[gmx-users] still problem of pr.mdp

Hi gmxusers, i have used below parameters those what you suggested , title = popc restrained define = -DPOSRES constraints = all-bonds integrator = md dt = 0.002; ps ! nsteps = 1; total 20 ps. nstcomm

[gmx-users] Concerning DSSP

Hello everyone. I'm new to this list and first of all I'd like to salute all the members and crew. I'm having a little problem with permissions with the DSSP program, should anybody help me I'd be glad. I've already read the forum but couldn't find an answer. I'm running GROMACS in two

Re: [gmx-users] Concerning DSSP

Ricardo Soares wrote: Hello everyone. I'm new to this list and first of all I'd like to salute all the members and crew. I'm having a little problem with permissions with the DSSP program, should anybody help me I'd be glad. I've already read the forum but couldn't find an answer. I'm

Re: [gmx-users] Concerning DSSP

Thanks David, Well, dsspcmbi is working fine without gromacs. So maybe the problem lies in the integration dssp-gromacs, with some user restrictions, isn't? -- ___ Ricardo Oliveira dos Santos Soares Post-graduation Student in Biological

Re: [gmx-users] Concerning DSSP

Ricardo Soares wrote: Thanks David, Well, dsspcmbi is working fine without gromacs. So maybe the problem lies in the integration dssp-gromacs, with some user restrictions, isn't? In that case it should also work in gromacs... I don't know what is going on. Do you have permission to write in

Re: [gmx-users] Harmonic dihedral restraints

Thanks for your replies. How do you include these dihedral restraints in the topology file? There isn't a [ dihedral_restraints ] section listed in Table 5.4. I presume this section should be formatted as: [ dihedral_restraints ] i j k l 1 phi_0 k delta_phi Is that

Re: [gmx-users] Harmonic dihedral restraints

Bob, The other way of putting what Mark said is that phi is only meaningful on some range (-pi to pi, or 0 to 2pi, depending on how you define it) and so what you require is that the potential be harmonic for the region in which phi is meaningful. You don't care what happens outside that. Or, in

[gmx-users] (no subject)

Hi, I am having a problem using pbc=full for crystalline polymers on Gromacs 3.3.2. I have input files that run in 3.3.1 with no problem, but the system explodes in 3.3.2. Here's a simplified cartoon of my system, dotted lines being box boundaries: (CH3) (CH3) |..| .

[gmx-users] pbc=full in 3.3.2

Sorry for the double post but I forgot my descriptive title... Hi, I am having a problem using pbc=full for crystalline polymers on Gromacs 3.3.2. I have input files that run in 3.3.1 with no problem, but the system explodes in 3.3.2. Here's a simplified cartoon of my system, dotted lines

Re: [gmx-users] Concerning DSSP

Yes, I have permission to both view and modify content. I even run the do_dssp command with the sudo (root user) option enabled. I think that the problem may then be related to sh: sh: /path/to/dssp: Permission denied I'll try to change its permissions and post another message later with the

Re: [gmx-users] Harmonic dihedral restraints

Not sure if anyone saw this...I had a question about how to include the dihedral restraints in the topology file. Unfortunately, this info doesn't seem to be in the manual. There isn't a [ dihedral_restraints ] section listed in Table 5.4. I presume this section should be formatted as: [

Re: [gmx-users] Harmonic dihedral restraints

Quoting Robert Johnson [EMAIL PROTECTED]: Not sure if anyone saw this...I had a question about how to include the dihedral restraints in the topology file. Unfortunately, this info doesn't seem to be in the manual. There isn't a [ dihedral_restraints ] section listed in Table 5.4. I presume

Re: [gmx-users] Concerning DSSP

Quoting Ricardo Soares [EMAIL PROTECTED]: Yes, I have permission to both view and modify content. I even run the do_dssp command with the sudo (root user) option enabled. I think that the problem may then be related to sh: sh: /path/to/dssp: Permission denied Perhaps a naive question, but

RE: [gmx-users] still problem of pr.mdp

Might be an idea to provide an image showing what you mean by this: but still i am getting tilting structure of POPC except water and protein stucture( fine) . I am using protein restrain force 1000 and my system box size is 7nm. Catch ya, Dallas Warren

[gmx-users] problem of general velocities

Hi gmx users, I am doing membrane simulations , In *pr.mdp file kept gen_vel =yes and in * md.mdp file kept no , can i use this like or viceversa I tried in different ways. Which way is acceptable. Pls suggest me. ___ gmx-users mailing list

Re: [gmx-users] problem of general velocities

- Original Message - From: sudheer babu [EMAIL PROTECTED] Date: Wednesday, February 27, 2008 4:42 pm Subject: [gmx-users] problem of general velocities To: gmx-users@gromacs.org Hi gmx users, I am doing membrane simulations , In *pr.mdp file kept gen_vel =yes and in *md.mdp file kept