. is there any way to center em.gro after energy
minimization?</div><br>I have attached the snapshots. Kindly see and suggest me that is it correct and should I continue with equilibrium step?<br><br>Kindly help me out...<br><br><div class="gmail_quote">On Thu, Nov 17, 2011 at 6:21 PM, <span dir="ltr"><<a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>></span> wrote:<br>
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Today's Topics:<br>
<br>
1. Regarding cosine content (bipin singh)<br>
2. Re: Strange problem.complex out of Box after EM (Justin A. Lemkul)<br>
3. Re: Umbrella Sampling - Justin tutorial (Steven Neumann)<br>
4. Re: Regarding cosine content (Tsjerk Wassenaar)<br>
5. Re: Regarding cosine content (bipin singh)<br>
6. Cuda not detected (Andrzej Rzepiela)<br>
7. Re: Regarding TIP4P structure (Justin A. Lemkul)<br>
<br>
<br>
----------------------------------------------------------------------<br>
<br>
Message: 1<br>
Date: Thu, 17 Nov 2011 16:52:48 +0530<br>
From: bipin singh <<a href="mailto:bipinelmat@gmail.com">bipinelmat@gmail.com</a>><br>
Subject: [gmx-users] Regarding cosine content<br>
To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
Message-ID:<br>
<<a href="mailto:CAKb2Z-FhAfSZ6KCRmLsQVQJqwbA0c_iNQdCgQAh2huOxGGwrMQ@mail.gmail.com">CAKb2Z-FhAfSZ6KCRmLsQVQJqwbA0c_iNQdCgQAh2huOxGGwrMQ@mail.gmail.com</a>><br>
Content-Type: text/plain; charset=ISO-8859-1<br>
<br>
Hello all,<br>
<br>
I have done PCA from 50ns long trajectory for two similar proteins<br>
(length 180 aa and RMSD 0.2 A).<br>
The equilibration time and final simulation condition were identical<br>
for both the protein.<br>
But when I checked the cosine content for PC1 for both proteins they<br>
were 0.9 and 0.5 respectively.<br>
What can be the reason for this huge difference in cosine content of<br>
the two proteins ?<br>
<br>
<br>
--<br>
-----------------------<br>
Regards,<br>
Bipin Singh<br>
<br>
<br>
------------------------------<br>
<br>
Message: 2<br>
Date: Thu, 17 Nov 2011 06:51:43 -0500<br>
From: "Justin A. Lemkul" <<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>><br>
Subject: Re: [gmx-users] Strange problem.complex out of Box after EM<br>
To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
Message-ID: <<a href="mailto:4EC4F54F.6060800@vt.edu">4EC4F54F.6060800@vt.edu</a>><br>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed<br>
<br>
<br>
<br>
Saba Ferdous wrote:<br>
> Dear Gromacs users<br>
><br>
> I am trying to simulate a protein complex. That complex has been<br>
> obtained after protein-protein docking.<br>
><br>
> I have geneated topology, defined box and solvate, added ions<br>
> successfully. My complex is centered in box.<br>
><br>
> but when I performed Energy minimization then my protein complex comes<br>
> out of box from one side.<br>
><br>
> can any body help me in fixing this problem so that i could proceed<br>
> towards equilibrium steps..<br>
><br>
<br>
There is no problem. It is odd that EM would cause periodicity issues, but<br>
suggests that your protein is not centered properly or that your box is not<br>
large enough to accommodate it. There may be some inconvenience for<br>
visualization (which can be fixed), but there is no such thing as "outside" in a<br>
periodic system.<br>
<br>
<a href="http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions" target="_blank">http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions</a><br>
<br>
-Justin<br>
<br>
--<br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | <a href="tel:%28540%29%20231-9080" value="+15402319080">(540) 231-9080</a><br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
========================================<br>
<br>
<br>
------------------------------<br>
<br>
Message: 3<br>
Date: Thu, 17 Nov 2011 11:55:31 +0000<br>
From: Steven Neumann <<a href="mailto:s.neumann08@gmail.com">s.neumann08@gmail.com</a>><br>
Subject: [gmx-users] Re: Umbrella Sampling - Justin tutorial<br>
To: <a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>, Discussion list for GROMACS users<br>
<<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
Message-ID:<br>
