Re: [gmx-users] Initial velocity

2013-05-12 Thread Brighter Agyemang
Thanks so much for your support, The point is that, I have this mathematical theory on coarse grain simulation for which is supposed to resolve the potential existing between atoms suspended by an angle theta(like the triangle share for two atoms). To solve for the potential, the theta between thes

[gmx-users] Initial velocity

2013-05-12 Thread Acoot Brett
Dear All, Will you please explain how the initial velocity may affect the MD results? What the initial velocity really means? How the velocity of the atoms in the protein changes in the MD process? What is the reasonable scope of the initial velocity? Any suggestions on how to manually input a

[gmx-users] MODIFYING GROMACS' bondfree.c

2013-05-12 Thread brighter
Please I am a beginner in GROMACS simulation and happens to be doing my undergraduate final year project on molecular dynamics simulation. I am working on the use of the martini model in simulation for coarse grain sugar. I have to modify the bondfree.c file to supply coordinates of the atoms, mixi

[gmx-users] Wednesday, 15 May: upgrading redmine.gromacs.org

2013-05-12 Thread Rossen Apostolov
Dear users and developers, On Wednesday the redmine server will be upgraded and moved to a new VM. Thus expect downtime of 1-2 hours (if it all goes well :-) ). Cheers, Rossen -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search

Re: [gmx-users] Inconsistent results in different clusters and cores

2013-05-12 Thread tarak karmakar
Oh ! Thanks a lot Justin. I'll rerun all my jobs with this corrected mdp. Restrains things I didn't follow properly, anyway I'll read about this. On Sun, May 12, 2013 at 11:27 PM, Justin Lemkul wrote: > > > On 5/12/13 1:53 PM, tarak karmakar wrote: > >> Thanks, >> >> I have used CGENFF force fi

Re: [gmx-users] question about energygrps

2013-05-12 Thread Hyunjin Kim
> > > On 5/12/13 1:53 PM, Hyunjin Kim wrote: >>> >>> >>> On 5/12/13 1:31 PM, Hyunjin Kim wrote: > > > On 5/12/13 1:14 PM, Hyunjin Kim wrote: >>> >>> >>> On 5/12/13 12:54 PM, Hyunjin Kim wrote: > > > On 5/12/13 2:25 AM, Hyunjin Kim wrote: >> De

Re: [gmx-users] question about energygrps

2013-05-12 Thread Justin Lemkul
On 5/12/13 1:53 PM, Hyunjin Kim wrote: On 5/12/13 1:31 PM, Hyunjin Kim wrote: On 5/12/13 1:14 PM, Hyunjin Kim wrote: On 5/12/13 12:54 PM, Hyunjin Kim wrote: On 5/12/13 2:25 AM, Hyunjin Kim wrote: Dear, I want to calculate LJ and Electrostatic energies between two groups defined in

Re: [gmx-users] Inconsistent results in different clusters and cores

2013-05-12 Thread Justin Lemkul
On 5/12/13 1:53 PM, tarak karmakar wrote: Thanks, I have used CGENFF force field parameters for the ligand generated from PARMCHEM with 0 penalties. For protein I have used CHARMM36 force field. my npt.mdp file is as follows, ; 7.3.3 Run Control integrator = md Bug 1021 was onl

Re: [gmx-users] question about energygrps

2013-05-12 Thread Hyunjin Kim
> > > On 5/12/13 1:31 PM, Hyunjin Kim wrote: >>> >>> >>> On 5/12/13 1:14 PM, Hyunjin Kim wrote: > > > On 5/12/13 12:54 PM, Hyunjin Kim wrote: >>> >>> >>> On 5/12/13 2:25 AM, Hyunjin Kim wrote: Dear, I want to calculate LJ and Electrostatic energies

Re: [gmx-users] Inconsistent results in different clusters and cores

2013-05-12 Thread tarak karmakar
Thanks, I have used CGENFF force field parameters for the ligand generated from PARMCHEM with 0 penalties. For protein I have used CHARMM36 force field. my npt.mdp file is as follows, ; 7.3.3 Run Control integrator = md tinit = 0 dt = 0.001 nste

Re: [gmx-users] Problem importing PDB to Gromacs

2013-05-12 Thread tarak karmakar
Remove all the hydrogens from the pdb file and then try to run pdb2gmx, I hope it'll do fine. Or you can also use -ignh option as suggested by Justin. Tarak On Fri, May 10, 2013 at 3:35 PM, Justin Lemkul wrote: > > > On 5/10/13 5:16 AM, Jernej Zidar wrote: > >> Hi, >>In CHARMM I generated

Re: [gmx-users] question about energygrps

2013-05-12 Thread Justin Lemkul
On 5/12/13 1:31 PM, Hyunjin Kim wrote: On 5/12/13 1:14 PM, Hyunjin Kim wrote: On 5/12/13 12:54 PM, Hyunjin Kim wrote: On 5/12/13 2:25 AM, Hyunjin Kim wrote: Dear, I want to calculate LJ and Electrostatic energies between two groups defined in index.ndx during rerun with original traje

Re: [gmx-users] Inconsistent results in different clusters and cores

2013-05-12 Thread Justin Lemkul
On 5/12/13 1:34 PM, tarak karmakar wrote: Thanks Justin for the Quick and Helpful reply. Yes. If I am right, the chaotic behavior of the simulations is inherent and can be assessed statistically by generating several independent trajectories and analyzing their similar outcomes. But with t

