http://www.charmm.org/ubbthreads-7-5-5/ubbthreads.php CHARMM forums: energy terms, constraints, restraints, and solvation CHARMM Forums - UBB.threads(tm) http://www.charmm.org/ubbthreads-7-5-5/ubbthreads.php?ubb=showflat&Number=27828#Post27828 Posted by mltan:
Thanks Rick. It works when I do the calculation on the cluster where the original simulation was done. It seemed there was some format incompatibility between local machine and cluster for the trajectory file. Ming ]]> Fri, 01 Jul 2011 14:52:35 CDT http://www.charmm.org/ubbthreads-7-5-5/ubbthreads.php?ubb=showflat&Number=27819#Post27819 Posted by hiva:
I actually need the lateral pressure profile along z-axis. I guess I should use another program then. I have a c-code that can read pdb, topology and prm files, and can calculate the non-bonded forces. So, to calculate the lateral pressure (without v]]> Thu, 30 Jun 2011 20:15:15 CDT http://www.charmm.org/ubbthreads-7-5-5/ubbthreads.php?ubb=showflat&Number=27732#Post27732 Posted by apredeus:
hiva, like I mentioned to you before, we have found that there are problems in BOUND. When we simulated a box of 125 TIP3P waters we saw very strange effects, such as waters aligning along certain lines, as if they were in crystal. And what d]]> Fri, 24 Jun 2011 03:53:47 CDT http://www.charmm.org/ubbthreads-7-5-5/ubbthreads.php?ubb=showflat&Number=27708#Post27708 Posted by rmv:
There is still a spherical cutoff with Ewald, imposed at CTOFNB, and is the boundary between explicit pairwise and reciprocal space calculations for a given atom. The unit cell is not the boundary for that. The simulation book by Allen and Tildesle]]> Tue, 21 Jun 2011 09:23:42 CDT http://www.charmm.org/ubbthreads-7-5-5/ubbthreads.php?ubb=showflat&Number=27706#Post27706 Posted by CHRM:
Thank you again.Helped a lot. sorry for the stupid questions. ]]> Tue, 21 Jun 2011 05:34:49 CDT http://www.charmm.org/ubbthreads-7-5-5/ubbthreads.php?ubb=showflat&Number=27697#Post27697 Posted by Yi He:
Thanks Sunhwan, Sorry, my force constant is 10.0( It is a typo that I didn't input the force constant). Yes, the molecule is placed in the restraint window( zref-droff]]> Mon, 20 Jun 2011 15:54:04 CDT http://www.charmm.org/ubbthreads-7-5-5/ubbthreads.php?ubb=showflat&Number=27648#Post27648 Posted by lennart:
eef1 is in principle the same as asp, just a faster implementation. ]]> Tue, 14 Jun 2011 05:20:34 CDT http://www.charmm.org/ubbthreads-7-5-5/ubbthreads.php?ubb=showflat&Number=27626#Post27626 Posted by lennart:
yes.]]> Fri, 10 Jun 2011 08:13:57 CDT http://www.charmm.org/ubbthreads-7-5-5/ubbthreads.php?ubb=showflat&Number=27623#Post27623 Posted by Newton:
Just a follow-up: I know you can use the scalar command to write the equations of a plane, but I found tcl scripting pretty useful, for visualizing while I was doing it. This is for anyone who wants to make a waterbox of any shape (this is an example]]> Wed, 08 Jun 2011 21:07:15 CDT http://www.charmm.org/ubbthreads-7-5-5/ubbthreads.php?ubb=showflat&Number=27561#Post27561 Posted by rmv:
You need to save velocity trajectories. ]]> Thu, 26 May 2011 13:00:09 CDT