Re: [gmx-users] How I extend command?

2015-02-23 Thread Chandan Choudhury
use -cpi state.cpt in the mdrun command Replace state.cpt file with the actual cpt file written by mdrun. On Tue, Feb 24, 2015 at 10:39 AM, Abid Channa wrote: > Hi gromacs users, > > I am working membrane complex simulation of 20 > ns, 100, steps , my simulation is reached 40,0 steps it

[gmx-users] How I extend command?

2015-02-23 Thread Abid Channa
Hi gromacs users, I am working membrane complex simulation of 20 ns, 100, steps , my simulation is reached 40,0 steps it stoped by mistakenly , How I can extend this 40 lac steps to 1 crore steps rather than starting , thanks in advance Abid Ali Channa, Junior Research Fellow, Lab No.

[gmx-users] Gromacs in windows 7 with GPU

2015-02-23 Thread 라지브간디
Dear all, I have a Windows 7 OS system which has i7, CPU @ 3.40GHz, 16 GB RAM and newly installed NVIDIA GeForce GX960 with 1 TB memory. Since i am familiar with gromacs in Linux system, i am not able to install in windows environment. Should i use cygwin or Visual Studio ? Though i tried V

[gmx-users] How I extend command

2015-02-23 Thread Abid Channa
Hi gromacs users, I am working membrane complex simulation of 20 ns, 100, steps , my simulation is reached 40,0 steps it stoped by mistakenly , How I can extend this 40 lac steps to 1 crore steps rather than starting , thanks in advance Abid Ali Channa, Junior Research Fellow, Lab No.

Re: [gmx-users] Beyond the KALP15 in DPPC tutorial and doing analysis in GROMACS

2015-02-23 Thread Justin Lemkul
On 2/23/15 6:13 PM, Thomas Lipscomb wrote: Dear gmx-users, I have finished the KALP15 in DPPC tutorial up to completing the molecular dynamics but not any of the analysis:http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/09_analysis.html I made one chang

[gmx-users] Beyond the KALP15 in DPPC tutorial and doing analysis in GROMACS

2015-02-23 Thread Thomas Lipscomb
Dear gmx-users, I have finished the KALP15 in DPPC tutorial up to completing the molecular dynamics but not any of the analysis:http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/09_analysis.html I made one change to the tutorial: using one maximin 3 molecule

Re: [gmx-users] Error during mdrun

2015-02-23 Thread Justin Lemkul
On 2/23/15 9:32 AM, soumadwip ghosh wrote: Dear all, I started an MDrun of Barstar protein in TIP3P water and 8M urea, neutralized by the required number of counterions. Until the mdrun, there was no issue with either energy minimization and equilibration steps. But whenever I wan

Re: [gmx-users] Error during mdrun

2015-02-23 Thread Rohit Farmer
Hi Soumadwip, I my understanding this error occurs when GROMACS can't distribute your job on the number of cores you are asking. Try to change the number of cores from 80 to something else, probably a fewer number of cores. I had this error once and I figured out that was the reason, but I am not

[gmx-users] Error during mdrun

2015-02-23 Thread soumadwip ghosh
Dear all, I started an MDrun of Barstar protein in TIP3P water and 8M urea, neutralized by the required number of counterions. Until the mdrun, there was no issue with either energy minimization and equilibration steps. But whenever I want to start MD run, a fatal error shows up saying

Re: [gmx-users] Simulation of polarizable Carbon nanotubes

2015-02-23 Thread Justin Lemkul
On 2/23/15 3:47 AM, Peter Kroon wrote: On 02/22/2015 05:33 PM, Jashimuddin Ashraf wrote: Thanks for your reply Dr. Lemkul I changed the bond length to zero in my topology file, forcefield file and in the n2t file. I also added the [ exclusion] section- If memory serves, you don't need a bo

Re: [gmx-users] g_rdf

2015-02-23 Thread Justin Lemkul
On 2/23/15 6:50 AM, leila salimi wrote: Dear all, I have a question regarding radial distribution function. Does g_rdf program work for non-cubic cell eg. triclinic? Yes. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdo

Re: [gmx-users] ffbond.itp

2015-02-23 Thread Justin Lemkul
On 2/23/15 1:04 AM, marzieh dehghan wrote: Hi every body 1- In the phosphate group, we have 4 oxygen atoms that bond to the phosphate. Two of them are as follow: CH2-O-P-OH and the others include: - A double bond is on the top of phosphor atom - A OH group is at the b

Re: [gmx-users] mdrun crash

2015-02-23 Thread Justin Lemkul
On 2/23/15 12:12 AM, rahul dhakne wrote: Dear Gromacs user, I am running mdrun to minimize (energy minimization) my structure co-ordinate, but every time it stuck by displaying following error Back Off! I just backed up em.log to ./#em.log.8# Reading file em.tpr, VERSION 5.0.4 (single pre

[gmx-users] g_rdf

2015-02-23 Thread leila salimi
Dear all, I have a question regarding radial distribution function. Does g_rdf program work for non-cubic cell eg. triclinic? Regards, Leila -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? R

Re: [gmx-users] Simulation of polarizable Carbon nanotubes

2015-02-23 Thread Peter Kroon
On 02/22/2015 05:33 PM, Jashimuddin Ashraf wrote: > Thanks for your reply Dr. Lemkul > > I changed the bond length to zero in my topology file, forcefield file and > in the n2t file. I also added the [ exclusion] section- If memory serves, you don't need a bond between a shell particle and it's "