[gmx-users] [Fwd: Gromacs installation]

Please keep correspondence on the gmx-users mailing list. This issue is routine, and is covered in the current installation guide. http://www.gromacs.org/index.php?title=Download_%26_Installation/Installation_Instructions Mark Original Message Subject:Gromacs install

[gmx-users] gromacs wall parameters

Hi everyone, I am trying to model an impenetrable wall for my simulation at z=0. I read the manual where this thing is discussed. I am still doubtful about the options to use. It seems that the wall parameters are designed to figure out the repulsive potential function based on wall_type, wall_at

Re: [gmx-users] A fragmented trajectory

Arik Cohen wrote: Dear users, I'll be most thankful if someone could give me an example as how to restart a MD simulation that is been fragmented into several sections. I have tried several flags according to the manual with no success. Every time a different problem emerges, i.e. either the

Re: [gmx-users] multiple processor running of gromacs-4.0.4

Jianhui Tian wrote: Hi, I have a small system of fullerene ball with waters. I want to simulation the system without pbc and pme, treating the coulomb and vdw without cutoff. The system can be run on single processor. But when I try to run it with multiple processors, it can't proceed. I am i

[gmx-users] A fragmented trajectory

Dear users, I'll be most thankful if someone could give me an example as how to restart a MD simulation that is been fragmented into several sections. I have tried several flags according to the manual with no success. Every time a different problem emerges, i.e. either the simulation get stuc

[gmx-users] multiple processor running of gromacs-4.0.4

Hi, I have a small system of fullerene ball with waters. I want to simulation the system without pbc and pme, treating the coulomb and vdw without cutoff. The system can be run on single processor. But when I try to run it with multiple processors, it can't proceed. I am including the error messag

Re: [gmx-users] top file in coarse-grained

Francesco Pietra wrote: Hi Justin: Could you please indicate the location of such scripts? They're on the MARTINI website, but given the further description of your system, they won't solve your problem. What I was referring to were scripts to build protein topologies. They won't help in

Re: [gmx-users] top file in coarse-grained

Hi Justin: Could you please indicate the location of such scripts? I have no trouble (in generating the .tpr file) with protein partly embedded in a double layer, by counting graphically the lipid residues and W residues remaining after creating the hole for the protein pore region. My trouble is

Re: [gmx-users] top file in coarse-grained

Francesco Pietra wrote: Hi: As I meet recurring problems in coarse-grained of the top file not matching the number of coordinates in coordinate file, is there any way to get the top file automatically like in all-atoms? Editing the top file to this regard proved difficult in my hands. I'm a

[gmx-users] top file in coarse-grained

Hi: As I meet recurring problems in coarse-grained of the top file not matching the number of coordinates in coordinate file, is there any way to get the top file automatically like in all-atoms? Editing the top file to this regard proved difficult in my hands. thanks francesco pietra ___

Re: [gmx-users] RE: gmx-users Digest, Vol 66, Issue 124

Thielges, Sabine wrote: Thielges, Sabine wrote: Hi everyone, I am currently doing a simulation which involves a dopamine receptor placed in a POPC membrane and an agonist or antagonist in the active site. The ligand was placed by VS and is closed to what the biology gives. My problem is th

[gmx-users] RE: gmx-users Digest, Vol 66, Issue 124

Thielges, Sabine wrote: >> Hi everyone, >> >> I am currently doing a simulation which involves a dopamine receptor >> placed in a POPC membrane and an agonist or antagonist in the active >> site. The ligand was placed by VS and is closed to what the biology >> gives. My problem is that the liga

Re: [gmx-users] Coarse-Grain: GROMACS bond information to VMD

Hello Thomas, I have a tcl script in my personal script library that might do what you want to do. I didn't use it for quite a while, but it was working well as far as I remember. I think it has been adapted from a script available on the VMD website, but I don't remember exactly its history.

Re: [gmx-users] Ligand during GPRC-membrane simulation

Thielges, Sabine wrote: Hi everyone, I am currently doing a simulation which involves a dopamine receptor placed in a POPC membrane and an agonist or antagonist in the active site. The ligand was placed by VS and is closed to what the biology gives. My problem is that the ligand get out of is

[gmx-users] Ligand during GPRC-membrane simulation

Hi everyone, I am currently doing a simulation which involves a dopamine receptor placed in a POPC membrane and an agonist or antagonist in the active site. The ligand was placed by VS and is closed to what the biology gives. My problem is that the ligand get out of is normal position during the s

Re: [gmx-users] Coarse-Grain: GROMACS bond information to VMD

Thomas Schmidt wrote: Dear Omer, many thanks for your answer, but your solution doesn't work for me. We have Protein-Lipid models in the CG scale. Only if I replace all atom names in the PDB file through "CA" I can use the "trace" drawing method, but get also wrong atoms connected to each other.

Re: Re: [gmx-users] Coarse-Grain: GROMACS bond information to VMD

Dear Omer, many thanks for your answer, but your solution doesn't work for me. We have Protein-Lipid models in the CG scale. Only if I replace all atom names in the PDB file through "CA" I can use the "trace" drawing method, but get also wrong atoms connected to each other. For example CG Beads wi

Re: [gmx-users] time steps and segmentation fault

albita...@virgilio.it wrote: Hi all, I carried out a MD simulation using the MARTINI CG force field and I had some problems. The simulation stops immediately, reporting a segmentation fault: **+ Making 1D domain decomposition 2 x 1 x 1 starting

Re: [gmx-users] time steps and segmentation fault

The type of system you are simulating and the manner you prepared are probably responsible for the crash ... You should have a good look at it! On Oct 19, 2009, at 3:29 PM, albita...@virgilio.it wrote: Hi all, I carried out a MD simulation using the MARTINI CG force field and I had some p

[gmx-users] time steps and segmentation fault

Hi all, I carried out a MD simulation using the MARTINI CG force field and I had some problems. The simulation stops immediately, reporting a segmentation fault: **+ Making 1D domain decomposition 2 x 1 x 1 starting mdrun 'FIB' 20 steps, 6000.0

RE: [gmx-users] a bit strange errors(Solved:Thanks to all)

Dear GMXers, I have solved the questions posted previously. It is not the unit and the transformation but the use of f'(x) instead of -f'(x) that leads to the issues. Anyway, thanks a lot for your attention and some suggestions from Berk and Mark Best wishes, Chaofu Wu, Dr. From: xiaowu..

Re: [gmx-users] Lennard Jones Parameters for Ammonia in ffoplsaa

Darrell Koskinen wrote: Hi, I see that the Lennard Jones parameters for the N & H atoms in ammonia, represented by opls_127 and opls_128 in the file ffoplsaanb.itp are: opls_127 NT 7 14.00670-1.020 A3.42000e-01 7.11280e-01 opls_128 H 1 1.00800 0.340 A

Re: [gmx-users] force field

Hi, leila karami wrote: I want to do MD simulation by gromacs but there are following force fields in gromacs program: ffG43a1- ffG43a2 - ffG43a3 - ffG43a5 - ffG43a6 - ffOPLS-AA - ffgmx - ffgmx2 - ffencads - ffencadv. How can I use other force fields such as AMBER or CHARMM. For AMBER, downl