RE: [gmx-users] find the relevant structure out

I do not know how to extract some special frames out (professionally), so I just simply use vim to take the relevant models out and put into a new pdb file. Are there some good ways to extract one or two frames at the end of those whole frames? Base on your answering, now I start to suspect I

[gmx-users] perl script for g_hbond / summary_HBmap.dat

Dear Justin Thank you so much for help. I used # symbol in where you said and problem was solved. a output was obtained with name summary_HBmap.dat. this file is as follows: #DonorAcceptor% Exist.

Re: [gmx-users] Problem with large number of frames only one frame can be read from trajectory bug ?

Resolved: I have found the error. Apparently I was using -dt 20, and the condition that t mod dt = first time (ps) was not being met because the first time was a funny number. Have rectified it. Apologies for the inconvenience. -- Maria G. Technical University of Denmark Copenhagen --

Re: [gmx-users] 3 questions of gromacs 4.5.2 for both CPU and GPU

Hi, On 11/24/10 2:59 AM, lin hen wrote: hi, I am testing the dhfr benchmarks with gromacs 4.5.2 1. for the benchmarks: dhfr-solv-RF-1nm.bench and dhfr-solv-RF-2nm.bench, set the steps = 1, The GPU version running results shows as following: ./mdrun-gpu Pre-simulation ~15s

Re: [gmx-users] perl script for g_hbond / summary_HBmap.dat

Quoting leila karami karami.lei...@gmail.com: Dear Justin Thank you so much for help. I used # symbol in where you said and problem was solved. a output was obtained with name summary_HBmap.dat. this file is as follows: #DonorAcceptor% Exist.

Re: [gmx-users] A periodic boundary trajectory with lots of objects: how to get rid of artefacts?

On 24/11/10 02:47, Mark Abraham wrote: On 24/11/2010 5:04 AM, ms wrote: On 23/11/10 17:00, Mark Abraham wrote: There is no general solution for bonds visualized on a single set of coordinates, however - over a trajectory, either molecules appear to diffuse out of the box, or appear to break.

[gmx-users] perl script for g_hbond / summary_HBmap.dat

Dear Justin thanks for your attention with chang of hbond.ndx file my problem was solved. I have another question about g_hbond: if I want to obtain same information (percentage of existence of each hbond during my trajectory) about water mediated hydrogen bonds between protein and dna, for

[gmx-users] Electric field: phosphate moves in the wrong direction

Dear users, I am applying an Electric Field along the z-axis to a system comprising a protein nanopore and a PO4- in order to see if gets into the pore. In some of the simulations the phosphate doesn't move on the opposite direction of the applied field but in the same direction! I wonder if

Re: [gmx-users] perl script for g_hbond / summary_HBmap.dat

Hi, If you mean interactions bridged by a watermolecule, Protein-H2O-DNA, then I don't know of any gromacs related tools for this. You need to write your own tool for this. One way would be to multiply the existence functions for hbonds between protein and water and the hbonds between water

[gmx-users] installation

Hi all, I'm trying to install gromacs.4.5.3 on fedora 13. I followed the instruction on the website, I completed my make install and this was the output: GROMACS is installed under /usr/local/gromacs. Make sure to update your PATH and MANPATH to find the programs and unix manual pages, and

Re: [gmx-users] installation

Quoting Rossella Noschese noschese.rosse...@gmail.com: Hi all, I'm trying to install gromacs.4.5.3 on fedora 13. I followed the instruction on the website, I completed my make install and this was the output: GROMACS is installed under /usr/local/gromacs. Make sure to update your PATH and

[gmx-users] g_hbond -ac -life

Dear gromacs users I used g_hbond -f .trr -s .tpr -n .ndx -ac -life. Can anyone clarify last 2 columns in hblife.xvg and last 4 columns hbac.xvg files by details. Also, I want to know what is difference between p(t) in hblife.xvg and c(t) in hbac.xvg file? which of them is more suitable for HB

Re: [gmx-users] installation

ok, but when I type luck it says command not found, where's my mistake? 2010/11/24 Justin A. Lemkul jalem...@vt.edu Quoting Rossella Noschese noschese.rosse...@gmail.com: Hi all, I'm trying to install gromacs.4.5.3 on fedora 13. I followed the instruction on the website, I completed my

Re: [gmx-users] g_hbond -ac -life

shahab shariati skrev 2010-11-24 16.24: Dear gromacs users I used g_hbond -f .trr -s .tpr -n .ndx -ac -life. Can anyone clarify last 2 columns in hblife.xvg and last 4 columns hbac.xvg files by details. Also, I want to know what is difference between p(t) in hblife.xvg and c(t) in hbac.xvg

Re: [gmx-users] installation

it was g_luck!!!it changed...ok, now it seems it wors! Thanks 2010/11/24 Rossella Noschese noschese.rosse...@gmail.com ok, but when I type luck it says command not found, where's my mistake? 2010/11/24 Justin A. Lemkul jalem...@vt.edu Quoting Rossella Noschese

