[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 molecu

Re: [gmx-users] g_rmsd

Hi sh-karbalaee, g_rmsf by default uses deviations from the average structure. You can write out that structure and use it as reference for g_rms. Cheers, Tsjerk On Thu, Dec 4, 2008 at 6:52 AM, shahrbanoo karbalaee <[EMAIL PROTECTED]> wrote: > Dear justin > I want to calculate rmsd or rmsf fro

[gmx-users] g_rmsd

Dear justin I want to calculate rmsd or rmsf from avg structure.Infact I calculate standard deviation from average structure.Can I do it with command g_rmsf and g_rmsd?thanks for your advise. best sh-karbalaee ___ gmx-users mailing listgmx-users@gro

[gmx-users] work from pulling simulation

1. What is Z_bead? 2. Could you give us a real .pdo file segment? 3. I can only assume AFM, or something similar, but need to see a pull code input file. Can you provide one? 4. What version of gromacs? This is all to say I don't have enough information. But from what I can see: 1. If you are

[gmx-users] work from pulling simulation

Hello GMXers, I am performing steered MD simulations using the pull code in 1-Dimension (z) and I'd like to calculate the work done on my system (in the z-direction) by the pulling spring. If my output PDO pulling file looks something like this: TimeZ_pulled_group Z_bead 0 0

[gmx-users] nested #include "./file" for .itp's no longer inherits directory in gromacs 4

Hello, I have noticed that gromacs 4.0.2 does not follow the gromacs 3.3.1 procedure for treating the directory in nested includes. Basically, if a .top includes file A and file A includes file B, then it was previously possible to put file B in the same directory as file A and to omit a full

Re: [gmx-users] Infinite force on an atom

Manik Mayur wrote: Hi, I have developed a co-ordinate file for Argon atoms bounded by wall atoms with properties same as Argon. When I am doing the energy minimization, it shows a max. force equal to inf. on a certain atom. This is for the case when I am using "simple" in the neighbour searc

[gmx-users] Infinite force on an atom

Hi, I have developed a co-ordinate file for Argon atoms bounded by wall atoms with properties same as Argon. When I am doing the energy minimization, it shows a max. force equal to inf. on a certain atom. This is for the case when I am using "simple" in the neighbour search, when I use "grid" it gi

Re: [gmx-users] Re: Re: problems running grompp with protein-ligand complex

Ragnarok sdf wrote: I am working with a system using ffamber99 forcefield and trying to set up a ligand protein complex system. I have encountered some problems with grompp now. In my past email, the problem was that : > Fatal error: Found a second defaults directive, file "ligand.itp", line 5.

[gmx-users] Re: Re: problems running grompp with protein-ligand complex

I am working with a system using ffamber99 forcefield and trying to set up a ligand protein complex system. I have encountered some problems with grompp now. In my past email, the problem was that : > Fatal error: Found a second defaults directive, file "ligand.itp", line 5. Then the following solu

RE: [gmx-users] REMD problem in concept

Hi, I think you are talking about two different concepts. At the moment of switching the replicas, the potential energy does not change, because the force field is temperature indepent. This is what Chris meant. As the system evolves in time, the potential energy will go up when a replica is swit

Re: [gmx-users] REMD problem in concept

[EMAIL PROTECTED] wrote: dG=dH-TdS so as T increases, so does the entropic contribution to the free energy (=available energy). The potential energies stay the same when using a temperature-independent forcefield (like all of the ones that come with gromacs). That's not quite right. The ave

[gmx-users] REMD problem in concept

dG=dH-TdS so as T increases, so does the entropic contribution to the free energy (=available energy). The potential energies stay the same when using a temperature-independent forcefield (like all of the ones that come with gromacs). Your system will easily cross barriers on the order of

RE: [gmx-users] test molecule insertion

Hi, The molecule you want to insert should be a single charge group. I guess you have miore than one charge group in the molecule. I will add a check in the code for this, so you get a more comprehensible error message. Berk > Date: Wed, 3 Dec 2008 12:34:23 +0100 > From: [EMAIL PROTECTED] > To

Re: [gmx-users] error

shahrbanoo karbalaee wrote: hi Dear justin would you please tell me about this error.I run by gromacs version 3.3 and my file consist of peptide,tfe ,water.I want to minimize that I get this error. Search the list archive, this has been reported dozens (if not hundreds) of times. Your sys

[gmx-users] error

hi Dear justin would you please tell me about this error.I run by gromacs version 3.3 and my file consist of peptide,tfe ,water.I want to minimize that I get this error. Steepest Descents: Tolerance (Fmax) = 1.0e+03 Number of steps= 2000 -

[gmx-users] test molecule insertion

Hi I have trouble inserting molecules for test particle insertion (with atoms there is no problem at all). I have defined my conf.gro, topology and index files, but it keeps saying that "Number of atoms in trajectory (7000) is not equal the number in the run input file (7005) minus the number o