[gmx-users] comparing gmx GB energy with Amber11

Hi, I am comparing single point amber ff energies from gmx4.5.5 (double precision) and Amber11. All bonded and non-bonded energy terms are in very good agreement (within 0.1 kJ/mol) except GB: gmx 'GB polarization' = -200 kJ/mol amber 11 'EGB' = -283 kJ/mol. I am basically trying to re

Re: [gmx-users] Double entries in block structure--problem with SHAKE

Oh ! I'm sorry Justin Actually in my system I need to fix three types of bonds 1) Metal-Ligand distance at a particular value given in PDB ( not covalent) 2) I need to fix some of the bond lengths (covalent) for the substrate molecule. 3) Lastly the covalent H-bonds ( C-H, N-H, O-H etc.) My inp

[gmx-users] Re: Running Gromacs in Clusters

On Wed, Nov 7, 2012 at 11:48 PM, Dr. Vitaly Chaban wrote: > On Wed, Nov 7, 2012 at 11:24 PM, Marcelo Depolo > wrote: >> I thought that at first, but other softwares run in parallel. If there's a >> problem, it' s somehow in the PBS. >> >> My guess is that my PBS don't allow the LAM library "see"

Fwd: [gmx-users] Re: Running Gromacs in Clusters

On Wed, Nov 7, 2012 at 11:24 PM, Marcelo Depolo wrote: > I thought that at first, but other softwares run in parallel. If there's a > problem, it' s somehow in the PBS. > > My guess is that my PBS don't allow the LAM library "see" others nodes. But > I have no clue where the problem could be. I w

Re: [gmx-users] Re: Running Gromacs in Clusters

I thought that at first, but other softwares run in parallel. If there's a problem, it' s somehow in the PBS. My guess is that my PBS don't allow the LAM library "see" others nodes. But I have no clue where the problem could be. I've tried eliminating the "node=X" and got the error. I've tried use

Re: [gmx-users] What algorithm does g_sas use?

Thanks Matt! I've seen some vmd tcl scripts using msms to get the surface area. However I think as gromacs using united atom, I need too change radii parameters or in a more simple way, add all hydrogen back before calculation Cheers Guang 2012/11/8, Matthew Zwier : > Hi Guang, > > Be care

Re: [gmx-users] Running Gromacs in Clusters

Hi, I usually go with openMPI. I think there are issues with LAM, but other probably know more about that. Erik 7 nov 2012 kl. 19.36 skrev Marcelo Depolo: > Hi guys. > > > I've tried your suggestions and had no sucess. I've got "no resources > available" error but I checked out and 50% of th

Re: [gmx-users] Double entries in block structure--problem with SHAKE

On 11/7/12 10:46 AM, tarak karmakar wrote: Dear All, As I am facing the following problem while using SHAKE to constrain some bonds, I have checked the mailing list but I think, this issue has not been resolved. So if anyone knows the solution kindly inform me. Program mdrun, VERSION 4.5.5 So

Re: [gmx-users] Running Gromacs in Clusters

Hi, I looked at one of my old pbs jobs and noted that the following line works for me: #PBS -l nodes=X:ppn=Y where X is the number of nodes and ppn is the number of cores per node. Perhaps your batch system uses a different "dialect". What errors do you get when you aim for more than one node?

Re: [gmx-users] Temperature Histogram

On 11/7/12 11:42 AM, Samadashvili Nino wrote: Hello, I would like to calculate temperature in my system along the axis. Could you please tell me if there is a way to make a temperature histogram with Gromacs? Use g_energy to extract temperatures from the .edr file, then g_analyze -dist

[gmx-users] Re: Self-diffusion in high temperature water

Sorry for the bump, but, please, does anybody know something of any study of the self-diffusion frequency spectrum of water done with GROMACS? I am not sure if it is something I am doing wrong, or if that is simple not possible to model with the program. Thanks, Ignacio On Tue, Oct 30, 2

Re: [gmx-users] Running Gromacs in Clusters

Hi Erik, That's good news! But i've got problems using more than one node per simulation (24 cores per node in my cluster). I don't know if it's a parallelization script problem or anything else. I'm using PBS scripts like this: *#!/bin/bash #PBS -N Gromacs #PBS -lselect=1:ncpus=24 #PBS -m ae #

[gmx-users] Temperature Histogram

Hello, I would like to calculate temperature in my system along the axis. Could you please tell me if there is a way to make a temperature histogram with Gromacs? Thank you for your attention. Cheers, Nino-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/lis

Re: [gmx-users] Running Gromacs in Clusters

Hi, Sure you can go beyond 24 cores. I'm currently simulating ~170 000 atoms on 192 cores at ~45 ns a day. with half the number of processors I get ~27 ns a day. It will of course depend on the hardware, particular algorithms, run parameters, and on the system details. Erik 7 nov 2012 kl. 16.

