[gmx-users] parallel run breaks !!

Dear Gromacs users I run DPPC monolayer on Tip4p2005 water layer system with gromacs 3.3 I had no problem before but when I run the system with command grompp_mpi -c .gro -f .mdp -n .ndx -p .top -o .tpr -np 8 and then qsub .ll   the run starts but it has break down several times, each ime after

[gmx-users] ask for help on connection to vpn from two computers

Dear gromacs users I connect via vpn to the university which I run my jobs using gromacs on its HPC system. I have Id password for that. now I want to know if I can connect from two computers in my lab to the vpn connection at the same time with one ID and password?   the computers are not

Re: [gmx-users] ask for help on connection to vpn from two computers

Hi Delara, This isn't really the place for these kind of questions, is it? Why not ask the system admins of your network? Cheers, Tsjerk On Apr 18, 2011 9:11 AM, delara aghaie d_agh...@yahoo.com wrote: Dear gromacs users I connect via vpn to the university which I run my jobs using gromacs

[gmx-users] fetal erorr while running pdb2gmx command

dear users after running the command pdb2gmx -f 1OL5.pdb -o 1OL5.gro -water spc ,i was faced with the erorr: Fatal error: Atom CG not found in residue seq.nr. 251 while adding atom. i used Gromacs 4.5.3 with AMBER99SB force field. it seems that some atomes are missing.should i be modeling the

Re: [gmx-users] fetal erorr while running pdb2gmx command

Hey Sajad, That sounds quite serious, having a fetal error (http://www.thefreedictionary.com/fetal)! But it seems you just have a missing atom, as is indicated in the output. Check the structure before trying to convert it. In particular, read the sections in the PDB file starting with 'REMARK

Re: [gmx-users] mdrun_mpi in HP_MPI LSF/SLURM setup

Ok. Solved it. Nothing wrong with the LSF/SLURM/MPI stuff. GMXRC.bash hadn't executed properly to set the environment up (typo) and the shared libraries weren’t being found. Seems this makes mdrun_mpi run like serial mdrun! Oops. Lee On 16/04/2011 22:51, Larcombe, Lee

Re: [gmx-users] diverging temperature with pressure coupling

Hello, oh this nasty ILs ;) I am currently investigating a similar problem, that deals with PR-coupling and my impression is that Leap-Frog is the problem and not PR. Currently I am running simulations with md-vv and MTTK to verify my ideas. On the other hand I am using two tc_groups for my ILs

Re: [gmx-users] diverging temperature with pressure coupling

On 2011-04-18 11.22, Dommert Florian wrote: Hello, oh this nasty ILs ;) I am currently investigating a similar problem, that deals with PR-coupling and my impression is that Leap-Frog is the problem and not PR. Currently I am running simulations with md-vv and MTTK to verify my ideas. On the

Re: [gmx-users] Re: energy group exclusions

Sikandar Mashayak wrote: Also, what about non-bonded interactions within the protein? Does exclusion group only exclude the non-bonded interactions between two different molecules and non-bonded interactions within the single molecule atoms are still computed? Nonbonded interactions are

Re: [gmx-users] diverging temperature with pressure coupling

On Mon, 2011-04-18 at 11:42 +0200, David van der Spoel wrote: On 2011-04-18 11.22, Dommert Florian wrote: Hello, oh this nasty ILs ;) I am currently investigating a similar problem, that deals with PR-coupling and my impression is that Leap-Frog is the problem and not PR. Currently I

[gmx-users] Cylinder Pulling output file pullx.xvg wron

That part of the pull code has a different printf statement in version 4.5.3. Can you test 4.0.7 output vs. 4.5.3 output and see if 4.5.3 is correct? You could simple use nsteps=0 genvel=no and load a .gro with no velocities in your mdrun. Chris. -- original message -- I am trying

[gmx-users] Simulation of CNT with Amber forcefield

Dear All, I am doing a DNA-CNT simulation, and I am trying to generate a topology of CNT using Amber99, which has been used for such systems, and CNT atoms are modeled using sp2 carbon parameters. But when I try to create topology file using: pdb2gmx -f cnt.pdb -p cnt.top, and Amber99

Re: [gmx-users] Simulation of CNT with Amber forcefield

majid hasan wrote: Dear All, I am doing a DNA-CNT simulation, and I am trying to generate a topology of CNT using Amber99, which has been used for such systems, and CNT atoms are modeled using sp2 carbon parameters. But when I try to create topology file using: pdb2gmx -f cnt.pdb -p

[gmx-users] protein-ligand complex tutorial

Dear Justin, You prepared a useful tutorial. if you used PO4 ligand (which has 2 molecule) instead of 1JZ4 ligand from 3HTB.pdb, Then, in the .itp and .gro files of ligand because of 2 molecule, what change? Can you give some hint? Thanks 3HTB.pdb TER 1365 ASN A 163 HETATM 1366 P PO4 A 165

