[gmx-users] Query regarding Domain decomposition

Greetings I have been trying to run a few set of simulations using high number of processors. Using the tutorial - http://compchemmpi.wikispaces.com/file/view/Domaindecomposition_KKirchner_27Apr2012.pdf I have done calculations to evaluate the set of nodes which would be optimal for the protein.

[gmx-users] Carbon monoxide topology

If you're happy that such parameters might work with your intended force field, then you only need to build them into a topology. Assuming you have some GROMACS experience, check out the relevant parts of chapters 4 and 5 of the manual. Mark On Jun 25, 2014 4:01 AM, "라지브간디" wrote: > Dear Dr. Vit

Re: [gmx-users] Hamiltonian Replica Exchange

Indeed. REST implemented in PLUMED seems a good bet. Mark On Jun 24, 2014 11:50 PM, "HANNIBAL LECTER" wrote: > I would think of using Replica Exchange with Solute Tempering in this case. > Look at the paper as to how one can implement this in Gromacs (doi: > 10.1002/jcc.21703). > > Without havin

Re: [gmx-users] Fwd: segmentation fault on gpus

In the Verlet scheme, mdrun will change rlist to conserve energy and maximize performance. Just leave it alone. Mark On Jun 24, 2014 10:18 PM, "ram bio" wrote: > so, is it that rlist should be less than rc? > > > On Tue, Jun 24, 2014 at 12:42 PM, Szilárd Páll > wrote: > > > On Tue, Jun 24, 2014

Re: [gmx-users] question about installation of gmx on Cray linux

Yes. Please start by reading the reply Justin made a few days ago. Your "normal" is unknown to us. Mark On Jun 24, 2014 10:29 PM, "Tom" wrote: > Dear Gromacs Developers and Experts: > > I noticed that the performance of gromacs on Cray linux clusters is only > 36.7% of the normal. > > > The foll

[gmx-users] topology file

Hi, I have a few technical questions regarding creating the topology file by using the command "g_x2top". I would like to use the following GROMACS's command: g_x2top -f device.gro -ff oplsaa -o device.top to convert the .gro file to .top. The problem that I have is that the force field for ca

[gmx-users] proteins break up in simulation

Dear all,In my NPT explicit solvent simulation on the proteins with multiple chains, sometimes the protein can break up and its chains leave far from each other. We wonder if this is caused by the instability of the protein or improper simulation conditions. Could anyone give me some suggestions

Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 122, Issue 103

Dear Dr. Vitaly V. Chaban, The charges and non-bonded interactions of Carbon monoxide are set to give approximate agreement with the experimental dipole & quardrupole moments ( J.E. Straub, M. Karplus, Chemical Physics, 1991). According to this article, with the specific point charges and LJ

Re: [gmx-users] Hamiltonian Replica Exchange

I would think of using Replica Exchange with Solute Tempering in this case. Look at the paper as to how one can implement this in Gromacs (doi: 10.1002/jcc.21703). Without having more details I would suggest to you to scale the Hamiltonian of each replica such that the Helix bundles are always cor

[gmx-users] Hamiltonian Replica Exchange

Greetings, I want to use the HREX implementation of GROMACS to study the dynamics of a heterodimeric protein. The structure is a two helix bundle (two helical monomers that are wrapped around each other) with disordered ends. I am mainly interested in the dynamics of the disordered ends because I

[gmx-users] question about installation of gmx on Cray linux

Dear Gromacs Developers and Experts: I noticed that the performance of gromacs on Cray linux clusters is only 36.7% of the normal. The following is the detail about the installation -- CC=gcc FC=ifort F77=ifort CXX=icpc CMAKE_PREFIX_PATH=/opt/cray/modulefiles/cray-mpich/6

Re: [gmx-users] Fwd: segmentation fault on gpus

so, is it that rlist should be less than rc? On Tue, Jun 24, 2014 at 12:42 PM, Szilárd Páll wrote: > On Tue, Jun 24, 2014 at 7:18 PM, Justin Lemkul wrote: > > > > > > On 6/24/14, 12:14 PM, ram bio wrote: > >> > >> hi Justin, > >> > >> Thanks, that makes sense, however I was able to use the sam

