Re: [gmx-users] simulation of protein in presence of ATP

Hi, We can use max 4 coloumns for naming atoms. But .rtp file has 5 coloumn atom names (AO1PG etc) That i modified to 4 letter name. But now the error is "atom N not found in residue 1ATP while combining tdb and rtp" From: Mark Abraham To: Discussion li

Re: [gmx-users] GROMACS file formats

Mark Abraham wrote: Santanu Ch wrote: Hi, I am looking for the documentation of GROMACS trajectory output file format and GROMACS .tpr file format. We have our own MD simualation program which is based on CHARMM. We would like to make this program output simulation trajectories in GROMAC

Re: [gmx-users] simulation of protein in presence of ATP

nikhil damle wrote: Hi, Thanks a lot for the reply. I am submitting ATP crds as ATP.pdb to pdb2gmx and receive the error as "No atoms found in pdb file ATP.pdb" I converted HETATM tag to ATOM tag. Still same error msg. Please find ATP.pdb file attached herewith. You've broken the PDB for

Re: [gmx-users] simulation of protein in presence of ATP

Hi, Thanks a lot for the reply. I am submitting ATP crds as ATP.pdb to pdb2gmx and receive the error as "No atoms found in pdb file ATP.pdb" I converted HETATM tag to ATOM tag. Still same error msg. Please find ATP.pdb file attached herewith. From: Mark

Re: [gmx-users] GROMACS file formats

Santanu Ch wrote: Hi, I am looking for the documentation of GROMACS trajectory output file format and GROMACS .tpr file format. We have our own MD simualation program which is based on CHARMM. We would like to make this program output simulation trajectories in GROMACS (so that we can us

[gmx-users] GROMACS file formats

Hi, I am looking for the documentation of GROMACS trajectory output file format and GROMACS .tpr file format. We have our own MD simualation program which is based on CHARMM. We would like to make this program output simulation trajectories in GROMACS (so that we can use some of the programs i

Re: [gmx-users] -bash: /home_soft/soft_chem/soft_install/gromac/bin/GMXRC.bash: No such file or directory

Jinyao Wang wrote: > Hi,gmx-users, > When I am installing Gromacs 4.0.3, I set environment variables in .bashrc > file like this: > > export > PATH=$PATH:/home_soft/soft/x86_64/apps/OpenSoft/Chem/gromacs/gromacs-4.0.3/bin > export > LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/home_soft/soft/x86_64/lib/M

Re: [gmx-users] How to increase the number of parameters in dihedral angle potentials?

bh...@princeton.edu wrote: Dear all, This is the problem I meet with. GROMACS provides a Ryckaert-Bellemans function with 6 parameters (C0, C1, C2, ..., C5) , while what I need is a function of summation over 8 terms, that is, 8 parameters from C0 to C7. I tried to add the values of the two add

Re: [gmx-users] -bash: /home_soft/soft_chem/soft_install/gromac/bin/GMXRC.bash: No such file or directory

Jinyao Wang wrote: > Hi,gmx-users, When I am installing Gromacs 4.0.3, I set environment variables > in .bashrc file like this: > > export > PATH=$PATH:/home_soft/soft/x86_64/apps/OpenSoft/Chem/gromacs/gromacs-4.0.3/bin > export > LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/home_soft/soft/x86_64/lib/M

Re: [gmx-users] problems with some calculated trajectories

Am 22.06.2009 um 17:19 schrieb Martin Höfling: Hey Bernhard, here some thoughts of mine: In principle, vmd should be able to read the trajectories if pdb2gmx tells you that the trajectory is ok. If this is not the case, you can use gmx_rescue64 to extract the undamaged parts.

Re: [gmx-users] problems with some calculated trajectories

Hey Bernhard, here some thoughts of mine: In principle, vmd should be able to read the trajectories if pdb2gmx tells you that the trajectory is ok. If this is not the case, you can use gmx_rescue64 to extract the undamaged parts. Reasons for damaged trajectories, even when gromacs runs thro

[gmx-users] -bash: /home_soft/soft_chem/soft_install/gromac/bin/GMXRC.bash: No such file or directory

Hi,gmx-users, When I am installing Gromacs 4.0.3, I set environment variables in .bashrc file like this: export PATH=$PATH:/home_soft/soft/x86_64/apps/OpenSoft/Chem/gromacs/gromacs-4.0.3/bin export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/home_soft/soft/x86_64/lib/Mathlib/fftw-3.2.1_bak/lib source /h

Re: [gmx-users] parallel computing

On Jun 22, 2009, at 4:43 PM, akalabya bissoyi wrote: hello everybody i am running my gromacs in PC, it takes me lot of time for running my simulation. Can anybody help me regarding parallel computing using my PC so that my simulation will be faster. Any materials/protocol so that i can m

RE: [gmx-users] How to extend correctly pulling simulation?

Hi, You don't say why you want to do it in several simulations and not in one. If it is just because your runtime per job is limited you can use the standard way to cut any simulation into parts. Make a tpr file with nsteps set to all steps. run it with mdrun -cpi -append -maxh Then mdrun will a

[gmx-users] parallel computing

hello everybody i am running my gromacs in PC, it takes me lot of time for running my simulation. Can anybody help me regarding parallel computing using my PC so that my simulation will be faster. Any materials/protocol so that i can make my own cluster using my PC (minimum resources) ? thank y

[gmx-users] How to increase the number of parameters in dihedral angle potentials?

Dear all, This is the problem I meet with. GROMACS provides a Ryckaert-Bellemans function with 6 parameters (C0, C1, C2, ..., C5) , while what I need is a function of summation over 8 terms, that is, 8 parameters from C0 to C7. I tried to add the values of the two additional pamameters at the

Re: [gmx-users] problems with some calculated trajectories

Hi, Could it be a periodicity issue? Have you tried using trjconv -pbc nojump ? /Erik Bernhard Knapp skrev: Dear users I performed some long-time simulations using gromacs 4.0. The longest simulation trajectory is about 62 ns. Unfortunately the trajectory seems to be damaged. If I calculate

[gmx-users] problems with some calculated trajectories

Dear users I performed some long-time simulations using gromacs 4.0. The longest simulation trajectory is about 62 ns. Unfortunately the trajectory seems to be damaged. If I calculate the RMSD of different interesting regions the values are beginning to jump up an down after about 17 ns in one

[gmx-users] How to extend correctly pulling simulation?

Hi all, I am trying to stretch protein using gromacs 4.0 umbrella options. (please see mdp file in attachment). This is quite large 136 amino acids protein which I want to stretch completely using sets of mdp files with 25 numbers of steps. To perform these simulations I have to be able to

[gmx-users] about stretch protein using gromacs 4.0 umbrella options

Hi all, I am trying to stretch protein using gromacs 4.0 umbrella options. (please see mdp file in attachment). This is quite large 136 amino acids protein which I want to stretch completely using sets of mdp files with 25 numbers of steps. To perform these simulations I have to be able to