<CAKZJqQG+oGcdDWLUPtNoONK=4igAZDJW518hP7=<a href="mailto:zB2CND97PPw@mail.gmail.com">zB2CND97PPw@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="iso-8859-1"<br>
<br>
Hi Justin,<br>
<br>
I am sorry for so many questions but I do not understand something.<br>
First we run the simulation of pulling Chain A from ChainB with constant<br>
force (pull_k1=1000) and constant velocity of pulling (pull_rate1=0.01) We<br>
extract windows as we discussed and then run simulations with those<br>
configurations as a starting point. I saw the trajectory of one of these<br>
simulations and it looks like normal MD simulation. My question is: Why do<br>
we have in mdp file still pull code as we do not pull protein chain any<br>
more? Pull rate is set to zero but force is still applied... why? Is this<br>
code just used to extract pullf.xvg and pullx.xvg which does not change too<br>
much?<br>
I would appreciate the explanation as without undesratnding the basics its<br>
not good to do any simulation like this.<br>
<br>
Thank you<br>
<br>
Steven<br>
<br>
<br>
<br>
<br>
Are my questions to trivial or noones knows? Please, help!<br>
<br>
On Wed, Nov 16, 2011 at 9:31 AM, Steven Neumann <<a href="mailto:s.neumann08@gmail.com">s.neumann08@gmail.com</a>>wrote:<br>
<br>
> Hi GMX Users,<br>
><br>
> I am doing Justin tutorial of Umbrella sampling. I have just finished<br>
> continous pulling of chainA from the reference chainB. I have some<br>
> questions. I looked at the trajectory of pulling and it has began with<br>
> dissociating residue 27Alanine from the ChainB following 26, 25, 24...1. My<br>
> question is why? As you apply pulling with the constant force to the COM of<br>
> the whole chain why does it start with terminal residue following then one<br>
> by one? Why not the middle one or any other?<br>
><br>
> The second thing I would like to extract starting configurations from from<br>
> my pulling. Till frame 189 the COM varies from 0.49 to 0.56 - makes sense<br>
> as the ChainA is still within ChainB. I would like to use configurations:<br>
><br>
> 0 - 0.50<br>
> 50 - 0.52<br>
> 100 - 0.51<br>
> 150 - 0.51<br>
> 200 - 0.62<br>
> 250 - 2.21<br>
> ....<br>
> 500 - 5.48<br>
><br>
> My question is: Do I have to use exactly the same e.g. 0.2 nm spacing or<br>
> this configuration above is ok? Can the spacing in nm vary?<br>
> And the last thing - is it required to use frames till 189 as the COM<br>
> varies in this area?<br>
><br>
> Thank you!<br>
><br>
> Steven<br>
><br>
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------------------------------<br>
<br>
Message: 4<br>
Date: Thu, 17 Nov 2011 13:04:14 +0100<br>
From: Tsjerk Wassenaar <<a href="mailto:tsjerkw@gmail.com">tsjerkw@gmail.com</a>><br>
Subject: Re: [gmx-users] Regarding cosine content<br>
To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
Message-ID:<br>
<<a href="mailto:CABzE1Si4jcNfj-gaN6QaRo-TOAcA1M72vpj36rd%2BJJRVosgnrQ@mail.gmail.com">CABzE1Si4jcNfj-gaN6QaRo-TOAcA1M72vpj36rd+JJRVosgnrQ@mail.gmail.com</a>><br>
Content-Type: text/plain; charset=ISO-8859-1<br>
<br>
Hi Bipin,<br>
<br>
It seems one of the proteins is taking longer to reach an equilibrium.<br>
Maybe it is undergoing a conformational change?<br>
Did you calculate the principal components per protein, or for the<br>
joint trajectories? It would have been better to echo the commands you<br>
used on the list, because it might result in a different<br>
interpretation. I also made some comments on the list a short while<br>
ago regarding the interpretation of projections and cosine content.<br>
Maybe they can help you form a picture of what is happening :)<br>
<br>
Hope it helps,<br>
<br>
Tsjerk<br>
<br>
<br>
On Thu, Nov 17, 2011 at 12:22 PM, bipin singh <<a href="mailto:bipinelmat@gmail.com">bipinelmat@gmail.com</a>> wrote:<br>
> Hello all,<br>
><br>
> I have done PCA from 50ns long trajectory for two similar proteins<br>
> (length 180 aa and RMSD 0.2 A).<br>
> The equilibration time and final simulation condition were identical<br>
> for both the protein.<br>
> But when I checked the cosine content for PC1 for both proteins they<br>
> were 0.9 and 0.5 respectively.<br>
