[gmx-users] Simulation Crash...Reg

the start of the simulation. What can be the possible reason for this kind of a behavior and what can be done to fix it? -- KRISHNA KISHORE@IIT-MADRAS -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http

[gmx-users] Re:Simulation Crash

DispCorr= EnerPres ; account for cut-off vdW scheme ; Velocity generation gen_vel = no ; assign velocities from Maxwell distribution -- KRISHNA KISHORE@IIT-MADRAS -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search

[gmx-users] CUT-OFFs for GROMOS96 43a1...Reg

/NPT equilibration and production MD run. So, someone please clarify me what the widely accepted values for these two would be. If at all I should use* rvdw = 1.4*, then should -d flag in editconf be atleast 1.4 or can it be less than that in the case of PBC conditions enabled. -- KRISHNA KISHORE

[gmx-users] Re: gmx-users Digest, Vol 83, Issue 188

gmx-users@gromacs.org Message-ID: 4d8e281b.5020...@vt.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed Please choose a relevant subject line and do not reply to the entire digest; it confuses the archive. Kishore wrote: Dear Mark, As you correctly pointed out, I had

[gmx-users] Re: gmx-users Digest, Vol 83, Issue 160

...@anu.edu.au Subject: Re: [gmx-users] Alcohol Dehydrogenase MD simulationReg To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 4d8942e6.8020...@anu.edu.au Content-Type: text/plain; charset=ISO-8859-1; format=flowed On 23/03/2011 4:38 AM, Kishore wrote: Dear All, I had

[gmx-users] Alcohol Dehydrogenase MD simulation....Reg

as a result of which important sidechain hydrogen bonds are being lost in the simulation. Is such behaviour expected or is it because of the non quantum mechanical treatment of the NADPH molecule that these kind of situations occur? If anyone has some experience please share it. -- KRISHNA KISHORE