Re: [gmx-users] How many ps needs a simulation?

On Wed, 10 May 2006 19:29:26 -0700 (PDT) jahanshah ashkani [EMAIL PROTECTED] wrote: Thanks, In fact I have a sequence with 1277 residue. It is stable even in 50ps. But when I continue to simulation my pc is restarted in 4 steps, automaticly. I should say that this step needs about 100 h

Re: [gmx-users] How many ps needs a simulation?

Dallas B. Warren wrote: How many ps needs a simulation? How long is a piece of string? rofl... didn't see until now we both had the same response to this question! Cheers, Mark ___ gmx-users mailing listgmx-users@gromacs.org

RE: [gmx-users] How many ps needs a simulation?

Mark, rofl... didn't see until now we both had the same response to this question! Yeah, spun me out a bit too when your repsonse arrived after I had sent mine ;-) Catch ya, Dr. Dallas Warren Lecturer Department of Pharmaceutical Biology and Pharmacology Victorian College of Pharmacy,

[gmx-users] question on pulling 2 groups in afm run

Dear gromacs users, I met a problem on pulling 2 groups in a afm pulling run. When mdrun processes input file, error messages such as unknown left-hand : group_2 appear for group_2, afm_rate2, afm_k2, afm_dir2 and afm_init2. However, pulling one group is OK. My pull.ppa is verbose =

Re: [gmx-users] How many ps needs a simulation?

Hi Jahan,You mention your computer restarted. Now that sounds serious. Can you give more details about that? What happens in the log-file before the crash. Was it gromacs or something else that caused it? Are you running windows or *nix? Furthermore, as mentioned before, how long the simulation

Re: [gmx-users] Value for bonded force constant (Kb)

Hi Gmxions, The value Kb = 1673.6 KJ/mol nm2 working good for restraining distance (type6, Harmonic potential) between Fe(II) and corresponding ligating atoms N and O (of amino acids) at the end of 5000 steps of energy minimization. That is newly introduced Kb value is able to restraint at around

[gmx-users] angle restraints

Dear users, I have a small system with a number of small peptides. I want to constraint the angle between the N-term to C-term vectors of different peptides. This works well, but if I do a FEP calculation the dG/dl becomes smaller than zero at some point. I expected it to be at least allways

[gmx-users] Re: question on pulling 2 groups in afm run

Hi Linchen, You may want to try adding the line ngroups=2 to the pull.ppa, right under runtype = afm. It's in the new manual (version 3.3, section 6.2.3). Otherwise, I believe the number of groups defaults to 1, and that's why mdrun gets confused about finding a group_2, afm_rate2, etc.

Re: [gmx-users] Topology question

Anthony Cruz wrote: Hi users: I made a small molecule topology using the PRODRG topology generation server but I want to use it with the G43a1 GROMOS96 43a1 Forcefield. How I could change the parameters from GROMACS to GROMOS??? thanks Anthony

Re: [gmx-users] Ngmx

karamyog singh wrote: Respected gentlemen, I have written another code for simulating atomic oxygen. the code is running fine. however when i view my run using ngmx, the entire box doesn't get filled up.It just shows one plane of atoms. I have a box of 27 atoms but ngmx shows only 9. Can any1

Re: [gmx-users] Ngmx

Karam,If you think you know why, please share your thoughts.. that can help us provide an answer.Still, gromacs supports all periodic boundary conditions, except for real exotic stuff like spherical (and I can think of a few others). But any crystal packing can be handled. Maybe the easiest for

Re: [gmx-users] Ngmx

the problem continues even if i rescale my box to 1.0 1.0 1.0 :(On 5/11/06, karamyog singh [EMAIL PROTECTED] wrote:hmm.. i know about the no. of atoms in bcc. please tell me what to do if i want more than 1 unit cell? gromacs is not supporting periodic boundary conditions for my cell and i think

Re: [gmx-users] afm pulling and comm_mode

Hi again, I pretty much went about the setting up of afm pulling calculations. Still I am a little bit concern about the results. When using gmx3.2.1 and applying a Linear removal of the center of mass (i.e. translation) I see the cell unit still moving during the simulation in a direction

[gmx-users] do_dssp : ssdump data

Where can I find the exhaustive list of one letter codes used from secondary structures? (H for helix, T for turn...) I looked at do_dssp.c to figure it out . the array map[]... semes to hold the relevant information, but I got very confused. Any help would be appreciated... Senthil

[gmx-users] position restraints

Dear all, I'm trying to figure out if there is currently a way to calculate the position restraint energy (for example, if I'm using a posre.itp file to harmonically restrain some atoms) on the fly. Can anyone give me some pointers? I haven't turned up anything useful on this since 2001 on the

Re: [gmx-users] position restraints

David Mobley wrote: Dear all, I'm trying to figure out if there is currently a way to calculate the position restraint energy (for example, if I'm using a posre.itp file to harmonically restrain some atoms) on the fly. Can anyone give me some pointers? I haven't turned up anything useful on

Re: [gmx-users] position restraints

David, OK, I am running MD using position restraints, and I don't get a separate energy output for restraint energy or some such; as far as I can tell the energy of the restraints is grouped in with the total potential energy and never reported separately. I would like it to be reported

[gmx-users] mdrun_mpi stops at random

Hi all, I have an issue doing parallel runs where the simulation would just hang at seemingly random intervals anywhere from an hour to a day. There are no error messages reported in the logs and nothing funny from dmesg. My set up is two dual-core Pentium D. I run with -np 4 to take

[gmx-users] Re: Re: angle restraints

David, Thanks for your reply. I am currently using 3.3.1 code. I am increase the force, to be able to calculate the free energy required of introducing the angle restraints in the system. I use small force increments each run, using a delta_lambda of 0. Decreasing or increasing in my view