[gmx-users] Regarding 2D simulation

Dear all Gromacs users, I am running the simulation using pbc in 2 directions instead of all directions. For example, pbc = xy instead of pbc = xyz. Kindly tell me how to run the simulation using pbc in two directions. Best Regards, Raju Lunkad -- Gromacs Users mailing list * Please search the

[gmx-users] Regarding energy calculation of head groups

ent energy groups I am not sure but in my opinion, the error is coming because of the N4 contains -0.5 charge and O2 contains -0.7 charge. Kindly tell me how to mention energy groups in "mdp file" with charged atoms. Best regards, Raju Lunkad -- Gromacs Users mailing list * Plea

[gmx-users] Mdrun with rdd option

affected using "rdd" option. Best Regards, Raju Lunkad -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For

[gmx-users] Regarding too many LINCS warnings

Dear all Gromacs Users, In one of my simulations when I use the command mdrun -v -deffnm nvt I face with this fatal error: Too many LINCS warnings (1056) I dont know what does it mean and how can I fix it! Regards, Raju Lunkad -- Gromacs Users mailing list * Please search the archive at http

Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 140, Issue 43

ll) >5. Re: Performance on multiple GPUs per node (Szil?rd P?ll) >6. Regarding generating itp file. (Raju Lunkad) >7. Re: Regarding generating itp file. (Justin Lemkul) > > > -- > > Message: 1 >

[gmx-users] Regarding generating itp file.

Dear GROMACS Admins, I want to generate itp file of crystal structure ( calcium oxalate monohyrate). Can anyone suggest me how to generate itp file. Thanking you, Yours sincerely, Raju Lunkad -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support

[gmx-users] Installing gmx 5.0.5 in mpi

n single PC contains 24 HPC processor. Its much appreciated if you can provide the best configuration to run gmx in best way, Thanks. Regards Raju -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * C

[gmx-users] gmx 5.0 installation with cuda

the gmx through following commands i gets following errors. Kindly give a suggestion to rectify this problem. Thanks. Cuda installed path whereis cuda cuda: /usr/local/cuda gmx installation [raju@ddteam build]$ gcc --version gcc (GCC) 4.7.2 20121015 (Red Hat 4.7.2-5) Copyright (C) 2012 Free

[gmx-users] Ligand moving during MD course.

Dear gmx users, I have simulated the crystal structure prion with its inhibitor using charmm27.ff force field by obtaining the inhibitor parameters from http://www.swissparam.ch/. After i ran the production for 10 ns, the output shows the inhibitor moving ~ 3 Angstrom from the cavity and con