Re: [gmx-users] Can I add extra LJ and electrostatic interactions for 1-2 or 1-3 interactions.

intelandamd wrote: Dear I want to add extra LJ and electrostatic interactions for 1-2 or 1-3 interactions between pairs of atoms in the [ pairs ] section and do free energy calculations by perturbing these interactions. If it is possible, how can I do that.Thank you. You start by reading

Re: [gmx-users] Pressure Coupling

Thank you very much for the reply, and I'll try to better search the board first :) Cheers, George Dallas B. Warren wrote: Issue like this has been discussed previously, try searching the emailing list for a solution first before posting. Means you get your answer faster :-) Pressure is a ma

RE: [gmx-users] Pressure Coupling

Issue like this has been discussed previously, try searching the emailing list for a solution first before posting. Means you get your answer faster :-) Pressure is a macroscopic property that is being monitored and adjusted on a microscopic scale. A variation of that order is entirely normal.

[gmx-users] Pressure Coupling

Hi, I want to fix the pressure during the simulation so I use pressure coupling. I set the reference potential to 1 (the unit is bar as the manual says). Nevertheless, the log file shows much higher pressures (can reach the order of 1e+03 and again it seems the unit is bar). Moreover, it

[gmx-users] Can I add extra LJ and electrostatic interactions for 1-2 or 1-3 interactions.

Dear I want to add extra LJ and electrostatic interactions for 1-2 or 1-3 interactions between pairs of atoms in the [ pairs ] section and do free energy calculations by perturbing these interactions. If it is possible, how can I do that.Thank you. Kind Regards

Re: [gmx-users] Initial Temperature

Thanks Dallas and Mark for your replies. Best regards, George Mark Abraham wrote: George Abadir wrote: Hi, When I do a Berendsen temperature coupling , I set the reference tepmerature to 300K. However, the log file says the initial temperature is 0K. Why does this happen and how can one

RE: [gmx-users] Initial Temperature

See the Chapter 7.3 of the manual, "Run Parameters". In particular "7.3.16 Velocity Generation", page 146. Catch ya, Dr. Dallas Warren Lecturer Department of Pharmaceutical Biology and Pharmacology Victorian College of Pharmacy, Monash University 381 Royal Parade, Parkville VIC 3010 [EMAIL PROTE

Re: [gmx-users] Initial Temperature

George Abadir wrote: Hi, When I do a Berendsen temperature coupling , I set the reference tepmerature to 300K. However, the log file says the initial temperature is 0K. Why does this happen and how can one control the initial temperature? Temperature is a function of molecular velocities

[gmx-users] Initial Temperature

Hi, When I do a Berendsen temperature coupling , I set the reference tepmerature to 300K. However, the log file says the initial temperature is 0K. Why does this happen and how can one control the initial temperature? Thank you very much, Regards, George _

Re: [gmx-users] use of -dt

[EMAIL PROTECTED] wrote: Hi, I know this should be trivial..but i cant understand what this option do: -dtOnly write frame when t MOD dt = first time (ps) would some explain what is MOD and how this is relevent to g_cluster or trjconv. MOD is the modulo operator, which returns the remain

[gmx-users] use of -dt

Hi, I know this should be trivial..but i cant understand what this option do: -dtOnly write frame when t MOD dt = first time (ps) would some explain what is MOD and how this is relevent to g_cluster or trjconv. Thank u ___ gmx-users mailing list

Re: [gmx-users] No such moleculetype FE

On 4/30/07, Sonali <[EMAIL PROTECTED]> wrote: hi everybody, i am running Gromacs simulation with the protein 1f9b.pdb. I had earlier got some errors with the ligands present i.e FE, BCT and 3ID so i had run prodrg with BCT and 3ID but as prodrg server doesnot support for FE i had obtaine4d itp

[gmx-users] No such moleculetype FE

hi everybody, i am running Gromacs simulation with the protein 1f9b.pdb. I had earlier got some errors with the ligands present i.e FE, BCT and 3ID so i had run prodrg with BCT and 3ID but as prodrg server doesnot support for FE i had obtaine4d itp and top files for FE by pdb2gmx. and ommiting the

Re: [gmx-users] g_energy sum

hello, you are right but "summing" over 1 term was done only for testing purposes. first i tried to sum up all lj terms but ran into the same problem. nevertheless i finally found the reason for the difference. the energy file is from a rerun. during the setup mdrun complained that not all fram