Re: [gmx-users] No such moleculetype NA+

Hello Shikha Replace NA+ with NA in your topol.top file. It will solve the problem as it recognise NA for NA+. Thanks Yuvraj IIIT Hyderabad On Sun, Dec 26, 2010 at 12:26 PM, gmx-users-requ...@gromacs.org wrote: Send gmx-users mailing list submissions to gmx-users@gromacs.org To

Re: [gmx-users] Replicating an experiment

On 26/12/2010 4:37 AM, NG HUI WEN wrote: Thank you David for your prompt and useful reply :) I am in fact simulating a membrane protein. It's good to know I can use the generate-new-starting-velocity method. But, do you mind to elaborate a bit more what you mean by if you simulate long

[gmx-users] topolbuild1_3 install problem

Hi all I downloaded topolbuild1_3 from the GROMACS website, and I run the command as follows: path: home/buct/topolbuild1_3 ” # tar -xvf topolbuild1_3.tgz #make -f Makefile ; (intel CPU) there were no any error messages. then I

[gmx-users] topolbuild1_3 install problem

Hi all I downloaded topolbuild1_3 from the GROMACS website, and I run the command as follows: path: home/buct/topolbuild1_3 ” # tar -xvf topolbuild1_3.tgz #make -f Makefile ; (intel CPU) there were no any error messages. then I

Re: [gmx-users] average pressure too high

Hi, what is the standard deviation and drift? Are you sure this is a significant difference to 1? Roland On Sun, Dec 26, 2010 at 12:28 AM, sreelakshmi ramesh sree.laks...@research.iiit.ac.in wrote: Dear users, I did nvt equil and after that npt equilbriation and i am using

Re: [gmx-users] amb2gmx.pl file

Hi Xiaodu, The fudgeLJ under defaults should be 1.0 for GLYCAM. I'm unable to check my own files right now so can't compare. When you run grompp check in the output that fudge is set to 1.0. So there will be no protein in your simulation correct? I think there is a way to do mixed scaling in

[gmx-users] Re: average pressure too high

On Sun, Dec 26, 2010 at 12:28 AM, sreelakshmi ramesh sree.laks...@research.iiit.ac.in wrote: Dear users,                  I did nvt equil and after that npt equilbriation and i am using parinello rahman as the barostat but the prob is even after 200 ps of equil the avg pressure is 1.5 bar

[gmx-users] number of DD cells

Hi, I am following umbrella sampling tutorial for my membrane protein system. While running continuous pulling simulation (mdrun). under step five: Generating Configurations of the tutorial. I get the below error. The system ran initially but corrupted very soon with warning The X-size of

Re: [gmx-users] How to suppress the error X particles communicated to PME node Y are more than a cell length out of the domain decomposition cell of their charge group

Hi, Mark, Thanks for the reply. As suggested, I tried a water in vacuum case. Initially the water droplet is a cubic 4nm-by-4nm-by-4nm water box, located in the middle of the simulation box. Everywhere else is just vacuum. The simulation box size is 8nm by 8nm by 8nm. SPC/E model is used to

[gmx-users] number of DD cells

Hi, To my earlier post on number of DD cells.i included -dds 0.6 and everything seems to run fine. Is this the possible solution to the error or is there other way to handle this warning ? Kind regards, chetan.

[gmx-users] umbrella sampling

Hi, I am working on membrane protein. In umbrella sampling tutorial...we saw the pulling of the peptide A away from peptide B. I want to pull the peptide deep into the hydrophobic core of the bilayer from outside (solvent environment). Please can someone suggest me how to go about this.

Re: [gmx-users] How to suppress the error X particles communicated to PME node Y are more than a cell length out of the domain decomposition cell of their charge group

On 27/12/2010 9:22 AM, WU Yanbin wrote: Hi, Mark, Thanks for the reply. As suggested, I tried a water in vacuum case. Initially the water droplet is a cubic 4nm-by-4nm-by-4nm water box, located in the middle of the simulation box. Everywhere else is just vacuum. The simulation box size is

Re: [gmx-users] number of DD cells

On 27/12/2010 7:51 AM, Poojari, Chetan wrote: Hi, I am following umbrella sampling tutorial for my membrane protein system. While running continuous pulling simulation (mdrun). under step five: Generating Configurations of the tutorial. I get the below error. The system ran initially but

Re: [gmx-users] topolbuild1_3 install problem

On 26/12/2010 10:07 PM, gromacs564 wrote: Hi all I downloaded topolbuild1_3 from the GROMACS website, and I run the command as follows: path: home/buct/topolbuild1_3 ?? # tar -xvf topolbuild1_3.tgz #make -f Makefile ; (intel CPU) there were no

RE: [gmx-users] number of DD cells

Hi Mark, I ran on 48 processors.the error is: The X-size of the box (5.312040) times the triclinic skew factor (1.00) is smaller than the number of DD cells (6) times the smallest allowed cell size (0.885281) Kind regards, chetan From:

Re: [gmx-users] number of DD cells

Poojari, Chetan wrote: Hi Mark, I ran on 48 processors.the error is: The X-size of the box (5.312040) times the triclinic skew factor (1.00) is smaller than the number of DD cells (6) times the smallest allowed cell size (0.885281) I would say this further confirms Mark's

Re: [gmx-users] umbrella sampling

Poojari, Chetan wrote: Hi, I am working on membrane protein. In umbrella sampling tutorial...we saw the pulling of the peptide A away from peptide B. I want to pull the peptide deep into the hydrophobic core of the bilayer from outside (solvent environment). Please can someone

RE: [gmx-users] Replicating an experiment

Thanks Mark, message noted:) -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Mark Abraham Sent: Sunday, December 26, 2010 6:03 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Replicating an experiment On