Re: [gmx-users] BD and SD equations

Thank you Mark. On Jul 8, 2011, at 11:17 AM, Mark Abraham wrote: On 9/07/2011 1:36 AM, Marcelo A. Carignano wrote: Hi all, Stochastic dynamics is described in section 3.8 of the Manual (v. 4.5) Equation 3.108 is dimensionally incorrect, or at least I cannot understand it. Left hand side

[gmx-users] BD and SD equations

Hi all, Stochastic dynamics is described in section 3.8 of the Manual (v. 4.5) Equation 3.108 is dimensionally incorrect, or at least I cannot understand it. Left hand side is a force, and the first term on the right hand side has a missing length in the numerator to be a force. This is accor

Re: [gmx-users] coordination number and g_analysis

I'll rather use: g_rdf -cn Marcelo. On Apr 4, 2011, at 4:17 PM, Nilesh Dhumal wrote: Hello, I want to calculat the coordination number of solute in first solvation shell. integration of (4*pi*r^2*g(r)) from 0 to 2.6 A(first solvation shell) If I calcualte the g_rdf for first solvation sh

[gmx-users] Postdoc position available

Hi all, A post-doctoral research position is available at Northwestern University at Evanston, IL. The position is in the field of computational physical chemistry, with a focus on molecular dynamics simulation and force field development. The systems to be studied include water/air, water/ic

RE: [gmx-users] cgnr

Thank you! Please disregard my last comment in bugzilla. Marcelo. -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Berk Hess Sent: Friday, May 05, 2006 8:48 AM To: gmx-users@gromacs.org Subject: RE: [gmx-users] cgnr I have fixed the bug. You can avoid th

RE: [gmx-users] cgnr

Done. Posted bug # 75. I hope my explanation is clear. Marcelo. -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of David van der Spoel Sent: Thursday, May 04, 2006 4:05 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] cgnr Marcelo A

RE: [gmx-users] cgnr

list for GROMACS users Subject: Re: [gmx-users] cgnr Marcelo A. Carignano wrote: > Thank you David, but there is no such a term in this case: > I see, make the cut-off larger. mdrun uses charge group based cutoff (see chap 4) and you are probably missing some interactions in the secon

RE: [gmx-users] cgnr

Mu-X Mu-Y Mu-Z T-rest Any other suggestion? Thank you, Marcelo. Marcelo A. Carignano wrote: > Dear all: > > I'm running a test case defining all the interaction parameters in the > topol.top file. My system c

[gmx-users] cgnr

Dear all: I'm running a test case defining all the interaction parameters in the topol.top file. My system consist of two NH3 molecules. Every thing goes well except for the role played by the "cgnr" values: Depending on how I assign these numbers the calculated Coulombic interaction changes. If I