Re: [gmx-users] protein-ligand complex tutorial

ahmet yıldırım wrote: Dear Justin, You prepared a useful tutorial. if you used PO4 ligand (which has 2 molecule) instead of 1JZ4 ligand from 3HTB.pdb, Then, in the .itp and .gro files of ligand because of 2 molecule, what change? Can you give some hint? Treat it like you would any other

[gmx-users] coordination file

Dear gromacs users, Thanks for your previous guidance. I used Drug/Enzyme complex solvation tutorial to run my simulation in nitrogen box. It finally worked. But I think that the *.gro coordination file of my solvent has problem beacuse when I run it, in my _b4ion.gro file the nitrogen molecules

Re: [gmx-users] protein-ligand complex tutorial

You need to get or calculate parameters for phosphate. These parameters are yet calculated for the AMBER forcefield, there are in http://personalpages.manchester.ac.uk/staff/Richard.Bryce/amber/cof/frcmod.phos. You need to install AmberTools and copy the frcmod.phos file in the URL above to

Re: [gmx-users] coordination file

sarah k wrote: Dear gromacs users, Thanks for your previous guidance. I used Drug/Enzyme complex solvation tutorial to run my simulation in nitrogen box. It finally worked. But I think that the *.gro coordination file of my solvent has problem beacuse when I run it, in my _b4ion.gro file the

Re: [gmx-users] protein-ligand complex tutorial

Dear Justin, without_JZ4_PO4_BME.pdb ( There arent ligands) 1.pdb2gmx -f without_JZ4_PO4_BME.pdb forcefield:43a1, water:spc Now I have topol.top and conf.gro files. 2.I have PO4.gro and PO4.itp from PRODRG using the following all lines. HETATM 1366 P PO4 A 165 15.430 -26.507 12.040 0.70

[gmx-users] no CUDA-capable device detected

Dear gromacs user, I have some problems getting a simulation running on a tesla T10 with CUDA driver version 3.20 running. My .mdp file looks like: ; title= ttt cpp= /lib/cpp include = -I../top constraints = none ;define

Re: [gmx-users] Simulation of CNT with Amber forcefield

Okay, so I am able to create cnt.rtp, and cnt.top file using g_x2top. But g_x2top only supports OPLSAA, and GROMOS forcefield, and if I use a different forcefield then I get this error: Fatal Error: No or incorrect atomname2type.n2t file found, which is because other forcefields don't contain

[gmx-users] question about adding two functions for one torsional angle

Dear all, I want to sum two functions for one torsional angle. Energy of the torsion (say, 1 2 3 4) is the combination of Ryckaert-Bellemans (function no.3) and compensated by periodic proper dihedral (function no.9). Is it possible that I simply type the follows, and GROMACS will add it up?

Re: [gmx-users] question about adding two functions for one torsional angle

On 2011-04-18 21.46, Ming-Tsung Lee wrote: Dear all, I want to sum two functions for one torsional angle. Energy of the torsion (say, 1 2 3 4) is the combination of Ryckaert-Bellemans (function no.3) and compensated by periodic proper dihedral (function no.9). Is it possible that I simply type

Re: [gmx-users] Simulation of CNT with Amber forcefield

majid hasan wrote: Okay, so I am able to create cnt.rtp, and cnt.top file using g_x2top. But g_x2top only supports OPLSAA, and GROMOS forcefield, and if I use a different forcefield then I get this error: Fatal Error: No or incorrect atomname2type.n2t file found, which is because other

Re: [gmx-users] protein-ligand complex tutorial

ahmet yıldırım wrote: Dear Justin, without_JZ4_PO4_BME.pdb ( There arent ligands) 1.pdb2gmx -f without_JZ4_PO4_BME.pdb forcefield:43a1, water:spc Now I have topol.top and conf.gro files. 2.I have PO4.gro and PO4.itp from PRODRG using the following all lines. HETATM 1366 P PO4 A 165

Re: [gmx-users] aminoacids.n.tdb

Hi Mark, Thanks again. Your suggestion of introducing the lauroic acid as a pseudo-amino acid seems to solve my problem. Below is my corrected aminoacids.rtp file for the 6-Carbon case as a test. (I used the Berger lipid parameters.) Just to be sure, could you have a look at the file (I used

Re: [gmx-users] protein-ligand complex tutorial

Dear Justin, Now, I added two PO4 to the coordinate file, then added two to the topology. I created PO4_1.gro and PO4_1.itp for first PO4 using PRODRG. Then, I created PO4_2.gro and PO4_2.itp for first PO4 using PRODRG. I added 10 atoms/lines into conf.gro from PO4.gro(5cordinate and PO4_2.gro

