[gmx-users] atomtype names case INsensitive?

Dear All, I have a complex A-B (not covalent bonded) I want to use oplsaa.ff atom types original for A and all are in .top files in which some parameters are changed and I have another directory with modified just atomtype names oplsaa.ff files (for B) that is ffbonded.itp, ffnopnbonded.itp, atom

[gmx-users] Distance travelled from time 0

Hi guys, What is the best way of calculating how far a residue has traveled from its starting position during a simulations? Thanks Natalie -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.o

Re: [gmx-users] atomtype names case INsensitive?

Probably Mark On Jun 20, 2013 11:42 AM, "gromacs query" wrote: > Dear All, > > I have a complex A-B (not covalent bonded) > > I want to use oplsaa.ff atom types original for A and all are in .top files > in which some parameters are changed and I have another directory with > modified just atomt

Re: [gmx-users] atomtype names case INsensitive?

Hi, GROMACS is indeed case insensitive when it comes to atomtypes. I had the same problem a while ago. The simplest way to deal with it is just to add a letter at the end of your atomtypes. 2013/6/20 Mark Abraham > Probably > > Mark > On Jun 20, 2013 11:42 AM, "gromacs query" wrote: > > > D

Re: [gmx-users] atomtype names case INsensitive?

Thanks Mark and Baptiste, yes its case insensitive for atomtype names. I have changed all names and its working now :-) regards, On Thu, Jun 20, 2013 at 2:55 PM, Baptiste Demoulin wrote: > Hi, > > GROMACS is indeed case insensitive when it comes to atomtypes. I had the > same problem a while ag

Re: [gmx-users] Distance travelled from time 0

Hi Natalie, You might want to look into g_rmsf, used to calculate the root mean squared fluctuation of atoms or residues. sample usage: g_rmsf -f trajectory.xtc -s struc_mass.tpr -oq rmsf.pdb -o rmsf.xvg Additional commands of interest: -res (when true, calculates residues as a whole) -b (first

Re: [gmx-users] Distance travelled from time 0

Hi, g_rmsf doesn't do distances. To answer the question, you can use g_rms with -fit none and a suitable index group. Does depend a bit on what you mean with distance. The distance traveled by a residue could well mean the average distance for all particles in the residue, which is what you'll get

[gmx-users] Re: Membrane Runs Crashing

Justin Lemkul wrote >> > > What was the outcome of EM before this? What if you try NVT before NPT? > Have > you tried reducing the timestep or the value of nstlist? > > I would try everything with ref_p = 1.0 instead of zero to make sure you > can get > a "normal" setup to work. > > -Justin

[gmx-users] System expansion

Dear Gromacs users, I experience a very strange problem. I have a well equilibrated system consisting of a protein, a ligand, ions and water. On most machines I run my simulations on, everything is just fine. Except for one compute cluster, where the system undergoes an extreme expansion when

Re: [gmx-users] System expansion

Hi Oliver - Hmm. Did you try to start from (a little bit) different configurations on the problematic machine? Or re-install gromacs there, perhaps? Dr. Vitaly Chaban On Thu, Jun 20, 2013 at 3:44 PM, Oliver Schillinger wrote: > Dear Gromacs users, > > I experience a very strange problem

[gmx-users] Error while using genion

I am new Gromacs user and I found Dr. Kerrigan's tutorial on the spider toxin peptide. I was going through the steps in the tutorial but got stuck with the genion command. When I am prompted to select a group, I get the error that it is not found. I tried many different ways of specifying thi

[gmx-users] Test Particle Insertion

Dear GMX Users, My name is Anh Phan, a PhD student at University of Oklahoma. I would like to calculate excess chemical potential of one gas molecule in water solvent using Widom test particle insertion with Gromacs. In this method, I will insert this gas molecule at a random position in each con

Re: [gmx-users] Test Particle Insertion

As far as I know it should not be included. Make a tpr file new .top and input file and run the mdrun with -rerun option as described here. " http://manual.gromacs.org/online/mdp_opt.html#run"; Cheers, Rajesh On Thu, Jun 20, 2013 at 3:08 PM, Phan, Anh T. wrote: > Dear GMX Users, > My name is

[gmx-users] Decouple

Hi , How do I  solve this problem in GROMACS: I have a system with 3 part A,B and C I have to put thermostat for A and C but not for  B. Gromacs   display error, what is temperature for B. How do aI decouple part B thanks  for help Hari -- gmx-users mailing listgmx-users@gromacs.org

Re: [gmx-users] Error while using genion

On 6/20/13 1:57 PM, Raji Viswanathan wrote: I am new Gromacs user and I found Dr. Kerrigan's tutorial on the spider toxin peptide. I was going through the steps in the tutorial but got stuck with the genion command. When I am prompted to select a group, I get the error that it is not found

Re: [gmx-users] Decouple

On 6/20/13 5:01 PM, Hari Pandey wrote: Hi , How do I solve this problem in GROMACS: I have a system with 3 part A,B and C I have to put thermostat for A and C but not for B. Gromacs display error, what is temperature for B. How do aI decouple part B Per the manual: "tau-t: [ps] tim

Re: [gmx-users] Test Particle Insertion

Dear Anh, You need to construct a .tpr file for the mdrun -rerun with: - a .gro file with the ligand to be inserted at the end, which _must_ be geometrically centered at 0,0,0 ; - a matching .top file (which means with the ligand topology appropriately inserted) ; - a .mdp file wit

Re: [gmx-users] Decouple

Please keep the discussion on the gmx-users mailing list; I am not a private tutor. Comments embedded below. On 6/20/13 8:35 PM, Hari Pandey wrote: Hi Justin, Thanks for last help. I have following (NVT.mdp) (NPT.mdp) and (NVE.mdp) . I have three parts of system, A, B and C. I want to

[gmx-users] (no subject)

Hi all  gromacs users I have following (NVT.mdp) (NPT.mdp)  and (NVE.mdp)   .  I have three parts of system, A, B and C. I want to put thermostat on A and C and couple the tempereture and do not put any thermostat on B. What I want is: after some ps,  temperature of A and C should be constant (

Re: [gmx-users] (no subject)

On 6/20/13 11:11 PM, Hari Pandey wrote: Hi all gromacs users I have following (NVT.mdp) (NPT.mdp) and (NVE.mdp) . I have three parts of system, A, B and C. I want to put thermostat on A and C and couple the tempereture and do not put any thermostat on B. What I want is: after some ps,

[gmx-users] can extract edr and cpt of one frame?

Hi, I want extract one frame from NPT to run MD because for md need npt.gro and npt.cpt So, if can we extract cpt of one frame? and because I want to check if this frame at equilibration state, use g_energy -f npt.edr So, if can we extract edr of one frame? Thank you very much! maggin

[gmx-users] GROMACS on GPU

Dear gromacs users,   Can anyone tell me how to make a mdp file for gromacs mdrun on NVIDIA GPU card, the following is a mdp file which runs well on cpu, but when I add the option "-testverlet" to mdrun in order to run it on GPU, it returns error "nonbond potiential is not supported". Could

[gmx-users] gromacs on GPU

 Can anyone tell me how to make a mdp file for gromacs mdrun on NVIDIA GPU card, the following is a mdp file which runs well on cpu, but when I add the option "-testverlet" to mdrun in order to run it on GPU, it returns error "nonbond potiential is not supported". Could you check the mdp fil