Re: [gmx-users] Fwd: segmentation fault on gpus

shall i do only two tc-grps protein and non-protein? On Tue, Jun 24, 2014 at 12:18 PM, Justin Lemkul wrote: > > > On 6/24/14, 12:14 PM, ram bio wrote: > >> hi Justin, >> >> Thanks, that makes sense, however I was able to use the same ligand >> toplogy >> files with earlier versions like gromacs

Re: [gmx-users] Fwd: segmentation fault on gpus

no , they are different protein-ligand complexes, the issues are with 1. the source one is from protein data bank and other is modelled protein 2. versions with older version i could simulate the modelled complex too On Tue, Jun 24, 2014 at 12:18 PM, Justin Lemkul wrote: > > > On 6/24/14, 12:14

Re: [gmx-users] Fwd: segmentation fault on gpus

On 6/24/14, 1:42 PM, Szilárd Páll wrote: On Tue, Jun 24, 2014 at 7:18 PM, Justin Lemkul wrote: On 6/24/14, 12:14 PM, ram bio wrote: hi Justin, Thanks, that makes sense, however I was able to use the same ligand toplogy files with earlier versions like gromacs 4.5.4 to simulate protein li

Re: [gmx-users] Fwd: segmentation fault on gpus

On Tue, Jun 24, 2014 at 7:18 PM, Justin Lemkul wrote: > > > On 6/24/14, 12:14 PM, ram bio wrote: >> >> hi Justin, >> >> Thanks, that makes sense, however I was able to use the same ligand >> toplogy >> files with earlier versions like gromacs 4.5.4 to simulate protein ligand >> complexes. I can si

Re: [gmx-users] Fwd: segmentation fault on gpus

On 6/24/14, 12:14 PM, ram bio wrote: hi Justin, Thanks, that makes sense, however I was able to use the same ligand toplogy files with earlier versions like gromacs 4.5.4 to simulate protein ligand complexes. I can simulate protein-ligand complexes with the current versions also but only for t

Re: [gmx-users] Fwd: segmentation fault on gpus

hi Justin, Thanks, that makes sense, however I was able to use the same ligand toplogy files with earlier versions like gromacs 4.5.4 to simulate protein ligand complexes. I can simulate protein-ligand complexes with the current versions also but only for the crystal structures that have ligand bo

Re: [gmx-users] Error in Umbrella sampling

On 6/24/14, 2:57 AM, Maziya Ibrahim wrote: Hello all, I have been running the umbrella sampling tutorial available on the bevan lab website. After the following steps: grompp -f md_pull.mdp -c npt.gro -p topol.top -n index.ndx -t npt.cpt -o pull.tpr mdrun -s pull.tpr trjconv -s pull.tpr -f

[gmx-users] Calculating the interaction energy as well individual energy?

Hello, Whats the way to calculate the individual residue energy (eg: His would have different energy upon different protonation)? How do we also calculate the interaction energy of ligand molecules with particular residues? -- Gromacs Users mailing list * Please search the archive at h

Re: [gmx-users] Charges & non-bonded interaction values usage in different force fields

Can you perhaps kindly explain us how "charges and non-bonded interaction values" were "experimentally determined"? Dr. Vitaly V. Chaban On Tue, Jun 24, 2014 at 10:37 AM, Rj wrote: > Dear all, > > > Experimentally determined charges and non-bonded interaction values for > ligand atoms ( Writte

[gmx-users] Charges & non-bonded interaction values usage in different force fields

Dear all, Experimentally determined charges and non-bonded interaction values for ligand atoms ( Written in charmm) can be used directly in gromacs provided charmm27.ff ? or does it need any conversion to use it in gromacs based charmm27.ff? -- Gromacs Users mailing list * Please search t