[gmx-users] gmx 4.6: incompatible gpu device

Hi, I've downloaded Gromacs 4.6: git checkout --track -b release-4-6 origin/release-4-6 With '-msse4.1' added to CMAKE_C_FLAGS it finally compiled. But a test run with 1 CPU & 1 GPU failed with the following message before it started : -- mdrun -deffnm gputest -gpu_id $g

Re: [gmx-users] Re: Regarding POPE " H " atom type modification

Hi, In both the cases i got the error as show below. xxx Step 0, time 0 (ps) LINCS WARNING relative constraint deviation after LINCS: max 2095.427979 (between atoms 4422 and 4424) rms 69.822533 bonds that rotated more than 30 degrees:

Re: [gmx-users] Regarding POPE " H " atom type modification

Hi, naga raju wrote: Dear gmx users, I am trying to equilibrate POPE lipid bilayer. As per mailing list (http://www.gromacs.org/pipermail/gmx-users/2006-May/021416.html.), C6/C12 parameters are converted into sigma/epsilon. I modified " H " atom type to opls_369 in pope.itp file(show

Re: [gmx-users] OPLSaa+Lipid.itp question

Hi Chris, Thanks Oliver, it's gratifying to know that everything is working for you. If you are not using the half-epsilon double-pairlist method for the lipid 1-4 interactions then you should note that opls-aa defaults are causing coulombic 1-4 scaling by 0.5 (non-standard for these lipid pa

Re: [gmx-users] Re: OPLSaa+Lipid.itp question

Hi Chris, thank you very much for your help. My test simulation is coming along well. The area per lipid is in good agreement with experimental values. Also the embedded membrane protein behaves quite well in terms of RMSD/F, but I have to play around with the protein insertion protocol. Now

Re: [gmx-users] Regarding POPE lipid parameters

Hi, I downloaded POPE.itp and lipid.itp file from Dr Tieleman website http://moose.bio.ucalgary.ca/index.php? page=Structures_and_Topologies. I am trying to convert C6/C12 parameters to sigma/epsilon as suggestions given by Dr.Chris neale in mailing list http://www.gromacs.org/pipermail/gmx-u