CHARMM forums: molecular dynamics

Re: cpt dynamics with implicit solvent

Fri, 08 Jul 2011 14:37:16 CDT

Posted by lennart:
There is an example that sets up a box for you: solvent-box.str. 1/ You need a larger executable, try install.com gnu xxlarge 2/ This is an old box from B Jorgensen, which was equilbrated using Monte Carlo for TIP water. This box happens to have th

Re: Residue seperation in COOR CONT and COOR DMAT

Fri, 01 Jul 2011 18:16:02 CDT

Posted by rmv:
Asuuming CTOF1 is a cutoff, the code snippet suggests CO is a array of distances between I1 and I2, with NCONTACT incremented when 0 < CO(I1,I2) < CTOF1

Re: Carbon nano tube analysis

Fri, 01 Jul 2011 08:41:07 CDT

Posted by rmv:
If you want all 6 values on one line, they should be printed with a single command; CHARMM is doing what it has been told to do.

Re: Size of Water Box w/ PBCs

Wed, 29 Jun 2011 14:51:23 CDT

Posted by Ascaris:
Thanks!

Re: free softwate with environment like QUANTA

Wed, 22 Jun 2011 05:42:48 CDT

Posted by sajad:
hello dears is there any "FREE" molecular mechanic software with features and environment like that of QUANTA? in fact I am using the book written by Martin Karplus on biomolecular simulation. but unfortunately i have no access to QUANTA and I can't

Re: hetero-atom

Mon, 20 Jun 2011 02:22:38 CDT

Posted by lennart:
Yes.

Re: calculation the bulk (water) solution residenttime

Wed, 15 Jun 2011 11:50:10 CDT

Posted by lennart:
It is a simple average over the hydrogen bonding events involving the atom. If an atom over the course of the trajectory forms hydrogen bonds at three times, with lifteimes of 100, 50, and 150 ps, respectively, the average hydrogen bond residence tim

Re: Lipid gel phase or fluid phase

Tue, 14 Jun 2011 17:10:21 CDT

Posted by rmv:
There's an older book on lipid bilayers by Derek Marsh that may be useful, but it's a little expensive (like most science books), and may be out of print. A web search for "DPPC diffraction" should lead to some useful articles, perhaps combined wi

Re: Diffusion Coefficient

Mon, 13 Jun 2011 22:29:28 CDT

Posted by Zeeshan:
Hi I am looking for the diffusion coeffiecient of the following mixtures: 1- Butanol and Iso Octane 2- Butanol and Iso Propyl Alcohol 3-Butanol and Ethanol 4- Butanol and n-Pentane If you please provide me information on this I

Re: tetrahedral order parameter for water

Fri, 10 Jun 2011 19:35:27 CDT

Posted by sairam.umb:
Hi All I am simulating a small peptide system and trying to compare the TIP3 and TIP5 water models. I need to calculate the tetrahedral order parameter to see if there is any local ordering effect which may be dependent on the water models.