Dear Mark Abraham, 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.
best regards, Uday. On Tue, Jun 21, 2011 at 4:05 AM, <gmx-users-requ...@gromacs.org> wrote: > Send gmx-users mailing list submissions to > gmx-users@gromacs.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://lists.gromacs.org/mailman/listinfo/gmx-users > or, via email, send a message with subject or body 'help' to > gmx-users-requ...@gromacs.org > > You can reach the person managing the list at > gmx-users-ow...@gromacs.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of gmx-users digest..." > > > Today's Topics: > > 1. Re: NVT equilibration of DMSO solvent (Charmm all-atom force > field) (Mark Abraham) > 2. Re: EM broke protein-lipid system (Mark Abraham) > 3. Re: doubt about your Umbrella Sampling tutorial (Justin A. Lemkul) > 4. Re: minimum image violation (Justin A. Lemkul) > 5. Re: error bars g_wham (Justin A. Lemkul) > 6. NMR chemical shift restraints (Thomas Evangelidis) > 7. Re: NMR chemical shift restraints (Mark Abraham) > 8. Re: Increase in charge after adding the ligand (bharat gupta) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 21 Jun 2011 03:51:53 +1000 > From: Mark Abraham <mark.abra...@anu.edu.au> > Subject: Re: [gmx-users] NVT equilibration of DMSO solvent (Charmm > all-atom force field) > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: <4dff88b9.4080...@anu.edu.au> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > On 21/06/2011 2:44 AM, udaya kiran marelli wrote: > > Dear GROMACS users, > > > > I have generated a 4*4*4 octahedral DMSO box containing 64 molecules > > (Charmm all-atom force field) which need to be NVT equilibrated in > > order to pass it for usage in genbox. Could one of you provide info > > on how to do the NVT and periodic boundary equilibration to remove the > > residual ordering of the solvent? > > Most tutorials will cover the details of such stages well. > > Mark > > > ------------------------------ > > Message: 2 > Date: Tue, 21 Jun 2011 03:54:57 +1000 > From: Mark Abraham <mark.abra...@anu.edu.au> > Subject: Re: [gmx-users] EM broke protein-lipid system > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: <4dff8971.2010...@anu.edu.au> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > On 21/06/2011 2:46 AM, Du Jiangfeng (BIOCH) wrote: > > Dear Gromacs Users, > > It comes to me with million problems per day during I am using gromacs. > :( > > Computational chemistry is rarely easy. The tasks are complex and > demanding, even when the software is mature and the documentation well > written... That said, you're tackling a difficult multi-phase system... > > > 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.... > > Any suggestions? > > I can only suggest that you find and follow suitable tutorial material, > simplifying your system as much as you can, adding complexity in stages. > > Mark > > > ------------------------------ > > Message: 3 > Date: Mon, 20 Jun 2011 17:03:56 -0400 > From: "Justin A. Lemkul" <jalem...@vt.edu> > Subject: [gmx-users] Re: doubt about your Umbrella Sampling tutorial > To: Rebeca Garc?a Fandi?o <rega...@hotmail.com> > Cc: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: <4dffb5bc.1060...@vt.edu> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > > > Rebeca García Fandiño wrote: > > Dear Justin, > > my name is Rebeca and I am a postdoctoral student in Santiago de > > Compostela University. Sorry for disturbing you to your personal mail, I > > have tried to post to the Gromacs-list first, but I did not get any > answer. > > I was traveling and not paying much attention to messages across the list. > I > will CC this reply to the list in the hopes that it is useful to others, as > well. > > > I am trying to obtain the PMF from Umbrella Sampling of the process of > > separating two monomers of a dimer, following your tutorial, and I have > > a pair of doubts: > > > > 1)In this tutorial the generation of configurations is done using a .mdp > > file for pulling one chain from another, but is it possible to generate > > the configurations for Umbrella Sampling "by hand", I mean, changing the > > z coordinate of the monomer I want to move, then solvating and then > > minimizing these configurations? Is there any problem with this protocol > > for the obtaining of the configurations? > > > > No problem at all. The tutorial is but one possible method. > > > 2) I have noticed that you use restraints in the md_umbrella.mdp for the > > fixed chain. Is that correct? I can understand the restraints in the > > pulling simulations for generate starting configurations, but once you > > have the configurations, is is necessary to restrain one part of the > > system? > > > > Not usually. The tutorial presents a special case. > > > Thanks a lot in advance for your help with this topic, and thank you > > very much also for publishing this interesting tutorial. There was > > nothing useful until that for Umbrella Sampling with Gromacs 4.0, so I > > think it is more than wellcome for all Gromacs users! > > Glad they're useful :) > > -Justin > > > Best wishes, > > Rebeca. > > > > Dr. Rebeca García Fandiño > > Department of Organic Chemistry and Center for Research in Biological > > Chemistry > > and Molecular Materials > > Santiago de Compostela University > > E-15782 Santiago de Compostela (Spain) > > e-mail: rebeca.garcia.fand...@usc.es > > Phone: 34-981563100 ext 15760 > > > > > > > > > > > > > > > > -- > ======================================== > > 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 > > ======================================== > > > ------------------------------ > > Message: 4 > Date: Mon, 20 Jun 2011 17:16:13 -0400 > From: "Justin A. Lemkul" <jalem...@vt.edu> > Subject: Re: [gmx-users] minimum image violation > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: <4dffb89d.8080...@vt.edu> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > > > Kavyashree M wrote: > > Dear users, > > > > I ran 100ns simulation for 4 proteins, 3 of them were > > non covalent dimers in solution, but only 1 is a covalent > > dimer connected by a disulphide bridge. I used monomers > > to run the job. > > Only in the case of covalent dimer I was getting severe > > minimum image violation ie. out of 50001 data points, > > 282 are <= 1.4nm > > 280 are < 1.4nm > > 144 are < 1.3nm > > 79 are < 1.2nm > > 28 are < 1.1nm > > 4 < 1.0nm > > > > I agree that this is quite wrong but I wanted to know whether > > any useful information can be gathered out of this simulation? > > > > Not likely. Nearly 2% of the saved frames are unusable, indicating that > potentially even more of the frames in the trajectory are useless, as well, > and > the dynamics that produced them are flawed. > > > In another data while calculating the energy terms it gives > > nan (not a number error) for rmsd alone eg - > > Energy Average Err.Est. RMSD Tot-Drift > > > ------------------------------------------------------------------------------- > > Temperature 300 9e-05 -nan -0.000501989 > (K) > > > > Energy Average Err.Est. RMSD Tot-Drift > > > ------------------------------------------------------------------------------- > > Pressure 0.99914 0.027 -nan 0.0174391 > (bar) > > > > Energy Average Err.Est. RMSD Tot-Drift > > > ------------------------------------------------------------------------------- > > Volume 517.755 0.0094 -nan 0.010871 > (nm^3) > > > > Initially i though some data points are missing but later > > gmxcheck gives that all the data points are present. > > now what could be the error? > > > > I had asked this question before and was instructed to check the > > trajectory. I checked the rmsd rmsf of this with the other proteins > > it similar but one of the segment has high rmsf compared to the other > > proteins. > > > > My advice to you was to *watch* the trajectory to see where the PBC > violations > occurred, not run more analysis. I doubt RMSF and RMSD will tell you > anything > useful. > > No one's been able to diagnose the problem based on this (continually > posted) > information. If it's a useless trajectory, why bother? > > -Justin > > > Thanking you > > With regards > > M. Kavyashree > > > > > > > > -- > ======================================== > > 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 > > ======================================== > > > ------------------------------ > > Message: 5 > Date: Mon, 20 Jun 2011 17:16:58 -0400 > From: "Justin A. Lemkul" <jalem...@vt.edu> > Subject: Re: [gmx-users] error bars g_wham > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: <4dffb8ca.90...