> What can be the reason for this huge difference in cosine content of<br>
> the two proteins ?<br>
><br>
><br>
> --<br>
> -----------------------<br>
> Regards,<br>
> Bipin Singh<br>
> --<br>
> gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
> <a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
> Please search the archive at <a href="http://www.gromacs.org/Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a> before posting!<br>
> Please don't post (un)subscribe requests to the list. Use the<br>
> www interface or send it to <a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>
> Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br>
><br>
<br>
<br>
<br>
--<br>
Tsjerk A. Wassenaar, Ph.D.<br>
<br>
post-doctoral researcher<br>
Molecular Dynamics Group<br>
* Groningen Institute for Biomolecular Research and Biotechnology<br>
* Zernike Institute for Advanced Materials<br>
University of Groningen<br>
The Netherlands<br>
<br>
<br>
------------------------------<br>
<br>
Message: 5<br>
Date: Thu, 17 Nov 2011 18:07:44 +0530<br>
From: bipin singh <<a href="mailto:bipinelmat@gmail.com">bipinelmat@gmail.com</a>><br>
Subject: Re: [gmx-users] Regarding cosine content<br>
To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
Message-ID:<br>
<<a href="mailto:CAKb2Z-FCCwxBRw69qFefRmyTeJsqq4iz35cOO%2BhOJzBCmhUJ9g@mail.gmail.com">CAKb2Z-FCCwxBRw69qFefRmyTeJsqq4iz35cOO+hOJzBCmhUJ9g@mail.gmail.com</a>><br>
Content-Type: text/plain; charset=ISO-8859-1<br>
<br>
Thanks for the reply...<br>
I calculated principal components per protein using the command<br>
g_anaeig -f md.xtc -s md.tpr -v eigenvec.trr -eig eigenval.xvg -comp<br>
eigcomp.xvg -rmsf eigrmsf.xvg -2d 2dproj.xvg -proj proj.xvg -tu ns<br>
-extr extr.pdb -filt filt.xtc -first 1 -last 2<br>
<br>
Also please suggest how one can differentiate between the two<br>
scenarios, when the high cosine content is due to random diffusion or<br>
conformational changes ?<br>
<br>
<br>
On Thu, Nov 17, 2011 at 17:34, Tsjerk Wassenaar <<a href="mailto:tsjerkw@gmail.com">tsjerkw@gmail.com</a>> wrote:<br>
> Hi Bipin,<br>
><br>
> It seems one of the proteins is taking longer to reach an equilibrium.<br>
> Maybe it is undergoing a conformational change?<br>
> Did you calculate the principal components per protein, or for the<br>
> joint trajectories? It would have been better to echo the commands you<br>
> used on the list, because it might result in a different<br>
> interpretation. I also made some comments on the list a short while<br>
> ago regarding the interpretation of projections and cosine content.<br>
> Maybe they can help you form a picture of what is happening :)<br>
><br>
> Hope it helps,<br>
><br>
> Tsjerk<br>
><br>
><br>
> On Thu, Nov 17, 2011 at 12:22 PM, bipin singh <<a href="mailto:bipinelmat@gmail.com">bipinelmat@gmail.com</a>> wrote:<br>
>> Hello all,<br>
>><br>
>> I have done PCA from 50ns long trajectory for two similar proteins<br>
>> (length 180 aa and RMSD 0.2 A).<br>
>> The equilibration time and final simulation condition were identical<br>
>> for both the protein.<br>
>> But when I checked the cosine content for PC1 for both proteins they<br>
>> were 0.9 and 0.5 respectively.<br>
>> What can be the reason for this huge difference in cosine content of<br>
>> the two proteins ?<br>
>><br>
>><br>
>> --<br>
>> -----------------------<br>
>> Regards,<br>
>> Bipin Singh<br>
>> --<br>
>> gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
>> <a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
>> Please search the archive at <a href="http://www.gromacs.org/Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a> before posting!<br>
>> Please don't post (un)subscribe requests to the list. Use the<br>
>> www interface or send it to <a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>
>> Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br>
>><br>
><br>
><br>
><br>
> --<br>
> Tsjerk A. Wassenaar, Ph.D.<br>
><br>
> post-doctoral researcher<br>
> Molecular Dynamics Group<br>
> * Groningen Institute for Biomolecular Research and Biotechnology<br>
> * Zernike Institute for Advanced Materials<br>
