Re: [gmx-users] tutorial umbrella sampling

On 11/27/15 5:36 PM, Matthias Kiesel wrote: Hi All, I am currently doing the umbrella sampling tutorial by Justin Lemkul, but i have a problem with creating the right configurations for the umbrella sampling run. After running the first pull simulation and the given perl script the com distanc

[gmx-users] Compile error in Gromacs-5.1 and icc2011+openmpi+cuda5.5

Hi, I was trying to install gromacs-5.0.4 with MPI(openmpi-1.4.4) and GPU support (cuda-5.5) using intel composer-xe 2011, but got error msg like icc: command line error: no files specified; for help type "icc -help" I also tried gromacs-5.1 with icc2011+cuda5.5+openmpi-1.4.4 and got the s

Re: [gmx-users] combine two pdb files

yes it's true. thank you all On Sat, Nov 28, 2015 at 3:31 PM, Peter Stern wrote: > Probably. So follow Chandan Choudhury's suggestion to use editconf -resnr > 1 to reorder the residue numbers too and then it should work. > > Peter > > -Original Message- > From: gromacs.org_gmx-users-bou

Re: [gmx-users] combine two pdb files

Probably. So follow Chandan Choudhury's suggestion to use editconf -resnr 1 to reorder the residue numbers too and then it should work. Peter -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf

Re: [gmx-users] combine two pdb files

hi yes that's right. but it's renuber atoms not residues. is the same residue number make an error? tnx : ) On Sat, Nov 28, 2015 at 1:57 AM, Peter Stern wrote: > AFAIK pdb2gmx doesn't care about the atom numbers in your pdb file since > in any case it reorders them and renumbers them after add