[gmx-users] dna, lipid simulation

Hi all, This is a question unrelated to gromacs but would pose it anyway to get some hints from the experts. I wish to set up DNA and DPPC lipid membrane simulation. Could someone please refer to a relevant forcefield/tutorial for simulation of lipids with DNA? Any help will be really appreciated

Re: [gmx-users] [OT] Generate random coil protein conformations?

On 05/12/10 00:26, Mark Abraham wrote: Sorry for the offtopic but my google-fu is apparently abandoning me. I am looking for a fast way to generate random coil protein configurations to use as startpoints for several simulations I'd like to do. All I managed to find is: - FOLDTRAJ which seems

Re: [gmx-users] [OT] Generate random coil protein conformations?

On 12/05/10, ms wrote: > Hi, > > Sorry for the offtopic but my google-fu is apparently abandoning me. I am > looking for a fast way to generate random coil protein configurations to use > as startpoints for several simulations I'd like to do. > > All I managed to find is: > - FOLDTRAJ which

[gmx-users] [OT] Generate random coil protein conformations?

Hi, Sorry for the offtopic but my google-fu is apparently abandoning me. I am looking for a fast way to generate random coil protein configurations to use as startpoints for several simulations I'd like to do. All I managed to find is: - FOLDTRAJ which seems unavailable and discontinued - the

[gmx-users] Desktop Freezes While Using mdrun-gpu

Hello friends, I'm writing today to see if anyone could offer further insight/commentary than the current available documentation and comments from the program itself concerning the following problem. I am currently using mdrun-gpu, v 4.5.3, utilizing my GPU, an NVIDIA GeForce GT 330M. When I

Re: [gmx-users] Ramachandran plot for non standar residues

Rebeca García Fandiño wrote: Hello, I am trying to calculate the Ramachandran plot for a molecules based on non-standar aminoacids, parametrized with the Gaff force field and simulated with Gromacs 4.0.7. When I try using g_rama -f trajectory.xtc -s topology.tpr -o rama.xvy I get: Found 0 p

[gmx-users] Ramachandran plot for non standar residues

Hello, I am trying to calculate the Ramachandran plot for a molecules based on non-standar aminoacids, parametrized with the Gaff force field and simulated with Gromacs 4.0.7. When I try using g_rama -f trajectory.xtc -s topology.tpr -o rama.xvy I get: Found 0 phi-psi combinations. I suppose

[gmx-users] MOPAC gromacs mdreun error

Dear gmx users          i have successfuly installed Mopac gromacs/interface. but when i run the QM/MM in mdrun_d  i have got hte following error QM/MM calculation requested. QM/MM calculation requested. there we go! there we go! Segmentation fault (core dumped) i am using 6 atoms f

Re: [gmx-users] two graphene sheets are blowing up

On 4/12/2010 7:48 PM, zhongjin wrote: Hi ALL, I am using GMX4.5.3. I have done a system, which include two graphenes and a CNT. I put two graphenes at both end of the CNT,and dig a hole to let water pass through CNT. I do not change any force fileld . I just treat all the carbon atoms as

[gmx-users] two graphene sheets are blowing up

Hi ALL, I am using GMX4.5.3. I have done a system, which include two graphenes and a CNT. I put two graphenes at both end of the CNT,and dig a hole to let water pass through CNT. I do not change any force fileld . I just treat all the carbon atoms as atoms in Benzene ring CA in AMBER03 forc

Re: [gmx-users] Which .tpr file to use for g_rms?

On 4/12/2010 6:45 PM, Anirban Ghosh wrote: Thanks a lot for the reply. But I am getting different results with the two .tpr files (first and last) using the following commands: trjconv -s *first.tpr *-f test.xtc -o str.gro -dump 1 -pbc nojump trjconv -s *last.tpr* -f test.xtc -o str.gro -d