[gmx-users] g_hbond -ac -life

Dear Erik thanks. thus -ac is only for determine the rate for hb breaking. is it true? or there is other usable case for -ac option? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at

[gmx-users] perl script for g_hbond / summary_HBmap.dat

Dear Erik I'm confused. is there h(t) in hbmap.xpm file? where is h(t)? which output file of g_hbond tool? -- Leila Karami Ph.D. student of Physical Chemistry K.N. Toosi University of Technology Theoretical Physical Chemistry Group -- gmx-users mailing listgmx-users@gromacs.org

[gmx-users] Re: perl script for g_hbond / summary_HBmap.dat

/pipermail/gmx-users/attachments/20101124/42b2e41d/att achment-0001.html -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un

Re: [gmx-users] installation

On Nov 24, 2010, at 4:04 PM, Rossella Noschese wrote: Hi all, I'm trying to install gromacs.4.5.3 on fedora 13. I followed the instruction on the website, I completed my make install and this was the output: GROMACS is installed under /usr/local/gromacs. Make sure to update your PATH and

[gmx-users] (no subject)

Dear gromacs users, I want to heat system from 0K till 300K. Than do equilibration dynamics in water. I can not find any .mdp files where the system is gradually heated from initial temperature (0K) till needed temperature. I can only find NVP and NVT equilibration dynamics. Please can you advice

Re: [gmx-users] (no subject)

Quoting Olga Ivchenko olga.ivche...@gmail.com: Dear gromacs users, I want to heat system from 0K till 300K. Than do equilibration dynamics in water. I can not find any .mdp files where the system is gradually heated from initial temperature (0K) till needed temperature. I can only find NVP

[gmx-users] heme

Dear all I am trying MD of cyt C containing heme. I am able to generate bonds with specbond.dat by pdb2gmx. After using editconf and genbox, when I tried grompp I got error about unrecognized bonds/angles. I made bond with MET SD and FE of Heme. As earlier suggested on this list I wrote to get

Re: [gmx-users] g_hbond -ac -life

shahab shariati skrev 2010-11-24 16.45: Dear Erik thanks. thus -ac is only for determine the rate for hb breaking. is it true? or there is other usable case for -ac option? And formation. And equillibrium constant. -- --- Erik Marklund, PhD

Re: [gmx-users] perl script for g_hbond / summary_HBmap.dat

Well, yes. The 'h' notation is never used in the xpm file. I just borrowed it from Luzar and chandler. Every line in the xpm data is the h(t) for a particular hydrogen bond. Erik leila karami skrev 2010-11-24 16.50: Dear Erik I'm confused. is there h(t) in hbmap.xpm file? where is h(t)?

Re: [gmx-users] heme

shahid nayeem skrev 2010-11-24 18.02: Dear all I am trying MD of cyt C containing heme. I am able to generate bonds with specbond.dat by pdb2gmx. After using editconf and genbox, when I tried grompp I got error about unrecognized bonds/angles. I made bond with MET SD and FE of Heme. As

[gmx-users] Nose-Hoover Thermostat for Non Equilibrium Simulations

Hello GROMACS users, I have a questions regarding how a Nose-Hoover thermostat works in non equilibrium simulations in GROMACS . If I apply some constant acceleration in the x direction, is the thermostat applied to all degrees of freedom or is it applied only in the y and z direction. Thanks.

[gmx-users] Martini parameters for formyl group

Dear users, I was wondering if there is Martini topology available for simple formyl (or aldehyde) group H - C = O. I would appreciate if somebody can direct me to the place where such force field parameters are discussed. Thanks, George -- George Khelashvili, Ph.D. Department of Physiology

Re: [gmx-users] heme

Erik Marklund wrote: shahid nayeem skrev 2010-11-24 18.02: Dear all I am trying MD of cyt C containing heme. I am able to generate bonds with specbond.dat by pdb2gmx. After using editconf and genbox, when I tried grompp I got error about unrecognized bonds/angles. I made bond with MET SD

[gmx-users] Reg: Interfacial tension

Hi all How to find the interfacial tension between two immiscible liquids in gromacs?. how one should start abou it. any help is highly is appreciated. Regards Vinoth -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive

Re: [gmx-users] heme

I am using ffG43a1 forcefield. its .rtp file contains topology of Heme but Met SD and FE bond is not there. Shahid Nayeem On Thu, Nov 25, 2010 at 5:11 AM, Justin A. Lemkul jalem...@vt.edu wrote: Erik Marklund wrote: shahid nayeem skrev 2010-11-24 18.02: Dear all I am trying MD of cyt C

[gmx-users] Reg: Interfacial tension

Hi all I want to calculate the interfacial tension of two immiscible liquids using the surface tension option in gromacs. when i do that i am getting the error message as One of the box vectors has become shorter than twice the cut-off length or box_yy-|box_zy| or box_zz has become smaller than

[gmx-users] RMSD and Resolution

Hi, Is there a relationship between RMSD value obtained from the calculation and Resolution value in PDB file? Thanks in advance -- Ahmet YILDIRIM -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at