<br><div id=":1t8" class="ii gt"><div id=":1t7">Dear Mark Abraham,<br><br>Thank
you for the reply. However, I am sorry to tell you that I could not
find a tutorial that really is explicit to explain the procedure. Could
you please suggest some tutorial covering the non-water solvent box
generation and optimization using all-atom charmm force-field on
GROMACS.<br>
<br>best regards,<br>Uday.</div></div><br><br><div class="gmail_quote">On Tue, Jun 21, 2011 at 4:05 AM, <span dir="ltr"><<a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">Send gmx-users mailing list submissions to<br>
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<br>
Today's Topics:<br>
<br>
1. Re: NVT equilibration of DMSO solvent (Charmm all-atom force<br>
field) (Mark Abraham)<br>
2. Re: EM broke protein-lipid system (Mark Abraham)<br>
3. Re: doubt about your Umbrella Sampling tutorial (Justin A. Lemkul)<br>
4. Re: minimum image violation (Justin A. Lemkul)<br>
5. Re: error bars g_wham (Justin A. Lemkul)<br>
6. NMR chemical shift restraints (Thomas Evangelidis)<br>
7. Re: NMR chemical shift restraints (Mark Abraham)<br>
8. Re: Increase in charge after adding the ligand (bharat gupta)<br>
<br>
<br>
----------------------------------------------------------------------<br>
<br>
Message: 1<br>
Date: Tue, 21 Jun 2011 03:51:53 +1000<br>
From: Mark Abraham <<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>><br>
Subject: Re: [gmx-users] NVT equilibration of DMSO solvent (Charmm<br>
all-atom force field)<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:4DFF88B9.4080302@anu.edu.au">4DFF88B9.4080302@anu.edu.au</a>><br>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed<br>
<br>
On 21/06/2011 2:44 AM, udaya kiran marelli wrote:<br>
> Dear GROMACS users,<br>
><br>
> I have generated a 4*4*4 octahedral DMSO box containing 64 molecules<br>
> (Charmm all-atom force field) which need to be NVT equilibrated in<br>
> order to pass it for usage in genbox. Could one of you provide info<br>
> on how to do the NVT and periodic boundary equilibration to remove the<br>
> residual ordering of the solvent?<br>
<br>
Most tutorials will cover the details of such stages well.<br>
<br>
Mark<br>
<br>
<br>
------------------------------<br>
<br>
Message: 2<br>
Date: Tue, 21 Jun 2011 03:54:57 +1000<br>
From: Mark Abraham <<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>><br>
Subject: Re: [gmx-users] EM broke protein-lipid system<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:4DFF8971.2010709@anu.edu.au">4DFF8971.2010709@anu.edu.au</a>><br>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed<br>
<br>
On 21/06/2011 2:46 AM, Du Jiangfeng (BIOCH) wrote:<br>
> Dear Gromacs Users,<br>
> It comes to me with million problems per day during I am using gromacs. :(<br>
<br>
Computational chemistry is rarely easy. The tasks are complex and<br>
demanding, even when the software is mature and the documentation well<br>
written... That said, you're tackling a difficult multi-phase system...<br>
<br>
> Maybe you are the right persons i should ask about coarse grained protein-lipid simulation. Right now I have a system with a bilayer (DOPCs) and a protein (Histone). After EM simulation, it worked quite well.... Then, this system was filled with water and was performed by EM again. Then it was scattered severely. Though I tried lipid constraint and many other methods, the problem is still here....<br>
> Any suggestions?<br>
<br>
I can only suggest that you find and follow suitable tutorial material,<br>
simplifying your system as much as you can, adding complexity in stages.<br>
<br>
Mark<br>
<br>
<br>
------------------------------<br>
<br>
Message: 3<br>
Date: Mon, 20 Jun 2011 17:03:56 -0400<br>
From: "Justin A. Lemkul" <<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>><br>
Subject: [gmx-users] Re: doubt about your Umbrella Sampling tutorial<br>
To: Rebeca Garc?a Fandi?o <<a href="mailto:regafan@hotmail.com">regafan@hotmail.com</a>><br>
Cc: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
Message-ID: <<a href="mailto:4DFFB5BC.1060507@vt.edu">4DFFB5BC.1060507@vt.edu</a>><br>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed<br>
<br>
<br>
<br>
Rebeca García Fandiño wrote:<br>
> Dear Justin,<br>
> my name is Rebeca and I am a postdoctoral student in Santiago de<br>
> Compostela University. Sorry for disturbing you to your personal mail, I<br>
> have tried to post to the Gromacs-list first, but I did not get any answer.<br>
<br>
I was traveling and not paying much attention to messages across the list. I<br>
will CC this reply to the list in the hopes that it is useful to others, as well.<br>
<br>
> I am trying to obtain the PMF from Umbrella Sampling of the process of<br>
