[gmx-users] Bug in g_energy for calculating heat capacity?
Hi, all, Actually I think others have also noticed this "bug": g_energy often generate incorrect heat capacity. When I checked the source code of gmx_energy.c, I found the calculation of heat capacity is only related with the fluctuation of temperature, which is actually the algorithm for NVE ensemble only (refer to Allen & Tildesley, Computer simulation of liquids, pp. 53, eqn. 2.82). For other ensembles, e.g. NVT ensemble, the heat capacity should be related with the fluctuation of energies. Another problem: even with the energy fluctuation algorithm for the heat capacity, I found it is not easy to get an convergent value. The most important factor is that the fluctuations are sensitively related with the temperature (pressure) coupling time constants for NVT (NPT) ensembles. I wonder if anyone can help me resolving this problem? Thanks a lot! Regards, zgzhang ___ gmx-users mailing listgmx-users@gromacs.org http://www.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
[gmx-users] Re: Re: How to calculate the local electric field?
Hi, Mark, Thanks for your reply. You mean g_potential in the program lists? It is related with electric field but can not give the local electric field, isn't it? Regards, zgzhang > Message: 4 > Date: Thu, 04 Dec 2008 19:26:40 +1100 > From: Mark Abraham <[EMAIL PROTECTED]> > Subject: Re: [gmx-users] How to calculate the local electric field? > To: Discussion list for GROMACS users > Message-ID: <[EMAIL PROTECTED]> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Zhang Zhigang wrote: > > Hi, all, > > Is it possible to use an established program in Gromacs 4.0 package > > to analysis the distributions of the local electric fields? > > Let me explain the situation clearer as following: > > In a pure water system, each molecule would "feel" a local electric > > field (from the other molecules). Now I want to know the statistical > > distribution and dynamics of the local electric fields that acts on the > > hydrogen atoms. > > I would really appreciate if any one can tell me where I can find > > the program directly without additional laborious programing. > > First port of call should be searching the manual. Section 7.4 has the > names of the utility programs sorted roughly by topic, which can guide > you to look up better information. There's one utility there that might > be useful. > > Mark > > ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] How to calculate the local electric field?
Hi, all, Is it possible to use an established program in Gromacs 4.0 package to analysis the distributions of the local electric fields? Let me explain the situation clearer as following: In a pure water system, each molecule would "feel" a local electric field (from the other molecules). Now I want to know the statistical distribution and dynamics of the local electric fields that acts on the hydrogen atoms. I would really appreciate if any one can tell me where I can find the program directly without additional laborious programing. Regards, zgzhang ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: RE: [gmx-users] Re: About entropic contribution to the potential of mean force
Dear Angel, Firstly I would quote a sentence of the manual: "Whether one needs to correct for this contribution depends on what the PMF should represent." Secondly, in my opinion, the so-called entropic contribution to the PMF (we abbreviate it as P0) is a kind of reference PMF. That is to say, P0 is just the PMF of two non-interacting masses (originated from centrifugal force). So, if we are interested in the "absolute" PMF, e.g. pull a substrate into a protein, P0 is surely not be substracted from PMF; otherwise, if we are interested in "excess" PMF, e.g. ionic PMF with the aim of inversion of radial distribution function (which is calculated with the reference of ideal gas), then P0 should be removed. zgzhang > Date: Fri, 28 Nov 2008 22:55:18 +0100 > From: ?ngel Pi?eiro <[EMAIL PROTECTED]> > Subject: RE: [gmx-users] Re: About entropic contribution to the >potential of mean force > To: "'Discussion list for GROMACS users'" > Message-ID: <[EMAIL PROTECTED]@usc.es> > Content-Type: text/plain; charset="iso-8859-1" > > Dear Zgzhang, > > I am interested in your answer to your own question since I asked basically > the same several months ago, could you explain it better? > > > > Angel. > > ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: About entropic contribution to the potential of mean force
