[gmx-users] Re: Re:NVT equilibration of DMSO solvent (Charmm all-atom force field)
udaya kiran marelli
kiran.udaya at gmail.com
Wed Jun 22 17:05:56 CEST 2011
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-request at gromacs.org> wrote:
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> 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.Abraham at 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 at gromacs.org>
> Message-ID: <4DFF88B9.4080302 at 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.Abraham at anu.edu.au>
> Subject: Re: [gmx-users] EM broke protein-lipid system
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4DFF8971.2010709 at 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" <jalemkul at vt.edu>
> Subject: [gmx-users] Re: doubt about your Umbrella Sampling tutorial
> To: Rebeca Garc?a Fandi?o <regafan at hotmail.com>
> Cc: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4DFFB5BC.1060507 at 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.fandino at 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" <jalemkul at vt.edu>
> Subject: Re: [gmx-users] minimum image violation
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4DFFB89D.8080001 at 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" <jalemkul at vt.edu>
> Subject: Re: [gmx-users] error bars g_wham
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4DFFB8CA.90608 at 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 <tevang3 at gmail.com>
> Subject: [gmx-users] NMR chemical shift restraints
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <BANLkTim95fLRCjFRyL3EzcN18CcqbUHsOw at 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: tevang at bioacademy.gr
>
> tevang3 at gmail.com
>
>
> website: https://sites.google.com/site/thomasevangelidishomepage/
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> ------------------------------
>
> Message: 7
> Date: Tue, 21 Jun 2011 11:06:43 +1000
> From: Mark Abraham <Mark.Abraham at anu.edu.au>
> Subject: Re: [gmx-users] NMR chemical shift restraints
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4DFFEEA3.9080403 at 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.monu at gmail.com>
> Subject: [gmx-users] Re: Increase in charge after adding the ligand
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <BANLkTimj0C3mTok3qhFGVZ5E=O9DKsBViQ at 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 : monu46010 at yahoo.com
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>
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