[gmx-users] How to neutralize net charge of protein and why
rituraj purohit
riturajpurohit at gmail.com
Sat Aug 29 17:00:32 CEST 2009
Dear Friends,
During first step of MD (pdb2gmx) I come to know that my protein having net
charge -42 e (it has two chain, A and B each having -21 e ).
Why neutral system is preferable for further steps of MD & what kind of
problem encounter with charged system ?
Should i have to add 21 Na+ to make it neutral, through "genion"?
Regards,
Rituraj
On 8/29/09, gmx-users-request at gromacs.org <gmx-users-request at gromacs.org>
wrote:
>
> Send gmx-users mailing list submissions to
> gmx-users at 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-request at gromacs.org
>
> You can reach the person managing the list at
> gmx-users-owner at 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: RE: Re: g_energy and g_analyze give different averages
> (Justin A. Lemkul)
> 2. Re: double precision (Justin A. Lemkul)
> 3. RE: RE: Re: g_energy and g_analyze give different averages
> (Berk Hess)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Fri, 28 Aug 2009 20:53:16 -0400
> From: "Justin A. Lemkul" <jalemkul at vt.edu>
> Subject: Re: [gmx-users] RE: Re: g_energy and g_analyze give different
> averages
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4A987BFC.2040304 at vt.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>
>
> Ragnarok sdf wrote:
> >
> >
> > I am terribly sorry. I have not expressed myself well. I meant the
> > standard error of the mean energy given by g_energy. So I believe I
> > would like to know the standard error estimate.
>
> Based on the output RMSD (standard deviation), it seems rather
> straightforward
> to calculate SE:
>
>
> http://en.wikipedia.org/wiki/Standard_error_(statistics)#Standard_error_of_the_mean
>
> -Justin
>
> >
> >
> > I don't understand what you want exactly.
> > Your g_energy command does exponential averaging, that happens
> > on the printed data points. So there g_analyze or any program will
> > do fine.
> > For the original data g_energy gives the exact standard deviation
> > over all MD steps, called RMSD.
> >
> > But do you really want the standard deviation, or do you want
> > a standard error estimate?
> >
> > Berk
> >
> > Date: Fri, 28 Aug 2009 09:30:37 -0300
> > From: fabracht1 at gmail.com <mailto:fabracht1 at gmail.com>
> > To: gmx-users at gromacs.org <mailto:gmx-users at gromacs.org>
> > Subject: [gmx-users] Re: g_energy and g_analyze give different
> averages
> >
> >
> > Is there a correct way to obtain the standard deviation for these
> > data sets?
> >
> >
> >
> >
> > >
> >
> > > Ragnarok sdf wrote:
> >
> > > > When analysing FEP simulations. After running g_energy -f
> > fep000.edr -f2
> >
> > > > fep_000-005.edr for obtaining the dF = -kT ln <
> > exp(-(EB-EA)/kT) >A I
> >
> > > tried
> >
> > > > to obtain the standard deviation for this ensemble average using
> >
> > > g_analyze
> >
> > > > -f runavg.xvg, but I've noticed that the average values are
> quite
> >
> > > different
> >
> > > >
> >
> > > >
> >
> > > g_energy takes all values during your simulation into account,
> > g_analyze
> >
> > > only the printed datapoints.
> >
> > >
> >
> > >
> >
> >
> >
> >
> > ------------------------------------------------------------------------
> >
> > _______________________________________________
> > gmx-users mailing list gmx-users at gromacs.org
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > Please search the archive at http://www.gromacs.org/search before
> posting!
> > Please don't post (un)subscribe requests to the list. Use the
> > www interface or send it to gmx-users-request at gromacs.org.
> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
>
>
> ------------------------------
>
> Message: 2
> Date: Fri, 28 Aug 2009 10:44:27 -0400
> From: "Justin A. Lemkul" <jalemkul at vt.edu>
> Subject: Re: [gmx-users] double precision
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4A97ED4B.9020604 at vt.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>
>
> abhijit kayal wrote:
> > Hi,
> > I am going to do the normal mode analysis of 1OMB.pdb.For this purpose I
> > have to run the GROMACS in double precision .For this i went through the
> > manual and made necessart changes in .mdp file.But when I gave grompp_d
> > it showed like this
> > [abhijit at SCFBioServer 1omb]$ grompp_d -v -f em.mdp -c b4em.gro -o em.tpr
> > -p 1OMB.top
> > -bash: grompp_d: command not found.
> > I am using GROMACS 4.0.4 version .So my question is why
> > it showed like this.
> >
>
> Did you specify --program-suffix=_d when doing the double-precision
> installation?
>
> -Justin
>
>
> > Thank you
> >
> > Abhijit Kayal
> >
> > IIT Delhi
> >
> >
> > ------------------------------------------------------------------------
> >
> > _______________________________________________
> > gmx-users mailing list gmx-users at gromacs.org
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > Please search the archive at http://www.gromacs.org/search before
> posting!
> > Please don't post (un)subscribe requests to the list. Use the
> > www interface or send it to gmx-users-request at gromacs.org.
> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
>
>
> ------------------------------
>
> Message: 3
> Date: Sat, 29 Aug 2009 10:35:05 +0200
> From: Berk Hess <gmx3 at hotmail.com>
> Subject: RE: [gmx-users] RE: Re: g_energy and g_analyze give different
> averages
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <COL113-W5761A7D698571E5044C8E18EF40 at phx.gbl>
> Content-Type: text/plain; charset="iso-8859-1"
>
>
> Hi,
>
> No, that assumes that all points are independent.
> Which they might be, but they are usually not.
>
> It is still not clear to me if you want the error of the exponential
> difference of the error of the direct energies.
>
> g_analyze -ee will give you an error estimate, but only based
> on the printed points.
>
> The simplest way is always to divide your set in 4 consecutive parts,
> determine the averages with g_energy -b -e
> and determine the error estimate through the method in Justin's link.
>
> Berk
>
> > Date: Fri, 28 Aug 2009 20:53:16 -0400
> > From: jalemkul at vt.edu
> > To: gmx-users at gromacs.org
> > Subject: Re: [gmx-users] RE: Re: g_energy and g_analyze give different
> averages
> >
> >
> >
> > Ragnarok sdf wrote:
> > >
> > >
> > > I am terribly sorry. I have not expressed myself well. I meant the
> > > standard error of the mean energy given by g_energy. So I believe I
> > > would like to know the standard error estimate.
> >
> > Based on the output RMSD (standard deviation), it seems rather
> straightforward
> > to calculate SE:
> >
> >
> http://en.wikipedia.org/wiki/Standard_error_(statistics)#Standard_error_of_the_mean
> >
> > -Justin
> >
> > >
> > >
> > > I don't understand what you want exactly.
> > > Your g_energy command does exponential averaging, that happens
> > > on the printed data points. So there g_analyze or any program will
> > > do fine.
> > > For the original data g_energy gives the exact standard deviation
> > > over all MD steps, called RMSD.
> > >
> > > But do you really want the standard deviation, or do you want
> > > a standard error estimate?
> > >
> > > Berk
> > >
> > > Date: Fri, 28 Aug 2009 09:30:37 -0300
> > > From: fabracht1 at gmail.com <mailto:fabracht1 at gmail.com>
> > > To: gmx-users at gromacs.org <mailto:gmx-users at gromacs.org>
> > > Subject: [gmx-users] Re: g_energy and g_analyze give different
> averages
> > >
> > >
> > > Is there a correct way to obtain the standard deviation for these
> > > data sets?
> > >
> > >
> > >
> > >
> > > >
> > >
> > > > Ragnarok sdf wrote:
> > >
> > > > > When analysing FEP simulations. After running g_energy -f
> > > fep000.edr -f2
> > >
> > > > > fep_000-005.edr for obtaining the dF = -kT ln <
> > > exp(-(EB-EA)/kT) >A I
> > >
> > > > tried
> > >
> > > > > to obtain the standard deviation for this ensemble average
> using
> > >
> > > > g_analyze
> > >
> > > > > -f runavg.xvg, but I've noticed that the average values are
> quite
> > >
> > > > different
> > >
> > > > >
> > >
> > > > >
> > >
> > > > g_energy takes all values during your simulation into account,
> > > g_analyze
> > >
> > > > only the printed datapoints.
> > >
> > > >
> > >
> > > >
> > >
> > >
> > >
> > >
> > >
> ------------------------------------------------------------------------
> > >
> > > _______________________________________________
> > > gmx-users mailing list gmx-users at gromacs.org
> > > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > > Please search the archive at http://www.gromacs.org/search before
> posting!
> > > Please don't post (un)subscribe requests to the list. Use the
> > > www interface or send it to gmx-users-request at gromacs.org.
> > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> >
> > --
> > ========================================
> >
> > Justin A. Lemkul
> > Ph.D. Candidate
> > ICTAS Doctoral Scholar
> > Department of Biochemistry
> > Virginia Tech
> > Blacksburg, VA
> > jalemkul[at]vt.edu | (540) 231-9080
> > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> >
> > ========================================
> > _______________________________________________
> > gmx-users mailing list gmx-users at gromacs.org
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > Please search the archive at http://www.gromacs.org/search before
> posting!
> > Please don't post (un)subscribe requests to the list. Use the
> > www interface or send it to gmx-users-request at gromacs.org.
> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
> _________________________________________________________________
> Express yourself instantly with MSN Messenger! Download today it's FREE!
> http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/
> -------------- next part --------------
> An HTML attachment was scrubbed...
> URL:
> http://lists.gromacs.org/pipermail/gmx-users/attachments/20090829/a806db6e/attachment-0001.html
>
> ------------------------------
>
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
>
> End of gmx-users Digest, Vol 64, Issue 198
> ******************************************
>
--
--------------------------------------------------------------------------------------------------
RITURAJ PUROHIT
Assistant Professor, Bioinformatics Division
School of Bio-sciences and Technology (SBST)
Vellore Institute of Technology, University
Address: SBST, VIT University, Vellore-632014,Tamilnadu, India.
Phone: +91-416-2202638 (Lab), +91-9944649073 (Mobile)
Fax; +91-416-2243092, E-mail: rituraj at vit.ac.in
------------------------------------------------------------------------------------------------------
"The future belongs to those who believe in the beauty of their dreams."
--------------------------------------------------------------------------------------------------------
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20090829/203f95f0/attachment.html>
More information about the gromacs.org_gmx-users
mailing list