[gmx-users] Double entries in block structure--problem with SHAKE

Dear All, As I am facing the following problem while using SHAKE to constrain some bonds, I have checked the mailing list but I think, this issue has not been resolved. So if anyone knows the solution kindly inform me. Program mdrun, VERSION 4.5.5 Source code file: invblock.c, line: 79 Fatal err

Re: [gmx-users] Protein at given pH

7 nov 2012 kl. 16.21 skrev Steven Neumann: > On Wed, Nov 7, 2012 at 2:55 PM, Erik Marklund wrote: >> Hi, >> >> I've used the H++ server myself at times. My experience is that it's rather >> sensitive to the very fine detail of the input structure in some cases. I've >> had situations where H+

Re: [gmx-users] Protein at given pH

On Wed, Nov 7, 2012 at 2:55 PM, Erik Marklund wrote: > Hi, > > I've used the H++ server myself at times. My experience is that it's rather > sensitive to the very fine detail of the input structure in some cases. I've > had situations where H++ suggest one protonation state, then a short md > s

Re: [gmx-users] What algorithm does g_sas use?

Hi Guang, Be careful with this tool. It's very fast and very good at what it's designed to do, but it does not appear to be designed to give accurate single-residue SASA (as you will read in the paper on the method employed). Definitely use g_sas for entire proteins or large cavities (it's blazing

Re: [gmx-users] Protein at given pH

Hi, I've used the H++ server myself at times. My experience is that it's rather sensitive to the very fine detail of the input structure in some cases. I've had situations where H++ suggest one protonation state, then a short md simulation takes the system to a slightly different conformation t

Re: [gmx-users] Protein at given pH

On Wed, Nov 7, 2012 at 12:20 PM, Justin Lemkul wrote: > > > On 11/7/12 7:10 AM, Steven Neumann wrote: >> >> On Wed, Nov 7, 2012 at 11:56 AM, Justin Lemkul wrote: >>> >>> >>> >>> On 11/7/12 4:19 AM, Steven Neumann wrote: Dear Gmx Users, I am trying to simulate protein-liga

Re: [gmx-users] Protein at given pH

On 11/7/12 7:10 AM, Steven Neumann wrote: On Wed, Nov 7, 2012 at 11:56 AM, Justin Lemkul wrote: On 11/7/12 4:19 AM, Steven Neumann wrote: Dear Gmx Users, I am trying to simulate protein-ligand interactions at specific pH=5. I processed my protein.pdb into the H++. As I see from th titrat

Re: [gmx-users] Protein at given pH

On Wed, Nov 7, 2012 at 11:56 AM, Justin Lemkul wrote: > > > On 11/7/12 4:19 AM, Steven Neumann wrote: >> >> Dear Gmx Users, >> >> I am trying to simulate protein-ligand interactions at specific pH=5. >> I processed my protein.pdb into the H++. As I see from th titration >> curve of the entire mole

Re: [gmx-users] Protein at given pH

On 11/7/12 4:19 AM, Steven Neumann wrote: Dear Gmx Users, I am trying to simulate protein-ligand interactions at specific pH=5. I processed my protein.pdb into the H++. As I see from th titration curve of the entire molecule it appears that at pH=5 the total charge should be equal to 2. When I

Re: [gmx-users] Polarisation model

On 2012-11-07 11:24, Volker Lesch wrote: On 11/07/2012 11:19 AM, David van der Spoel wrote: On 2012-11-07 10:21, Volker Lesch wrote: Dear all, I am a new Gromacs user. In the past I used AMBER, but because of performance and technical reason I want to switch to Gromacs. Actually, I have one bi

Re: [gmx-users] Polarisation model

On 11/07/2012 11:19 AM, David van der Spoel wrote: On 2012-11-07 10:21, Volker Lesch wrote: Dear all, I am a new Gromacs user. In the past I used AMBER, but because of performance and technical reason I want to switch to Gromacs. Actually, I have one big problem namely polarisation. In AMBER I

Re: [gmx-users] Polarisation model

On 2012-11-07 10:21, Volker Lesch wrote: Dear all, I am a new Gromacs user. In the past I used AMBER, but because of performance and technical reason I want to switch to Gromacs. Actually, I have one big problem namely polarisation. In AMBER I used the atomic point dipole model but this one is n

Re: [gmx-users] converting amber distributed parameters to gromacs.

There is not too much to say: the script is self-explanatory. Look also: http://www.gromacs.org/Documentation/Terminology/Force_Fields/AMBER?highlight=antechamber On 11/07/2012 10:27 AM, Rajiv Gandhi wrote: Could you please tell how do i use this script over amber file? Thanks. On Wed, Nov 7

Re: [gmx-users] converting amber distributed parameters to gromacs.

Could you please tell how do i use this script over amber file? Thanks. On Wed, Nov 7, 2012 at 5:58 PM, Felipe Pineda, PhD < luis.pinedadecas...@lnu.se> wrote: > ffamber.cnsm.csulb.edu/**amb2gmx.pl > > > > On 11/07/2012 09:45 AM, Rajiv Gandhi wrote: > >>

[gmx-users] Polarisation model

Dear all, I am a new Gromacs user. In the past I used AMBER, but because of performance and technical reason I want to switch to Gromacs. Actually, I have one big problem namely polarisation. In AMBER I used the atomic point dipole model but this one is not implemented in Gromacs (please corr

Re: [gmx-users] converting amber distributed parameters to gromacs.

ffamber.cnsm.csulb.edu/amb2gmx.pl On 11/07/2012 09:45 AM, Rajiv Gandhi wrote: Dear Gromacs user, I have found the parameters file for my ligand which is available in AMBER distribution parameter database, Could you advice me how do i use them in running over MD in gromacs? Thanks in advance,