Re: [gmx-users] question about energygrps

2013-05-12 Thread Hyunjin Kim
> > > On 5/12/13 1:14 PM, Hyunjin Kim wrote: >>> >>> >>> On 5/12/13 12:54 PM, Hyunjin Kim wrote: > > > On 5/12/13 2:25 AM, Hyunjin Kim wrote: >> Dear, >> >> I want to calculate LJ and Electrostatic energies between two groups >> defined in index.ndx during rerun with ori

Re: [gmx-users] Inconsistent results in different clusters and cores

2013-05-12 Thread tarak karmakar
Thanks Justin for the Quick and Helpful reply. Yes. If I am right, the chaotic behavior of the simulations is inherent and can be assessed statistically by generating several independent trajectories and analyzing their similar outcomes. But with the same '.mdp' file I am getting TOO much diffe

Re: [gmx-users] Inconsistent results in different clusters and cores

2013-05-12 Thread Justin Lemkul
On 5/12/13 1:17 PM, tarak karmakar wrote: Dear All, I am simulating a protein in water to check the ligand movement over a time span. I haveminimized the system in STEEP and CG and after that heated from 0K - 300K within a time span of 300 ps. Then, I performed the NPT production run

Re: [gmx-users] question about energygrps

2013-05-12 Thread Justin Lemkul
On 5/12/13 1:14 PM, Hyunjin Kim wrote: On 5/12/13 12:54 PM, Hyunjin Kim wrote: On 5/12/13 2:25 AM, Hyunjin Kim wrote: Dear, I want to calculate LJ and Electrostatic energies between two groups defined in index.ndx during rerun with original trajectory. The following is what I tried: 1.

[gmx-users] Inconsistent results in different clusters and cores

2013-05-12 Thread tarak karmakar
Dear All, I am simulating a protein in water to check the ligand movement over a time span. I haveminimized the system in STEEP and CG and after that heated from 0K - 300K within a time span of 300 ps. Then, I performed the NPT production runs. In two clusters I have got different results

Re: [gmx-users] question about energygrps

2013-05-12 Thread Hyunjin Kim
> > > On 5/12/13 12:54 PM, Hyunjin Kim wrote: >>> >>> >>> On 5/12/13 2:25 AM, Hyunjin Kim wrote: Dear, I want to calculate LJ and Electrostatic energies between two groups defined in index.ndx during rerun with original trajectory. The following is what I tried: >

Re: [gmx-users] question about energygrps

2013-05-12 Thread Justin Lemkul
On 5/12/13 12:54 PM, Hyunjin Kim wrote: On 5/12/13 2:25 AM, Hyunjin Kim wrote: Dear, I want to calculate LJ and Electrostatic energies between two groups defined in index.ndx during rerun with original trajectory. The following is what I tried: 1. insert "energygrps r_1 r_25" in the test.

Re: [gmx-users] question about energygrps

2013-05-12 Thread Hyunjin Kim
> > > On 5/12/13 2:25 AM, Hyunjin Kim wrote: >> Dear, >> >> I want to calculate LJ and Electrostatic energies between two groups >> defined in index.ndx during rerun with original trajectory. >> >> The following is what I tried: >> >> 1. insert "energygrps r_1 r_25" in the test.mdp file. >> >> 2. g

Re: [gmx-users] g_dist

2013-05-12 Thread Justin Lemkul
On 5/12/13 8:48 AM, mohammad agha wrote: Dear GROMACS Specialists, I want to obtain number of instances the different atoms was found within a spherical shell of width 0.02 nm at a distance r from the micelle COM. For this, I use g_dist -dist, but when I select for example 0.04, it also resu

[gmx-users] g_dist

2013-05-12 Thread mohammad agha
Dear GROMACS Specialists, I want to obtain number of instances the different atoms was found within a spherical shell of width 0.02 nm at a distance r from the micelle COM. For this, I use g_dist -dist, but when I select for example 0.04, it also result all instances in 0-0.02, whereas I want on

Re: [gmx-users] system hangs while running perl distances.pl

2013-05-12 Thread Justin Lemkul
On 5/12/13 6:40 AM, Arunima Shilpi wrote: Respected Sir many many thanks for your reply to my last mail. while running trjconv -s pull.tpr -f traj.xtc -o conf.gro -sep I selected group 0 for the system... but while i run perl distances.pl it says processing file 236...and than the system

Re: [gmx-users] question about energygrps

2013-05-12 Thread Justin Lemkul
On 5/12/13 2:25 AM, Hyunjin Kim wrote: Dear, I want to calculate LJ and Electrostatic energies between two groups defined in index.ndx during rerun with original trajectory. The following is what I tried: 1. insert "energygrps r_1 r_25" in the test.mdp file. 2. grompp -f test.mdp -c x.gro -

[gmx-users] system hangs while running perl distances.pl

2013-05-12 Thread Arunima Shilpi
Respected Sir many many thanks for your reply to my last mail. while running trjconv -s pull.tpr -f traj.xtc -o conf.gro -sep I selected group 0 for the system... but while i run perl distances.pl it says processing file 236...and than the system hangs, no more blinking along the terminal.