I've got it! Thanks myself. ^_^ So, it seems that the prior calculations by, i.e. Ciccotti, et al, Chem. Phys. 129, 241 (1989), Guardia, et al, J. Chem. Phys. 95, 2823 (1991) are flawy since they have not corrected the entropic effects at all. Cheers, zgzhang > Date: Wed, 26 Nov 2008 15:55:05 +0800 > From: "Zhang Zhigang" <[EMAIL PROTECTED]> > Subject: [gmx-users] About entropic contribution to the potential of >meanforce > To: gmx-users@gromacs.org > Message-ID: ><[EMAIL PROTECTED]> > Content-Type: text/plain; charset="iso-8859-1" > > Hi, >In the manual of gromacs, the entropic contribution to the pmf is > emphasized. In my opinion, this contribution is originated from the > rotations of the constrained groups. >However, according to the manual suggestion, "...when calculating a PMF > between two solutes in a solvent, for the purpose of simulating without > solvent, the entropic contribution should be removed." I'm really confused > with this. >If, e.g., in a infinite dilute solution of NaCl (only one Na+ and Cl- > and many water molecules), I want to calculate the potential of mean force > of NaCl, should I count the contributions from the entropic effects? >According to Hess et al., (2006), JCP, 124: 164509, this effect should > surely be added. >So, any one experienced with similar researches can give me an answer > for this: when should I add the entropic contribution to the pmfs? and, > what > the really physical explanation for this effect? >Thanks in advance! > > Regards, > > zgzhang > ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] About entropic contribution to the potential of mean force
Hi, In the manual of gromacs, the entropic contribution to the pmf is emphasized. In my opinion, this contribution is originated from the rotations of the constrained groups. However, according to the manual suggestion, "...when calculating a PMF between two solutes in a solvent, for the purpose of simulating without solvent, the entropic contribution should be removed." I'm really confused with this. If, e.g., in a infinite dilute solution of NaCl (only one Na+ and Cl- and many water molecules), I want to calculate the potential of mean force of NaCl, should I count the contributions from the entropic effects? According to Hess et al., (2006), JCP, 124: 164509, this effect should surely be added. So, any one experienced with similar researches can give me an answer for this: when should I add the entropic contribution to the pmfs? and, what the really physical explanation for this effect? Thanks in advance! Regards, zgzhang ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] About the gromacs 4.0 manual and parallel running
Hi, I'm using the newly published Gromacs 4.0 package these days. Compared with the prior versions, this version seems to have been improved a lot. From the ftp site, I've downloaded a manual for this version. But this manual seems to be incompleted, which can be revealed in the descriptions of the instructions for parallel runnings. I wonder: 1. When will the final official manual be published for 4.0? 2. How to run a parallel simulation with Gromacs 4.0? Are there any special tips for a optimized parallel run? I've tried a set of runnings but found the accelerations are not good enough as I expected. Thank you for your possible suggestions! zgzhang ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Problems of test particle insertion with gromacs 4.0
Hi all, I'm trying to use gromacs 4.0 to carried out some calculations with test particle insertion algorithm. Here are my operations: 0. Carried out a common NPT simulation with N molecules, I got the .trr file; 1. prepare .top and .gro with N+1 molecules (including the test particle); 2. use grompp to get the .tpr for mdrun; 3. mdrun -rerun .trr. In this way, I finally got two files tpi.xvg and tpidist.xvg. The procedure seems fine, isn't it? Nevertheless, I have some problems here: 1. when I was trying to use pme (or EWALD) for the electrostatics, the grompp stopped with an error: "TPI does not work with full electrostatics". But if I use cut-off, the grompp works but generates a warning to recommend the use of pme or reaction field. What's wrong here? 2. The final output of mu seems to be sensitive to the choice of nsteps (I've tried from 1000 to 1). How to choose an appropriate one? Thanks for your possible suggestions! zgzhang ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