Re: [gmx-users] protein-ligand complex tutorial

ahmet yıldırım wrote: Dear Justin, Now, I added two PO4 to the coordinate file, then added two to the topology. I created PO4_1.gro and PO4_1.itp for first PO4 using PRODRG. Then, I created PO4_2.gro and PO4_2.itp for first PO4 using PRODRG. I added 10 atoms/lines into conf.gro from

Re: [gmx-users] protein-ligand complex tutorial

Dear Justin, But I doesn't see any error in the conf.gro. Am I wrong? *conf.gro:* LYSOZYME 2363 1MET N1 0.556 -1.596 -0.893 ... 388HOHHW2 2353 1.763 -1.939 1.371 1PO4 O2 1 1.456 -2.557 1.128 1PO4 P 2 1.543 -2.651 1.204 1PO4 O3

Re: [gmx-users] protein-ligand complex tutorial

ahmet yıldırım wrote: Dear Justin, But I doesn't see any error in the conf.gro. Am I wrong? _conf.gro:_ LYSOZYME 2363 1MET N1 0.556 -1.596 -0.893 ... 388HOHHW2 2353 1.763 -1.939 1.371 1PO4 O2 1 1.456 -2.557 1.128 1PO4 P 2 1.543

Re: [gmx-users] protein-ligand complex tutorial

Dear Justin, I rearranged conf.gro but Gromacs is giving the same errors again. I think I am going mad :-( *conf.gro* 388HOHHW2 2353 1.763 -1.939 1.371 1PO4 O2 1 1.456 -2.557 1.128 1PO4 P 2 1.543 -2.651 1.204 1PO4 O3 3 1.507 -2.801 1.181

Re: [gmx-users] protein-ligand complex tutorial

ahmet yıldırım wrote: Dear Justin, I rearranged conf.gro but Gromacs is giving the same errors again. I think I am going mad :-( In the absence of the corresponding topology, there is no way to help you other than to say you're still doing something wrong. Your coordinates still appear

Re: [gmx-users] protein-ligand complex tutorial

ahmet yıldırım wrote: Dear Justin, If I send your e-mail the conf.gro, topol.top and PO4.itp files, can you look at them? do you have a little time? There are many problems with the files you sent me. 1. The [molecules] section in no way reflects the contents of the system. You have:

Re: [gmx-users] aminoacids.n.tdb

On 4/19/2011 6:55 AM, Emine Deniz Tekin wrote: Hi Mark, Thanks again. Your suggestion of introducing the lauroic acid as a pseudo-amino acid seems to solve my problem. Below is my corrected aminoacids.rtp file for the 6-Carbon case as a test. (I used the Berger lipid parameters.) Looks

Re: [gmx-users] mdrun_mpi in HP_MPI LSF/SLURM setup

On 4/18/2011 6:44 PM, Larcombe, Lee wrote: Ok. Solved it. Nothing wrong with the LSF/SLURM/MPI stuff. GMXRC.bash hadn't executed properly to set the environment up (typo) and the shared libraries weren’t being found. Seems this makes mdrun_mpi run like serial mdrun! OK, but failing to pick up

Re: [gmx-users] coordination file

On 4/19/2011 4:06 AM, Justin A. Lemkul wrote: sarah k wrote: Dear gromacs users, Thanks for your previous guidance. I used Drug/Enzyme complex solvation tutorial to run my simulation in nitrogen box. It finally worked. But I think that the *.gro coordination file of my solvent has problem

Re: [gmx-users] parallel run breaks !!

On 4/18/2011 4:39 PM, delara aghaie wrote: Dear Gromacs users I run DPPC monolayer on Tip4p2005 water layer system with gromacs 3.3 I had no problem before but when I run the system with command grompp_mpi -c .gro -f .mdp -n .ndx -p .top -o .tpr -np 8 and then qsub .ll the run starts but it

Re: [gmx-users] Re: energy group exclusions

On 4/18/2011 1:43 PM, Sikandar Mashayak wrote: Also, what about non-bonded interactions within the protein? Does exclusion group only exclude the non-bonded interactions between two different molecules and non-bonded interactions within the single molecule atoms are still computed? The sets

Re: [gmx-users] Re: energy group exclusions

so that means if I define a index group GRP and energy exclusion GRP GRP then all the non-boned interactions between atoms belonging to GRP group are excluded? On Mon, Apr 18, 2011 at 7:43 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 4/18/2011 1:43 PM, Sikandar Mashayak wrote: Also,

Re: [gmx-users] Re: energy group exclusions

On 4/19/2011 2:57 PM, Sikandar Mashayak wrote: so that means if I define a index group GRP and energy exclusion GRP GRP then all the non-boned interactions between atoms belonging to GRP group are excluded? What does manual 7.3.19 say? Mark On Mon, Apr 18, 2011 at 7:43 PM, Mark Abraham