> University of Groningen<br>
> The Netherlands<br>
> --<br>
> gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
> <a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
> Please search the archive at <a href="http://www.gromacs.org/Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a> before posting!<br>
> Please don't post (un)subscribe requests to the list. Use the<br>
> www interface or send it to <a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>
> Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br>
><br>
<br>
<br>
<br>
--<br>
-----------------------<br>
Regards,<br>
Bipin Singh<br>
<br>
<br>
------------------------------<br>
<br>
Message: 6<br>
Date: Thu, 17 Nov 2011 13:23:15 +0100<br>
From: Andrzej Rzepiela <<a href="mailto:Andrzej.Rzepiela@physik.uni-freiburg.de">Andrzej.Rzepiela@physik.uni-freiburg.de</a>><br>
Subject: [gmx-users] Cuda not detected<br>
To: <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
Message-ID:<br>
<<a href="mailto:F2E137B5-6631-4588-8F18-ECB451C46D96@physik.uni-freiburg.de">F2E137B5-6631-4588-8F18-ECB451C46D96@physik.uni-freiburg.de</a>><br>
Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes<br>
<br>
Hey,<br>
<br>
I am playing with the gpu version of mdrun and could make it run with:<br>
<br>
~/gromacs/gpu/bin/mdrun-gpu -s topol.tpr -device<br>
"OpenMM:platform=Cuda,memtest=15,deviceid=0,force-device=yes"<br>
<br>
However after reboot of the machine ( which is a testing machine)<br>
<br>
I get the following error:<br>
<br>
<br>
-------------------------------------------------------<br>
Program mdrun-gpu, VERSION 4.5.5<br>
Source code file: /home/weber/gromacs/gromacs-4.5.5_gpu/src/kernel/<br>
openmm_wrapper.cpp, line: 1272<br>
<br>
Fatal error:<br>
The requested platform "Cuda" could not be found.<br>
<br>
<br>
echo $LD_LIBRARY_PATH:/opt/software/ganglia-3.1.7/lib64:/opt/software/<br>
htop-0.8.3:/usr/local/cuda/lib64:/usr/local/cuda/lib:/home/weber/<br>
OpenMM3.1.1-Linux64/lib<br>
<br>
echo $PATH/usr/local/bin:/usr/bin:/bin:/usr/X11R6/bin:/usr/games:/usr/<br>
lib64/jvm/jre/bin:/opt/software/nvidia/3.2.16/cuda/bin:/opt/software/<br>
ganglia-3.1.7/bin:/opt/software/htop-0.8.3/bin:/usr/lib/mit/bin:/usr/<br>
lib/mit/sbin:.:/usr/local/cuda/bin:/home/weber/cmake-2.8.6/bin<br>
<br>
<br>
I run a simple gpu test program and it works.<br>
<br>
I believe something is not linked correctly, maybe someone can give me<br>
a hint.<br>
<br>
Thank You<br>
<br>
Andrzej<br>
<br>
<br>
<br>
------------------------------<br>
<br>
Message: 7<br>
Date: Thu, 17 Nov 2011 08:19:44 -0500<br>
From: "Justin A. Lemkul" <<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>><br>
Subject: Re: [gmx-users] Regarding TIP4P structure<br>
To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
Message-ID: <<a href="mailto:4EC509F0.1030103@vt.edu">4EC509F0.1030103@vt.edu</a>><br>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed<br>
<br>
<br>
<br>
Ravi Kumar Venkatraman wrote:<br>
> Dear all,<br>
> Could anybody send me the link for getting the tip4p tip3p<br>
> and tip5p single water structure in gro/pdb or in anyother format.<br>
><br>
<br>
A single water molecule? Copy and paste the coordinates from the existing .gro<br>
files in $GMXLIB.<br>
<br>
-Justin<br>
<br>
--<br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | <a href="tel:%28540%29%20231-9080" value="+15402319080">(540) 231-9080</a><br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
========================================<br>
<br>
<br>
------------------------------<br>
<font color="#888888"><br>
--<br>
gmx-users mailing list<br>
<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
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Please search the archive at <a href="http://www.gromacs.org/Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a> before posting!<br>
<br>
End of gmx-users Digest, Vol 91, Issue 119<br>
******************************************<br>
</font></blockquote></div><br><br clear="all"><br>-- <br>Saba Ferdous<div>Research Scholar (M. Phil)</div><div>National Center for Bioinformatics</div><div>Quaid-e-Azam University, Islamabad</div><div>Pakistan</div><br>