[gmx-users] Announcement: Structure-based model webtool for Gromacs

to prepare production simulations. Questions, comments and suggestions regarding this model and webtool should be directed to sbm-h...@ctbp.ucsd.edu, and not the gmx-users list. Hope you find this resource useful. Paul Whitford ___ gmx-users mailing list

[gmx-users] periodic boundary issue

I am having the following issue with Gromacs 4.0.2: I run a simulation with pbc=xyz. By the end of the simulation my molecule is split by the boundary (half of the molecule appears on one side and the other half on the opposite side). This is not a problem. The problem occurs when I use tpbco

[gmx-users] Re: gmx-users Digest, Vol 56, Issue 32

I am extending the run with tpbconv and a trajectory file. I also get this error if I change the number of steps in the tpr by using tpbconv and then using a checkpoint to start the next run. I get this error in both serial and parallel. I used this same procedure for a system that did not cross

RE: [gmx-users] periodic boundary issue

My apologies for not providing the appropriate subject line before. You can delete the last post, to keep the archive more organized. -- I am extending the run with tpbconv and a trajectory file. I also get this error if I change the number of steps in the tpr by using tpbconv and then

[gmx-users] MPI issue

I am running gromacs on a machine with altivec support. My understanding is I have to use MVAPICH on this machine. I occasionally have runs crash and I receive the following error n559(0): Loaded with Money n536(14): 14 - MPI_ALLREDUCE : Null communicator n536(14): [14] [] Aborting Program! n5

[gmx-users] Unable to minimize energy

This is likely an embarrassingly trivial problem, but let's see. I am following the energy minimization scheme presented in the groningen tutorial http://md.chem.rug.nl/education/mdcourse/MDpract.html I believe I follow the directions exactly, yet I can not minimize below Fmax~500 I download 1A

[gmx-users] g_sas and vdwradii.dat

Gromacs users, I have 3 easy questions regarding the use of g_sas 1) I am trying to understand exactly how gromacs computed the SAS. I looked at vdwradii.dat and it says ; Very approximate VanderWaals radii ; only used for drawing atoms as balls or for calculating atomic overlap. Does atomic

[gmx-users] PBC, lincs and bonds breaking

I am trying to simulate my own structure based simulation using 3.3.2. I have developed the forcefield and it works fine without periodic boundary conditions. When I use pbc=xyz atoms that are connected in the [bonds] section of the topology get broken. What happens is 1 of the two atoms will cr

[gmx-users] PBC, lincs and bonds breaking

>>* I am trying to simulate my own structure based simulation using 3.3.2. * >What sort of structure? RNA with a ligand (the ligand is the trouble) >>* I *>>* have developed the forcefield and it works fine without periodic boundary *>*> conditions. When I use pbc=xyz atoms that are connected in

[gmx-users] Periodic Boundary conditions

I am running v3.3.2. I am running an RNA strand with a homemade potential. When I run a single molecule in a periodic box, the system is fine until one nucleic acid crosses the boundary. THen the entire nucleic acid gets moved to the opposite side of the box. Since there are bonds this results i

[gmx-users] replica exchange: >4 processors

I am using 3.3.2 and 3.3.1 and I get the following problem with both of them. If I run replica exchange on >4 processors (2 and 4 are fine), the simulations finish, but mpi gives the following errors, thus the job never terminates this is the end of my log file -