[gmx-users] simulating only few residues from whole protein]
Original Message Subject: simulating only few residues from whole protein From:preetichoudh...@iisermohali.ac.in Date:Tue, March 19, 2013 10:45 am To: gmx-users@gromacs.org -- Original Message Subject: From:preetichoudh...@iisermohali.ac.in Date:Tue, March 19, 2013 10:44 am To: gmx-users@gromacs.org -- Hi, can anyone tell me how to carry out simulations in which we take the whole protein pdb structure but simulate only a certain part of it(only some residues). what will be the mdp files for such simulations ??? please help me if you know how to do it. -thankyou -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] [Fwd: implicit solvation]
Original Message Subject: implicit solvation From:preetichoudh...@iisermohali.ac.in Date:Fri, March 15, 2013 1:58 pm To: gmx-users@gromacs.org -- hi, I am trying to simulate a 50 residue protein in implicit water.Can anyone tell me that why we usually set the cuttoff to be 0. coulombtype = Cut-off vdwtype = Cut-off nstype = grid nstlist = 0 rlist = 0 rcoulomb = 0 rvdw = 0. I HAVE SEEN THAT PEOPLE KEEP NO CONSTRAINTS ON THE SYSTEM.Can you explain why this is being done. Also we dont need to do nvt and npt equlibration here.We dont neutralise our system too.But it keeps on showing in note: NOTE 1 [file topol.top, line 7412]: System has non-zero total charge: -2.00 Total charge should normally be an integer. See http://www.gromacs.org/Documentation/Floating_Point_Arithmetic for discussion on how close it should be to an integer. Correct me if I am wrong. Also while doing production run,I am getting this error:- WARNING 1 [file topol.top, line 7412]: The bond in molecule-type Protein_chain_W between atoms 17 OG and 18 HG has an estimated oscillational period of 9.0e-03 ps, which is less than 5 times the time step of 2.0e-03 ps. Maybe you forgot to change the constraints mdp option. thankyou -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] implicit solvation
hi, I am trying to simulate a 50 residue protein in implicit water.Can anyone tell me that why we usually set the cuttoff to be 0. coulombtype = Cut-off vdwtype = Cut-off nstype = grid nstlist = 0 rlist = 0 rcoulomb = 0 rvdw = 0. I HAVE SEEN THAT PEOPLE KEEP NO CONSTRAINTS ON THE SYSTEM.Can you explain why this is being done. Also we dont need to do nvt and npt equlibration here.We dont neutralise our system too.But it keeps on showing in note: NOTE 1 [file topol.top, line 7412]: System has non-zero total charge: -2.00 Total charge should normally be an integer. See http://www.gromacs.org/Documentation/Floating_Point_Arithmetic for discussion on how close it should be to an integer. Correct me if I am wrong. Also while doing production run,I am getting this error:- WARNING 1 [file topol.top, line 7412]: The bond in molecule-type Protein_chain_W between atoms 17 OG and 18 HG has an estimated oscillational period of 9.0e-03 ps, which is less than 5 times the time step of 2.0e-03 ps. Maybe you forgot to change the constraints mdp option. thankyou -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
