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-requ...@gromacs.org <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: 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" <jalem...@vt.edu> > Subject: Re: [gmx-users] RE: Re: g_energy and g_analyze give different > averages > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: <4a987bfc.2040...@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: fabrac...@gmail.com <mailto:fabrac...@gmail.com> > > To: gmx-users@gromacs.org <mailto:gmx-users@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@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-requ...@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" <jalem...@vt.edu> > Subject: Re: [gmx-users] double precision > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: <4a97ed4b.9020...@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 > > [abhi...@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@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-requ...@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 <g...@hotmail.com> > Subject: RE: [gmx-users] RE: Re: g_energy and g_analyze give different > averages > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: <col113-w5761a7d698571e5044c8e18e...@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: jalem...@vt.edu > > To: gmx-users@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: fabrac...@gmail.com <mailto:fabrac...@gmail.com> > > > To: gmx-users@gromacs.org <mailto:gmx-users@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@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-requ...@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@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-requ...@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@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: ritu...@vit.ac.in ------------------------------------------------------------------------------------------------------ "The future belongs to those who believe in the beauty of their dreams." --------------------------------------------------------------------------------------------------------
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