Dear Friends,<br>
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 ).<br>
Why neutral system is preferable for further steps of MD & what kind of problem encounter with charged system ?<br>
Should i have to add 21 Na+ to make it neutral, through "genion"?<br>
<br>
Regards,<br>
Rituraj<br>
<br><br><div><span class="gmail_quote">On 8/29/09, <b class="gmail_sendername"><a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a></b> <<a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>> wrote:</span><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
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<br> When replying, please edit your Subject line so it is more specific<br> than "Re: Contents of gmx-users digest..."<br> <br> <br> Today's Topics:<br> <br> 1. Re: RE: Re: g_energy and g_analyze give different averages<br>
(Justin A. Lemkul)<br> 2. Re: double precision (Justin A. Lemkul)<br> 3. RE: RE: Re: g_energy and g_analyze give different averages<br> (Berk Hess)<br> <br> <br> ----------------------------------------------------------------------<br>
<br> Message: 1<br> Date: Fri, 28 Aug 2009 20:53:16 -0400<br> From: "Justin A. Lemkul" <<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>><br> Subject: Re: [gmx-users] RE: Re: g_energy and g_analyze give different<br>
averages<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:4A987BFC.2040304@vt.edu">4A987BFC.2040304@vt.edu</a>><br>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed<br> <br> <br> <br> Ragnarok sdf wrote:<br> ><br> ><br> > I am terribly sorry. I have not expressed myself well. I meant the<br> > standard error of the mean energy given by g_energy. So I believe I<br>
> would like to know the standard error estimate.<br> <br> Based on the output RMSD (standard deviation), it seems rather straightforward<br> to calculate SE:<br> <br> <a href="http://en.wikipedia.org/wiki/Standard_error_(statistics)#Standard_error_of_the_mean">http://en.wikipedia.org/wiki/Standard_error_(statistics)#Standard_error_of_the_mean</a><br>
<br> -Justin<br> <br> ><br> ><br> > I don't understand what you want exactly.<br> > Your g_energy command does exponential averaging, that happens<br> > on the printed data points. So there g_analyze or any program will<br>
> do fine.<br> > For the original data g_energy gives the exact standard deviation<br> > over all MD steps, called RMSD.<br> ><br> > But do you really want the standard deviation, or do you want<br>
> a standard error estimate?<br> ><br> > Berk<br> ><br> > Date: Fri, 28 Aug 2009 09:30:37 -0300<br> > From: <a href="mailto:fabracht1@gmail.com">fabracht1@gmail.com</a> <mailto:<a href="mailto:fabracht1@gmail.com">fabracht1@gmail.com</a>><br>
> To: <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a> <mailto:<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br> > Subject: [gmx-users] Re: g_energy and g_analyze give different averages<br>
><br> ><br> > Is there a correct way to obtain the standard deviation for these<br> > data sets?<br> ><br> ><br> ><br> ><br> > ><br> ><br> > > Ragnarok sdf wrote:<br>
><br> > > > When analysing FEP simulations. After running g_energy -f<br> > fep000.edr -f2<br> ><br> > > > fep_000-005.edr for obtaining the dF = -kT ln <<br> > exp(-(EB-EA)/kT) >A I<br>
><br> > > tried<br> ><br> > > > to obtain the standard deviation for this ensemble average using<br> ><br> > > g_analyze<br> ><br> > > > -f runavg.xvg, but I've noticed that the average values are quite<br>
><br> > > different<br> ><br> > > ><br> ><br> > > ><br> ><br> > > g_energy takes all values during your simulation into account,<br> > g_analyze<br> ><br>
> > only the printed datapoints.<br> ><br> > ><br> ><br> > ><br> ><br> ><br> ><br> ><br> > ------------------------------------------------------------------------<br>
><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">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
> Please search the archive at <a href="http://www.gromacs.org/search">http://www.gromacs.org/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/mailing_lists/users.php">http://www.gromacs.org/mailing_lists/users.php</a><br> <br> --<br> ========================================<br> <br> Justin A. Lemkul<br>
Ph.D. Candidate<br> ICTAS Doctoral Scholar<br> Department of Biochemistry<br> Virginia Tech<br> Blacksburg, VA<br> jalemkul[at]<a href="http://vt.edu">vt.edu</a> | (540) 231-9080<br> <a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br> ========================================<br> <br> <br> ------------------------------<br> <br> Message: 2<br> Date: Fri, 28 Aug 2009 10:44:27 -0400<br> From: "Justin A. Lemkul" <<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>><br>
Subject: Re: [gmx-users] double precision<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:4A97ED4B.9020604@vt.edu">4A97ED4B.9020604@vt.edu</a>><br>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed<br> <br> <br> <br> abhijit kayal wrote:<br> > Hi,<br> > I am going to do the normal mode analysis of 1OMB.pdb.For this purpose I<br> > have to run the GROMACS in double precision .For this i went through the<br>
> manual and made necessart changes in .mdp file.But when I gave grompp_d<br> > it showed like this<br> > [abhijit@SCFBioServer 1omb]$ grompp_d -v -f em.mdp -c b4em.gro -o em.tpr<br> > -p 1OMB.top<br> > -bash: grompp_d: command not found.<br>
> I
am using GROMACS 4.0.4 version .So my question is why<br> > it showed like this.<br> ><br> <br> Did you specify --program-suffix=_d when doing the double-precision installation?<br> <br> -Justin<br> <br> <br> > Thank you<br>
><br> > Abhijit Kayal<br> ><br> > IIT Delhi<br> ><br> ><br> > ------------------------------------------------------------------------<br> ><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">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
