Re: [gmx-users] g_dipoles -slab option

+++ Bob Johnson [Wed, May 24, 2006 at 08:37:01PM -0400]: > for some reason and I can't interepret it. The first column is the position of > the water slab. I can only assume that column 2 is the dipole in the x > direction and column 3 is the dipole in the y direction and so on. Is that > correct?

Re: [gmx-users] Simulating crystalls

karamyog singh wrote: I am trying to simulate a crystal too. I have a box size of .65 nm and there are 8 bcc crystals in the system. Lattice parameter = 0.287 nm. I get a segmentation fault after mdrun -v. Is an atom with co-ordinates 0.574 0.000 0.000 equivalent to 0.287 0.000 0.000 in such a

[gmx-users] g_dipoles -slab option

Hello everyone, Water tends to align at a hydrophobic surface in a way to maximize H-bonds. Doing this leads to a dipole moment that is perpendicular to the surface (pointing away from the surface). Is this correct? I'm trying to verify this with a simulation. I have an uncharged surface in the xz

RE: [gmx-users] g_h2order still makes problem

> the g_h2order still makes problem, i divided the box > into 1 slice but it told me there are 2405777 water in the slice >while the system has only 2827 tip4p water molecules. > and the mu and cos generated is tortured! > can it be any mistakes from th

Re: [gmx-users] POPC simulation

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[gmx-users] POPC simulation

http://www.gromacs.org/mailman/listinfo/gmx-users > 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 > -- next part -- An HTML atta

Re: [gmx-users] POPC simulation

Arindam, I fixed this problem a while ago and it was pretty difficult to figure out. I tinkered with so many things, once I got it to work I didn't even know what steps I took to fix it! Here's something to try: GROMACS doesn't like the fact popc.itp has a four-character residue name (si

[gmx-users] Re: Simulating crystalls

Mark Abraham <[EMAIL PROTECTED]> writes: > > David van der Spoel wrote: > > Gale, Ella wrote: > > > >> > >> Thanks for the advice, but my force-field has no charges and hence no > >> coulomb potential, so I want the atoms to interact with itself via the > >> Van der Waals functions. I'm using

[gmx-users] POPC simulation

Hi Steffen, thanks for the reply. this is what i have done. my topol.top looks like this now #inlcude ffgmx.itp inlcude popc.itp. as per your last reply i have copied the contents of lipid.itp to ffgmxbon.itp and ffgmxnb.itp without removing the contents of the respective file. basically just app

[gmx-users] Stange results of bonds fep

Dear all, I'm trying to calculate dG of transition between alpha and pi conformation in some part of my protein. I indended to use fep and perform this conversion in three steps: first, I want to fix alpha conformation gradually by indroducing bonded interactions between i'th H, i+4 and i+5'th O,

Re: [gmx-users] Position restrain

Alessandro Mattozzi wrote: Hi How should my posres.itp look like? Is there any template available? Thank Regards genpr does generate position rstrains ... -- -- Xavier Periole - Ph.D. Dept. of Biophysical Chemistry / MD Group Univ. of Groningen Nijenborgh

[gmx-users] Position restrain

Title: Position restrain Hi How should my posres.itp look like? Is there any template available? Thank Regards Alessandro Mattozzi M.Phil., Ph.D. student Dept. of Fibre and Polymer Technology Royal Institute of Technology Stockholm, Sweden ___

Re: [gmx-users] Simulating crystalls

I am trying to simulate a crystal too. I have a box size of .65 nm and there are 8 bcc crystals in the system. Lattice parameter = 0.287 nm. I get a segmentation fault after mdrun -v. Is an atom with co-ordinates 0.574 0.000 0.000 equivalent to 0.287 0.000 0.000 in such a system? What I am trying

[gmx-users] CHARMM force field in GROMACS

Hi, I am making available under GPL two perl scripts, one of which converts a CHARMM27 .prm file into the necessary .itp files for pdb2gmx to use to produce .top files, and another that massages that .top file into something that will produce a .tpr file that will get CHARMM energy & force evalu

[gmx-users] error in gromppp

Dear All, I'm trying to simulate a dendrimer using AMBER and when running grompp i get the error message: file /usr/share/gromacs/top/spc.itp Atom index (1) in settles out of bounds (1-0). I didn't make any change in spc.itp file so that sounds a bit strange. The [settles] field contains the lin

RE: [gmx-users] fep calculation of L-Asn - D-Asn transition

From: Alexandra Patriksson <[EMAIL PROTECTED]> Reply-To: Discussion list for GROMACS users To: gmx-users@gromacs.org Subject: [gmx-users] fep calculation of L-Asn - D-Asn transition Date: Wed, 24 May 2006 11:11:38 +0200 Dear all, I'm trying to do a fep calculation of the L to D transition o

[gmx-users] g_h2order still makes problem

Hello, gmx-users， the g_h2order still makes problem, i divided the box into 1 slice but it told me there are 2405777 water in the slice while the system has only 2827 tip4p water molecules. and the mu and cos generated is tortured! can it be any mi

[gmx-users] fep calculation of L-Asn - D-Asn transition

Dear all, I'm trying to do a fep calculation of the L to D transition of a amino acid in a small peptide. We have done some changes to the dihedrals and the charges in the topology file (see below), but still we get dH/dlambda values that are far too large. Does anyone have an idea what could

Re: [gmx-users] Ions close to protein

From: David van der Spoel <[EMAIL PROTECTED]> Reply-To: Discussion list for GROMACS users To: Discussion list for GROMACS users Subject: Re: [gmx-users] Ions close to protein Date: Tue, 23 May 2006 20:13:32 +0200 David Mobley wrote: Joanne, >When I add ions to my system to neutralise it s

Re: [gmx-users] POPC simulation

Arindam Ganguly wrote: Hi Steffen, Thanks very much for the prompt reply. i made the changes as mentioned such that my popc.top looks like this :- #include "ffgmx.itp" #include "lipid.itp" #include "popc.itp" #include "ffgmx2nb.itp" #include "ffgmx2bon.itp" however is still get the same messag

Re: [gmx-users] g_h2order problem

Rongliang Wu wrote: Hello, gmx-users， my system has just 2827 water molecules, but the g_h2order command told me that there are more than 2807 waters in each slice. there are only one group in my index file and in O H H sequence. why? this is the sum over all frames. so this i