i am using GBMV with dynamics and I see a huge drift in temp(rise) when i use time step of .002 with shake. Re-running with .002 only leads to a small drift but i am afriad if i run longer i might still see it rising. What do you suggest to avoid this temp jump w/o larger time step?
From earlier post, i realized two things. One use of "UPDATE 1" and another use of "Langevin" dynamics.
1) Can I still use 2fs step and shake with GBMV and langevin dynamics? 2) Use of Langevin for dynamics run and not equilibration should i use "IEQFRQ=0"? 3) SHould i run equilibration and dynamics,both using langevin dynamics or can i just begin a new dynamics run without restarting from equilibrated run for GBMV?
I'm not familiar with "UPDATE 1"; but then again I'm not very familiar with GBMV, either. Have you considered using another of the many implicit water models in CHARMM, such as SCPISM?
SHAKE BONH PARAM should always be used with a 2 fs timestep.
There should not be a problem using Langevin dynamics with implicit solvent; it provides T control, and the use of low friction (SCALAR FBETA SET 2.0) accelerates barrier crossings (torsional state changes) w/o affecting populations. You may have to run some test simulations to determine if a 2 fs timestep is reasonable for your case or not.
For Langevin dynamics, IHTFRQ, IEQFRQ, and ICHECW should all be zero; these represent a different T control method.
ECHECK should not be so large; even ECHECK 1000. may be excessive.
ISVFRQ is not really needed; it's a legacy feature from early on when computers used to crash a lot more often.
However, after use of update 1, i am getting better energy conservation.
But, I will also try another implict solvent you suggested. When i run parallel charmm on my supercmputers, i find use of "isvfreq" necessary. If i don't specify it and if the job terminates on exceeding the run time limit, it dosen't write the restart file until the required number of steps have finished(or dynamics run is finished).
I am currently using "fbeta=10" from another test file. You recommend, "fbeta=2" is better?