> Please search the archive at <a href="http://www.gromacs.org/search">http://www.gromacs.org/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/mailing_lists/users.php">http://www.gromacs.org/mailing_lists/users.php</a><br> <br> --<br> ========================================<br> <br> Justin A. Lemkul<br>
Ph.D. Candidate<br> ICTAS Doctoral Scholar<br> Department of Biochemistry<br> Virginia Tech<br> Blacksburg, VA<br> jalemkul[at]<a href="http://vt.edu">vt.edu</a> | (540) 231-9080<br> <a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br> ========================================<br> <br> <br> ------------------------------<br> <br> Message: 3<br> Date: Sat, 29 Aug 2009 10:35:05 +0200<br> From: Berk Hess <<a href="mailto:gmx3@hotmail.com">gmx3@hotmail.com</a>><br>
Subject: RE: [gmx-users] RE: Re: g_energy and g_analyze give different<br> averages<br> To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br> Message-ID: <COL113-W5761A7D698571E5044C8E18EF40@phx.gbl><br>
Content-Type: text/plain; charset="iso-8859-1"<br> <br> <br> Hi,<br> <br> No, that assumes that all points are independent.<br> Which they might be, but they are usually not.<br> <br> It is still not clear to me if you want the error of the exponential<br>
difference of the error of the direct energies.<br> <br> g_analyze -ee will give you an error estimate, but only based<br> on the printed points.<br> <br> The simplest way is always to divide your set in 4 consecutive parts,<br>
determine the averages with g_energy -b -e<br> and determine the error estimate through the method in Justin's link.<br> <br> Berk<br> <br> > Date: Fri, 28 Aug 2009 20:53:16 -0400<br> > From: <a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a><br>
> To: <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br> > Subject: Re: [gmx-users] RE: Re: g_energy and g_analyze give different averages<br> ><br> ><br> ><br> > Ragnarok sdf wrote:<br>
> ><br> > ><br> > > I am terribly sorry. I have not expressed myself well. I meant the<br> > > standard error of the mean energy given by g_energy. So I believe I<br> > > would like to know the standard error estimate.<br>
><br> > Based on the output RMSD (standard deviation), it seems rather straightforward<br> > to calculate SE:<br> ><br> > <a href="http://en.wikipedia.org/wiki/Standard_error_(statistics)#Standard_error_of_the_mean">http://en.wikipedia.org/wiki/Standard_error_(statistics)#Standard_error_of_the_mean</a><br>
><br> > -Justin<br> ><br> > ><br> > ><br> > > I don't understand what you want exactly.<br> > > Your g_energy command does exponential averaging, that happens<br> > > on the printed data points. So there g_analyze or any program will<br>
> > do fine.<br> > > For the original data g_energy gives the exact standard deviation<br> > > over all MD steps, called RMSD.<br> > ><br> > > But do you really want the standard deviation, or do you want<br>
> > a standard error estimate?<br> > ><br> > > Berk<br> > ><br> > > Date: Fri, 28 Aug 2009 09:30:37 -0300<br> > > From: <a href="mailto:fabracht1@gmail.com">fabracht1@gmail.com</a> <mailto:<a href="mailto:fabracht1@gmail.com">fabracht1@gmail.com</a>><br>
> > To: <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a> <mailto:<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br> > > Subject: [gmx-users] Re: g_energy and g_analyze give different averages<br>
> ><br> > ><br> > > Is there a correct way to obtain the standard deviation for these<br> > > data sets?<br> > ><br> > ><br> > ><br> > ><br> > > ><br>
> ><br> > > > Ragnarok sdf wrote:<br> > ><br> > > > > When analysing FEP simulations. After running g_energy -f<br> > > fep000.edr -f2<br> > ><br> > > > > fep_000-005.edr for obtaining the dF = -kT ln <<br>
> > exp(-(EB-EA)/kT) >A I<br> > ><br> > > > tried<br> > ><br> > > > > to obtain the standard deviation for this ensemble average using<br> > ><br> > > > g_analyze<br>
> ><br> > > > > -f runavg.xvg, but I've noticed that the average values are quite<br> > ><br> > > > different<br> > ><br> > > > ><br> > ><br> > > > ><br>
> ><br> > > > g_energy takes all values during your simulation into account,<br> > > g_analyze<br> > ><br> > > > only the printed datapoints.<br> > ><br> > > ><br>
> ><br> > > ><br> > ><br> > ><br> > ><br> > ><br> > > ------------------------------------------------------------------------<br> > ><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">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
> > Please search the archive at <a href="http://www.gromacs.org/search">http://www.gromacs.org/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/mailing_lists/users.php">http://www.gromacs.org/mailing_lists/users.php</a><br> ><br> > --<br> > ========================================<br> ><br>
> Justin A. Lemkul<br> > Ph.D. Candidate<br> > ICTAS Doctoral Scholar<br> > Department of Biochemistry<br> > Virginia Tech<br> > Blacksburg, VA<br> > jalemkul[at]<a href="http://vt.edu">vt.edu</a> | (540) 231-9080<br>
> <a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br> ><br> > ========================================<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">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
> Please search the archive at <a href="http://www.gromacs.org/search">http://www.gromacs.org/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>
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</blockquote></div><br><br clear="all"><br>-- <br>--------------------------------------------------------------------------------------------------<br>RITURAJ PUROHIT<br>Assistant Professor, Bioinformatics Division<br>School of Bio-sciences and Technology (SBST)<br>
Vellore Institute of Technology, University<br>Address: SBST, VIT University, Vellore-632014,Tamilnadu, India.<br>Phone: +91-416-2202638 (Lab), +91-9944649073 (Mobile)<br>Fax; +91-416-2243092, E-mail: <a href="mailto:rituraj@vit.ac.in">rituraj@vit.ac.in</a><br>
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