> separating two monomers of a dimer, following your tutorial, and I have<br>
> a pair of doubts:<br>
><br>
> 1)In this tutorial the generation of configurations is done using a .mdp<br>
> file for pulling one chain from another, but is it possible to generate<br>
> the configurations for Umbrella Sampling "by hand", I mean, changing the<br>
> z coordinate of the monomer I want to move, then solvating and then<br>
> minimizing these configurations? Is there any problem with this protocol<br>
> for the obtaining of the configurations?<br>
><br>
<br>
No problem at all. The tutorial is but one possible method.<br>
<br>
> 2) I have noticed that you use restraints in the md_umbrella.mdp for the<br>
> fixed chain. Is that correct? I can understand the restraints in the<br>
> pulling simulations for generate starting configurations, but once you<br>
> have the configurations, is is necessary to restrain one part of the<br>
> system?<br>
><br>
<br>
Not usually. The tutorial presents a special case.<br>
<br>
> Thanks a lot in advance for your help with this topic, and thank you<br>
> very much also for publishing this interesting tutorial. There was<br>
> nothing useful until that for Umbrella Sampling with Gromacs 4.0, so I<br>
> think it is more than wellcome for all Gromacs users!<br>
<br>
Glad they're useful :)<br>
<br>
-Justin<br>
<br>
> Best wishes,<br>
> Rebeca.<br>
><br>
> Dr. Rebeca García Fandiño<br>
> Department of Organic Chemistry and Center for Research in Biological<br>
> Chemistry<br>
> and Molecular Materials<br>
> Santiago de Compostela University<br>
> E-15782 Santiago de Compostela (Spain)<br>
> e-mail: <a href="mailto:rebeca.garcia.fandino@usc.es">rebeca.garcia.fandino@usc.es</a><br>
> Phone: 34-981563100 ext 15760<br>
><br>
><br>
><br>
><br>
><br>
><br>
><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: 4<br>
Date: Mon, 20 Jun 2011 17:16:13 -0400<br>
From: "Justin A. Lemkul" <<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>><br>
Subject: Re: [gmx-users] minimum image violation<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:4DFFB89D.8080001@vt.edu">4DFFB89D.8080001@vt.edu</a>><br>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed<br>
<br>
<br>
<br>
Kavyashree M wrote:<br>
> Dear users,<br>
><br>
> I ran 100ns simulation for 4 proteins, 3 of them were<br>
> non covalent dimers in solution, but only 1 is a covalent<br>
> dimer connected by a disulphide bridge. I used monomers<br>
> to run the job.<br>
> Only in the case of covalent dimer I was getting severe<br>
> minimum image violation ie. out of 50001 data points,<br>
> 282 are <= 1.4nm<br>
> 280 are < 1.4nm<br>
> 144 are < 1.3nm<br>
> 79 are < 1.2nm<br>
> 28 are < 1.1nm<br>
> 4 < 1.0nm<br>
><br>
> I agree that this is quite wrong but I wanted to know whether<br>
> any useful information can be gathered out of this simulation?<br>
><br>
<br>
Not likely. Nearly 2% of the saved frames are unusable, indicating that<br>
potentially even more of the frames in the trajectory are useless, as well, and<br>
the dynamics that produced them are flawed.<br>
<br>
> In another data while calculating the energy terms it gives<br>
> nan (not a number error) for rmsd alone eg -<br>
> Energy Average Err.Est. RMSD Tot-Drift<br>
> -------------------------------------------------------------------------------<br>
> Temperature 300 9e-05 -nan -0.000501989 (K)<br>
><br>
> Energy Average Err.Est. RMSD Tot-Drift<br>
> -------------------------------------------------------------------------------<br>
> Pressure 0.99914 0.027 -nan 0.0174391 (bar)<br>
><br>
> Energy Average Err.Est. RMSD Tot-Drift<br>
> -------------------------------------------------------------------------------<br>
> Volume 517.755 0.0094 -nan 0.010871 (nm^3)<br>
><br>
> Initially i though some data points are missing but later<br>
> gmxcheck gives that all the data points are present.<br>
> now what could be the error?<br>
><br>
> I had asked this question before and was instructed to check the<br>
> trajectory. I checked the rmsd rmsf of this with the other proteins<br>
> it similar but one of the segment has high rmsf compared to the other<br>
> proteins.<br>
><br>
<br>
My advice to you was to *watch* the trajectory to see where the PBC violations<br>
occurred, not run more analysis. I doubt RMSF and RMSD will tell you anything<br>
useful.<br>
<br>
No one's been able to diagnose the problem based on this (continually posted)<br>
information. If it's a useless trajectory, why bother?<br>
<br>
-Justin<br>
<br>
> Thanking you<br>
> With regards<br>
> M. Kavyashree<br>
><br>
><br>
><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: 5<br>
Date: Mon, 20 Jun 2011 17:16:58 -0400<br>
