[gmx-users] recognising phos group

Hi ! I am attempting to simulate a protein that is phosphorylated below is a part of the PDF file HETATM 460 P PO3 A 200 14.995 1.523 4.011 1.00 0.89 P HETATM 461 O1 PO3 A 200 14.287 1.882 5.272 1.00 1.16 O HETATM 462 O2 PO3 A 200 15.841 0.179 4.048 1.00 0

[gmx-users] continuation run in parallel with shuffle and, sort option

While the previously posted script seems like a valid approach, the usefulness of -sort depends entirely on how long your trajectory is. If you only sort once at the beginning, then after <<10ns your waters will be mostly redistributed and I think that you will have totally lost the benifits of

Re: [gmx-users] x2top, error generating topology

Vitaly Chaban wrote: Hello All, I've got a problem with x2top in gromacs 3.3.3. Trying to obtain atopology from ".pdb" structure I do the following: 1. Add C C 1 C ; CNT Carbon with one bond C C 2 C C ; CNT double bonded Carbon to ffencadv.n2t. 2. Add the following lines [ bondtypes ] ; i j f

[gmx-users] x2top, error generating topology

Hello All, I've got a problem with x2top in gromacs 3.3.3. Trying to obtain atopology from ".pdb" structure I do the following: 1. Add >> C C 1 C ; CNT Carbon with one bond >> C C 2 C C ; CNT double bonded Carbon to ffencadv.n2t. 2. Add the following lines [ bondtypes ] ; i j func b0 kb C C 1 0.1

Re: [gmx-users] inconsistent shifts

Bert wrote: Hi all, I use pbc=full in my system, and all runs are ok except for the "inconsistent shifts" warnings when I use some analysis tools, such as g_density, g_densmap, etc. I have searched the whole list related to this problem, and I doubt several analysis tools are not coded with

[gmx-users] inconsistent shifts

Hi all, I use pbc=full in my system, and all runs are ok except for the "inconsistent shifts" warnings when I use some analysis tools, such as g_density, g_densmap, etc. I have searched the whole list related to this problem, and I doubt several analysis tools are not coded with consideration of f

Re: [gmx-users] mix solvent

I gave you advice: http://www.gromacs.org/pipermail/gmx-users/2008-April/033307.html So what have you done to help yourself? Asking the same question without demonstrating that you've attempted to respond to the advice given will surely get you nowhere. -Justin Quoting Mahnam <[EMAIL PROTECTE

[gmx-users] continuation run in parallel with shuffle and sort option

Hi, I was running a DPPC system with 128 DPPC and 3655 water molecules in 16 CPU with -shuffle -sort option. But I am unable to continue the job in parallel. I read a lots of posts in mailing list, but could not understand the proper way, as I don't know the script languages. So whatever is menti

Re: [gmx-users] mdrun exectutable

On Tue, 08 Apr 2008 15:49:10 +0200 Marilisa Neri <[EMAIL PROTECTED]> wrote: I am trying to compile by hand the mdrun executable. For this reason, I have selected just the routines that I need. Why don't you run the configure and then use "make mdrun" I think it will do what you want! I collec

[gmx-users] mix solvent

In God We Trust Hello GMX users I want to equilibrate my protein in a mix solvent, befor this work, I made a cubic box that it contained 215 spc water and 5 proline molecule (without protein) with 20*20*20 angestrom and then I minimized it. when I do position restrain with NPT e

Re: [gmx-users] mdrun exectutable

Marilisa Neri wrote: I am trying to compile by hand the mdrun executable. For this reason, I have selected just the routines that I need. I collected a list of file.c, file.h, and file.s . I compiled the files .c and .s with this command: (i) mpicc -c *.[cs] -I. -I /fftw-2.1.5/include/ -DHA

[gmx-users] mdrun exectutable

I am trying to compile by hand the mdrun executable. For this reason, I have selected just the routines that I need. I collected a list of file.c, file.h, and file.s . I compiled the files .c and .s with this command: (i) mpicc -c *.[cs] -I. -I /fftw-2.1.5/include/ -DHAVE_CONFIG_H -DGMXLIB

Re: [gmx-users] (no subject)

Is your simulation box (20*20*20 A^3) big enough? 2008/4/7 Mahnam <[EMAIL PROTECTED]>: > In God We Trust > Hello GMX users > I want to equilibrate my protein in a mix solvent, befor this work, I made > a cubic box that it contained 215 spc water and 5 proline molecule (without > protein) with

Re: [gmx-users] bilayer simulation crashes after 2 ns or 7 ns of stable runs. why does system explode

What will happen if pbc=full is used? 2008/4/4 maria goranovic <[EMAIL PROTECTED]>: > Dear All > > I am running a 128-lipid bilayer simulation with standard parameters. The > simulation abruptly crashed after 2 ns, and a look into the pdb files > suggested that bonds were being broken and eve

RE: [gmx-users] AA not present in the ffG43a1.rtp

You find those definitions in ffG43a1bon.itp. As far as I know, they are simply placeholders for the explicit data. Probably you can insert the explicit data into the rtp file. Andreas > -Original Message- > From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] > On Behalf Of Mattia Sturles

Re: [gmx-users] AA not present in the ffG43a1.rtp

Quoting Mattia Sturlese <[EMAIL PROTECTED]>: > Dear all, > I have a protein with an oxidated Cys( to sulfinic acid) , this > residue is not present in the residue database. I use PRODGR to obtain > the .itp file of the residue but I don't start grompp Be aware that the charges given by

[gmx-users] AA not present in the ffG43a1.rtp

Dear all, I have a protein with an oxidated Cys( to sulfinic acid) , this residue is not present in the residue database. I use PRODGR to obtain the .itp file of the residue but I don't start grompp How I insert this residue in the rtp file?? I trying insert the parameters manually

Re: [gmx-users] g msd freeze

Quoting Kateøina Hyn¹tová <[EMAIL PROTECTED]>: > The simulated system is a carbon chain of 1000 united atom units. Ive tried > bothmaking the system smaller (less units or extracting the trajectory for > one unit)and taking very short time of simulation using the flags -b and -e, > the system respo

Re: [gmx-users] CPMD and gmx

Thanks, Vasilii. >From publ it's clear that 5 a.u. is standart for all CP MD simulations, I was confused by examples from Biswas page :) It's time to start cp md and will go deeper in theory :) On Mon, Apr 7, 2008 at 9:39 PM, Vasilii Artyukhov <[EMAIL PROTECTED]> wrote: > Dear Andrey, > > The ma

[gmx-users] g msd freeze

>Kateřina Hynštová wrote: >> Dear users, >> >> >> >> I would like to calculate the mean square displacement. >> >> Using the >> >> >> >> g_msd -f traj.xtc -s input.tpr -n index.ndx -o msd.xvg >> >> >> >> I get >> >> >> >> Reading file input.tpr, VERSION 3.3.2(single precision) >>