[gmx-users] how to do dPCA

Dear gromacs users, I have done simulations of 20 residues length peptide for 300ns. As I would like to do explore the conformational space I have chosen the dPCA to find flexible regions. I have gone through the dPCA tutorial from gromacs site and followed it. First I have generated the index

[gmx-users] constant surface tension in gormacs

Dear Justin and all GROMACS users, I'm simulating a monolayer system using the surface tension command in gromacs to set the surface tension and obtain the area( per molecule). Although my system is 2d and uniform : a slab of water covered with surfactant molecules and the surface tension

Re: [gmx-users] KALP15 in DPPC

hi . I want to measure the distance between center of membrane and a peptide . how can i use gmx distance ?? On Wed, Jan 31, 2018 at 8:13 PM, Justin Lemkul wrote: > > > On 1/30/18 7:00 PM, negar habibzadeh wrote: > >> hi. in my dopc.gro file i have 128 dopc ,5120 water (sol)

[gmx-users] Pull group at constant speed

Hi, gmx users, I have a question on pulling a group of molecules at a constant speed. Let's say, I want move a protein in the vacuum at a constant speed of 0.01 nm/ps. I am aware that I can specify the pull rate in the COM pulling. I am using gromacs 5.1.2. Following is my pulling code: ;pull

Re: [gmx-users] Can I put b-factor into xtc file?

Hi, I don't know what your intended use case is, but there are various approaches to get a single PDB frame from a trajectory (e.g. trjconv -dump) and to combine that with B-factors (e.g. editconf -bf), but frankly the latter stage is probably easier with your own script, e.g. building on

Re: [gmx-users] Can I put b-factor into xtc file?

Thank you Mark for this fascinating tng format. I think I could not modify it using C/C++ at this moment. For your "easier approach", do you mean I can convert xtc to pdb frame with b-factor assigned, if I provide the b-factor file? How to do this? -- Original

Re: [gmx-users] Can I put b-factor into xtc file?

Hi, No, the format is not extensible. The TNG format offers better compression than XTC, and in principle can be extended for this kind of purpose, but you'd have to write some C/C++ to get that organized. An easier approach is to keep your B factors in some file that you keep in sync with the

[gmx-users] Can I put b-factor into xtc file?

Dear Gromacs, I have residue-based b-factor values for a protein. In the past, they were assigned to the b-factor columns of pdb files. It would take a lot of space if I extract all the pdb files. As the pdb files come from the xtc file, I wonder, if I can modify the xtc file directly? Thank

[gmx-users] Running long MD simulation

Hi I want to run a long MD 200 ns, but I want the outputs of every 5 ns to be saved separately ... Is there a way or a script to do this? Kind Regards,Ahmed -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

[gmx-users] simulation of water

Dear all users, I am new to Gromacs and I want to simulate a box of pure water.I want to know is there any tutorial for this simulation with Gromacs? or Could anyone kindly help me? Thanks in advance,Negar -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] paralllelized gromacs run creating same file in many times -reg

Hi, Yes, that's another point of failure - the command to launch the MPI executable needs to provide the correct context, including linking the right libraries. Mark On Thu, Feb 1, 2018 at 2:40 PM Peter Kroon wrote: > Hi, > > Digging through my old submission scripts show

Re: [gmx-users] Rupture force definition

On 2/1/18 7:59 AM, Rakesh Mishra wrote: Dear Justin Here I am applying pull for two groups with respect to two reference group as following. ; Pull code pull= yes pull_ngroups= 4 pull_ncoords= 1 pull_group1_name= chain_A8 (reference

Re: [gmx-users] paralllelized gromacs run creating same file in many times -reg

Hi, Digging through my old submission scripts show that when I ran gromacs with `srun` MPI communication would not work, and I would end up with a lot of files. If I ran with `mpirun` everything worked as expected. Which was why I blamed my cluster and their OpenMPI installation. I'm not sure

Re: [gmx-users] Rupture force definition

Dear Justin Here I am applying pull for two groups with respect to two reference group as following. ; Pull code pull= yes pull_ngroups= 4 pull_ncoords= 1 pull_group1_name= chain_A8 (reference also immobile ) pull_group2_name=

Re: [gmx-users] paralllelized gromacs run creating same file in many times -reg

Hi, The fact that the binary you ran was named gmx_mpi yet does not seem to be compiled with MPI is suspicious - either the cmake process that was used handled suffixes explicitly (which is unnecessary if all you want is the standard thing) and was wrong, or we implemented the standard suffixing

Re: [gmx-users] paralllelized gromacs run creating same file in many times -reg

Hi Venkat, I've seen similar behaviour with OpenMPI and a home-patched version of Gromacs. I blamed OpenMPI/the cluster and contacted the admins (but I don't remember what the result was). In the end I solved/worked around the issue by compiling Gromacs with IntelMPI. HTH Peter On 01-02-18