Re: [gmx-users] g_dipole ? => dipole moment ?

On 2010-10-18 03.30, Chih-Ying Lin wrote: HI I confined one molecule in the center of box and issue the g_dipole command. The average dipole moment is still around 32. It is the molecule with 33 atoms / united atoms of most carbon groups, isn't the dipole moment around 32 too high? How can I test

Re: [gmx-users] Simulation parameter problem about protein unfolding

Hi, If I can add to this discussion, I think that your results are very reasonable. Proteins in solution are not straight lines, but fold to some extent. If you wish to have en elongated protein you have to pull it like it is being done in AFM experiments. Itamar On 18/10/10 3:56 PM, chris.

[gmx-users] Simulation parameter problem about protein unfolding

Generally, forcefields are not parameterized for temperatures other than 298K, so simulations are not expected to reproduce the expected properties (like boiling water and the correct temperature denaturation of proteins). There's almost certainly other issues here (including the fact that

[gmx-users] Simulation parameter problem about protein unfolding

Hi All, I met a problem when I try to unfold a protein using Gromacs, It seemed the protein cannot be totally unfolded! The simulated system has one Engrailed Homeodomain (En) protein (a three helix bundle protein with 54 residues, 629 atoms), total 4848 spce waters, and 7 Cl- used to neutrali

[gmx-users] Re: [gmx-developers] More than one settle type

I am CC'ing this message to the gmx-users list; please continue any future discussion there. I hadn't realized it was initially posted to gmx-developers, which is the wrong forum for such questions. Comments inline below. Emanuel Birru wrote: Hi Jestin, Thanks for your advise. Just to mak

Re: [gmx-users] The trouble with dihedral restraints: frozen peptide backbones

- Original Message - From: ms Date: Monday, October 18, 2010 8:23 Subject: [gmx-users] The trouble with dihedral restraints: frozen peptide backbones To: Discussion list for GROMACS users > Hi, > > It's a bit long but bear with me if you can. I'm getting quite > mad with this. Thank

Re: [gmx-users] Problems when simulating a protein in its crystal matrix.

Try a smaller integration timestep while you equilibrate. Set nstxout = 1 and look closely at the region that starts to break. Try without constraints. Alternatively, simplify/change the problem by (say) stripping all the crystal waters before adding, or solvating only one copy of the protein (t

[gmx-users] g_dipole ? => dipole moment ?

HI I confined one molecule in the center of box and issue the g_dipole command. The average dipole moment is still around 32. It is the molecule with 33 atoms / united atoms of most carbon groups, isn't the dipole moment around 32 too high? How can I test next and know that the dipole moment aro

[gmx-users] Problems when simulating a protein in its crystal matrix.

Hi All, I wish to simulate a protein in its crystal form. The crystal is a triclinic box with a C2 symmetry. I have built the unit cell, which has 4 copies of the protein, and add some water on top of the ones in the pdb. Then minimized and run positional restrained MD followed by a non restr

[gmx-users] The trouble with dihedral restraints: frozen peptide backbones

Hi, It's a bit long but bear with me if you can. I'm getting quite mad with this. Thanks :) Now. I am using Gromacs (4.0.7 currently) to create a custom coarse-grained, no-solvent MD peptide model -one that contains the backbone but has only C-alphas, no side chains. To enforce chirality i

Re: [gmx-users] analysis

Dear justin Thank you I will do that. On Sun, Oct 17, 2010 at 7:12 PM, Justin A. Lemkul wrote: > > > mohsen ramezanpour wrote: > >> Dear Gromacs users >> >> I am searching for a good text for underestanding analysis tools. >> Of course I had read the user manual (chapter 8),But I think I need mo

Re: [gmx-users] analysis

mohsen ramezanpour wrote: Dear Gromacs users I am searching for a good text for underestanding analysis tools. Of course I had read the user manual (chapter 8),But I think I need more about them.for example I want a mathematical description and an easy explanation of analysis tool's results

[gmx-users] analysis

Dear Gromacs users I am searching for a good text for underestanding analysis tools. Of course I had read the user manual (chapter 8),But I think I need more about them.for example I want a mathematical description and an easy explanation of analysis tool's results from a MD trajectory. Please let

Re: [gmx-users] g_dipole ? => dipole moment ?

-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 On 10/16/2010 10:28 PM, David van der Spoel wrote: > On 2010-10-16 21.36, Chih-Ying Lin wrote: >> >> Hi >> I issue the g_dipole command on Gromacs => And, the following >> information is shown. >> There are 10 molecules in the selection, >> Does the Av

Re: [gmx-users] A very strange problem about version of pdb2gmx

英雄不再寂寞 wrote: Dear gmxers, Yesterday, I posted a mail titled "pdb2gmx stop at "AtomType 1" " where I mentioned that I used gmx-4.5.1. The resulting problem is again posted below. Today, I turn to the gmx-4.0.7, and use the same pdb and rtp files with the name modified to compatible to the

[gmx-users] A very strange problem about version of pdb2gmx

Dear gmxers, Yesterday, I posted a mail titled "pdb2gmx stop at "AtomType 1" " where I mentioned that I used gmx-4.5.1. The resulting problem is again posted below. Today, I turn to the gmx-4.0.7, and use the same pdb and rtp files with the name modified to compatible to the version. Strangely