[gmx-users] grompp for minimization: note & warning

2013-09-15 Thread shahab shariati
Dear gromacs users My system contains 3 components: DOPC & cholesterol lipids + drug + water molecules. In minimization step, when I use grompp -f em.mdp -c system.gro -p topol.top -o em.tpr, I encountered with following note and warning: WARNING 1 [file em.mdp]: The sum of the two largest charg

[gmx-users] grompp for minimization: note & warning

2013-09-15 Thread shahab shariati
Dear gromacs users Nember of groups in each of charge groups is less than or equal 3. charge groups in my itp files are as follows: DOPC.itp: [ atoms ] ; nr type resnr residue atom cgnr char

[gmx-users] identical results or exactly the same results?

2013-09-15 Thread Albert
Hello: I've got a md.tpr file generated by grompp, I am just wondering will the results be identical or would be exactly the same if I run it in different machine? thank you very much. best Albert -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/g

Re: [gmx-users] identical results or exactly the same results?

2013-09-15 Thread Dr. Vitaly Chaban
The [numerical] results will depend on architecture you are running on. No matter where the binary input file was prepared. Dr. Vitaly V. Chaban On Sun, Sep 15, 2013 at 10:22 AM, Albert wrote: > Hello: > > I've got a md.tpr file generated by grompp, I am just wondering will the > results be

[gmx-users] grompp for minimization: note & warning

2013-09-15 Thread shahab shariati
Dear gromacs users I used -maxwarn option, but after using this command: mdrun -s em.tpr -o em.trr -c em.gro -e em.edr -g em.log I encountered with: Fatal error: There is no domain decomposition for 4 nodes that is compatible with the given box and a minimum cell size of 6.61528 nm Change the

Re: [gmx-users] grompp for minimization: note & warning

2013-09-15 Thread Justin Lemkul
On 9/15/13 3:44 AM, shahab shariati wrote: Dear gromacs users My system contains 3 components: DOPC & cholesterol lipids + drug + water molecules. In minimization step, when I use grompp -f em.mdp -c system.gro -p topol.top -o em.tpr, I encountered with following note and warning: WARNING 1

Re: [gmx-users] grompp for minimization: note & warning

2013-09-15 Thread Justin Lemkul
On 9/15/13 8:17 AM, shahab shariati wrote: Dear gromacs users I used -maxwarn option, but after using this command: mdrun -s em.tpr -o em.trr -c em.gro -e em.edr -g em.log I encountered with: Fatal error: There is no domain decomposition for 4 nodes that is compatible with the given box an

Re: [gmx-users] identical results or exactly the same results?

2013-09-15 Thread Justin Lemkul
On 9/15/13 4:22 AM, Albert wrote: Hello: I've got a md.tpr file generated by grompp, I am just wondering will the results be identical or would be exactly the same if I run it in different machine? http://www.gromacs.org/Documentation/Terminology/Reproducibility -Justin --

[gmx-users] Regarding g_sgangle index file

2013-09-15 Thread Venkat Reddy
Dear Gmx-users, My system has cholesterol molecules and I want to do the orientation analysis for the cholesterol rings. I found g_sgangle is the suitable tool to calculate the angle between two cholesterol rings. But the problem is, I want to do this analysis for my whole system, which has 40 chol

[gmx-users] Number Density

2013-09-15 Thread Sun Moon
Dear users, To calculate "Number Density" of solvent via size box for a bilayer membrane, I used g_density program as the following: g_density -f md.xtc -s md.tpr -o density-Num-SOL.xvg -d z -dens number -n index-group.ndx I got @    title "Partial densities" @    xaxis  label "Box (nm)" @    yaxi

Re: [gmx-users] Number Density

2013-09-15 Thread Dr. Vitaly Chaban
I would guess that the density is zero at the center, since you do not have solvent molecules inside the membrane. Yes, the output density is number of interaction sites per nm^3, calculated in each slice, whose size you had specified. Dr. Vitaly V. Chaban On Sun, Sep 15, 2013 at 5:23 PM, Sun

[gmx-users] Installation of gromacs 4.5.4 on windows using cygwin

2013-09-15 Thread Muthukumaran R
hello, I am trying to install gromacs in cygwin but after issuing "make", installation stops with the following error Makefile:1315: recipe for target `gmx_tune_pme.lo' failed make[3]: *** [gmx_tune_pme.lo] Error 1 make[3]: Leaving directory `/usr/local/gromacs-4.5.1/src/tools' Makefile:301: reci

Re: [gmx-users] segfault on Gromacs 4.6.3 (cuda)

2013-09-15 Thread Szilárd Páll
Hi, On Tue, Sep 10, 2013 at 2:03 AM, Guanglei Cui wrote: > Hi Szilard, > > Thanks again for getting back. You may remember the previous thread I > started on regression test failure with icc 11.x compiled binary. Falling As it was not referenced, I did not recall your previous mail at the time of

Re: [gmx-users] Installation of gromacs 4.5.4 on windows using cygwin

2013-09-15 Thread Szilárd Páll
Looks like you are compiling 4.5.1. You should try compiling the latest version in the 4.5 series, 4.5.7. -- Szilárd On Sun, Sep 15, 2013 at 6:39 PM, Muthukumaran R wrote: > hello, > > I am trying to install gromacs in cygwin but after issuing "make", > installation stops with the following erro

Re: Fwd: [gmx-users] SD integrator

2013-09-15 Thread HANNIBAL LECTER
Thanks. From your publications it seems that you have been simulating with infinite CNTs. I am trying to use finite CNTs and I am generating my topology files according to http://chembytes.wikidot.com/grocnt. I am modeling the peripheral Carbon atoms with two bonds by specifying it in the atomnam

Re: Fwd: [gmx-users] SD integrator

2013-09-15 Thread Dr. Vitaly Chaban
Are you sure that the source of instability is the CNT, not the protein? If yes, what makes you to think so? If you freeze all the atoms of the CNT, does it work well? Dr. Vitaly V. Chaban On Sun, Sep 15, 2013 at 11:07 PM, HANNIBAL LECTER < hanniballecte...@gmail.com> wrote: > Thanks. From yo