@vt.edu> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > > > Gavin Melaugh wrote: > > Hi all > > > > I have read the manual and the recent JCTC paper on g_wham, and I was > > wondering how to actually get the error bars on the profile.xvg file > > outputted from g_wham. > > A suitable combination of g_wham -bs-method -nBootstrap, etc. See g_wham > -h. > > -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 > > ======================================== > > > ------------------------------ > > Message: 6 > Date: Tue, 21 Jun 2011 01:30:06 +0300 > From: Thomas Evangelidis <teva...@gmail.com> > Subject: [gmx-users] NMR chemical shift restraints > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: <banlktim95flrcjfryl3ezcn18ccqbuh...@mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > Dear GROMACS users, > > I've read in the manual and in previous posts that NMR chemical shifts can > be computed from phi/psi angles. However, it was unclear whether the > inverse > is possible with GROMACS, namely to use chemical shifts (1H, 13C, 15N) as > restraints (possibly as secondary structure restraints with a given > propensity) during MD simulations. I would be grateful if any experienced > member could clarify this for me. > > thanks in advance, > Thomas > > > > > -- > > ====================================================================== > > Thomas Evangelidis > > PhD student > > Biomedical Research Foundation, Academy of Athens > > 4 Soranou Ephessiou , 115 27 Athens, Greece > > email: tev...@bioacademy.gr > > teva...@gmail.com > > > website: https://sites.google.com/site/thomasevangelidishomepage/ > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://lists.gromacs.org/pipermail/gmx-users/attachments/20110621/aee9c0d1/attachment-0001.html > > ------------------------------ > > Message: 7 > Date: Tue, 21 Jun 2011 11:06:43 +1000 > From: Mark Abraham <mark.abra...@anu.edu.au> > Subject: Re: [gmx-users] NMR chemical shift restraints > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: <4dffeea3.9080...@anu.edu.au> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > On 21/06/2011 8:30 AM, Thomas Evangelidis wrote: > > Dear GROMACS users, > > > > I've read in the manual and in previous posts that NMR chemical shifts > > can be computed from phi/psi angles. However, it was unclear whether > > the inverse is possible with GROMACS, namely to use chemical shifts > > (1H, 13C, 15N) as restraints (possibly as secondary structure > > restraints with a given propensity) during MD simulations. I would be > > grateful if any experienced member could clarify this for me. > > > Various kinds of (time-averaged) restraints can be imposed (details in > the manual), and NMR data can be the source for these. For details of > the latter, I can only suggest searching the literature for publications > that report how they derived such restraints. > > Mark > > > ------------------------------ > > Message: 8 > Date: Tue, 21 Jun 2011 11:05:13 +0900 > From: bharat gupta <bharat.85.m...@gmail.com> > Subject: [gmx-users] Re: Increase in charge after adding the ligand > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: <BANLkTimj0C3mTok3qhFGVZ5E=o9dksb...@mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > Hi, > > Initially while preparing the structure , -2 charge was there on the > protein. Next, after adding the ligand and executing grompp statement It > showing -9.9 charge. So I added 9 sodium ions. but still its showing +8 > charge on the system. what shall I do in this case ?? > > -- > Bharat > Ph.D. Candidate > Room No. : 7202A, 2nd Floor > Biomolecular Engineering Laboratory > Division of Chemical Engineering and Polymer Science > Pusan National University > Busan -609735 > South Korea > Lab phone no. - +82-51-510-3680, +82-51-583-8343 > Mobile no. - 010-5818-3680 > E-mail : monu46...@yahoo.com > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://lists.gromacs.org/pipermail/gmx-users/attachments/20110621/924ca4d1/attachment.html > > ------------------------------ > > -- > gmx-users mailing list > gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > > End of gmx-users Digest, Vol 86, Issue 124 > ****************************************** >
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