From: "Justin A. Lemkul" <<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>><br>
Subject: Re: [gmx-users] error bars g_wham<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:4DFFB8CA.90608@vt.edu">4DFFB8CA.90608@vt.edu</a>><br>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed<br>
<br>
<br>
<br>
Gavin Melaugh wrote:<br>
> Hi all<br>
><br>
> I have read the manual and the recent JCTC paper on g_wham, and I was<br>
> wondering how to actually get the error bars on the profile.xvg file<br>
> outputted from g_wham.<br>
<br>
A suitable combination of g_wham -bs-method -nBootstrap, etc. See g_wham -h.<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: 6<br>
Date: Tue, 21 Jun 2011 01:30:06 +0300<br>
From: Thomas Evangelidis <<a href="mailto:tevang3@gmail.com">tevang3@gmail.com</a>><br>
Subject: [gmx-users] NMR chemical shift restraints<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:BANLkTim95fLRCjFRyL3EzcN18CcqbUHsOw@mail.gmail.com">BANLkTim95fLRCjFRyL3EzcN18CcqbUHsOw@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="iso-8859-1"<br>
<br>
Dear GROMACS users,<br>
<br>
I've read in the manual and in previous posts that NMR chemical shifts can<br>
be computed from phi/psi angles. However, it was unclear whether the inverse<br>
is possible with GROMACS, namely to use chemical shifts (1H, 13C, 15N) as<br>
restraints (possibly as secondary structure restraints with a given<br>
propensity) during MD simulations. I would be grateful if any experienced<br>
member could clarify this for me.<br>
<br>
thanks in advance,<br>
Thomas<br>
<br>
<br>
<br>
<br>
--<br>
<br>
======================================================================<br>
<br>
Thomas Evangelidis<br>
<br>
PhD student<br>
<br>
Biomedical Research Foundation, Academy of Athens<br>
<br>
4 Soranou Ephessiou , 115 27 Athens, Greece<br>
<br>
email: <a href="mailto:tevang@bioacademy.gr">tevang@bioacademy.gr</a><br>
<br>
<a href="mailto:tevang3@gmail.com">tevang3@gmail.com</a><br>
<br>
<br>
website: <a href="https://sites.google.com/site/thomasevangelidishomepage/" target="_blank">https://sites.google.com/site/thomasevangelidishomepage/</a><br>
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<br>
Message: 7<br>
Date: Tue, 21 Jun 2011 11:06:43 +1000<br>
From: Mark Abraham <<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>><br>
Subject: Re: [gmx-users] NMR chemical shift restraints<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:4DFFEEA3.9080403@anu.edu.au">4DFFEEA3.9080403@anu.edu.au</a>><br>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed<br>
<br>
On 21/06/2011 8:30 AM, Thomas Evangelidis wrote:<br>
> Dear GROMACS users,<br>
><br>
> I've read in the manual and in previous posts that NMR chemical shifts<br>
> can be computed from phi/psi angles. However, it was unclear whether<br>
> the inverse is possible with GROMACS, namely to use chemical shifts<br>
> (1H, 13C, 15N) as restraints (possibly as secondary structure<br>
> restraints with a given propensity) during MD simulations. I would be<br>
> grateful if any experienced member could clarify this for me.<br>
<br>
<br>
Various kinds of (time-averaged) restraints can be imposed (details in<br>
the manual), and NMR data can be the source for these. For details of<br>
the latter, I can only suggest searching the literature for publications<br>
that report how they derived such restraints.<br>
<br>
Mark<br>
<br>
<br>
------------------------------<br>
<br>
Message: 8<br>
Date: Tue, 21 Jun 2011 11:05:13 +0900<br>
From: bharat gupta <<a href="mailto:bharat.85.monu@gmail.com">bharat.85.monu@gmail.com</a>><br>
Subject: [gmx-users] Re: Increase in charge after adding the ligand<br>
To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
Message-ID: <BANLkTimj0C3mTok3qhFGVZ5E=<a href="mailto:O9DKsBViQ@mail.gmail.com">O9DKsBViQ@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="iso-8859-1"<br>
<br>
Hi,<br>
<br>
Initially while preparing the structure , -2 charge was there on the<br>
protein. Next, after adding the ligand and executing grompp statement It<br>
showing -9.9 charge. So I added 9 sodium ions. but still its showing +8<br>
charge on the system. what shall I do in this case ??<br>
<br>
--<br>
Bharat<br>
Ph.D. Candidate<br>
Room No. : 7202A, 2nd Floor<br>
Biomolecular Engineering Laboratory<br>
Division of Chemical Engineering and Polymer Science<br>
Pusan National University<br>
Busan -609735<br>
South Korea<br>
Lab phone no. - <a href="tel:%2B82-51-510-3680" value="+82515103680">+82-51-510-3680</a>, <a href="tel:%2B82-51-583-8343" value="+82515838343">+82-51-583-8343</a><br>
Mobile no. - 010-5818-3680<br>
E-mail : <a href="mailto:monu46010@yahoo.com">monu46010@yahoo.com</a><br>
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