[gmx-users] entropy from eigenfrequency

Dear Gromacs Users, I was just wondering if the formula and the units which I use for getting the entropy is absolutely correct. The eigenfrequency (v) in cm-1 are obtained from eigenfreq.xvg.( GMX ver 4.0.7, using normal mode calculations) TS = [alpha/exp(alpha)-1] -  log[1-exp(-alpha)]

[gmx-users] Invitation to connect on LinkedIn

LinkedIn Ting Zhou requested to add you as a connection on LinkedIn: -- Chinmay, I'd like to add you to my professional network on LinkedIn. - Ting Accept invitation from Ting Zhou

Re: [gmx-users] Invalid angle type 0 error during minimization.

sreelakshmi ramesh wrote: Dear all, i am trying to simulate a double walled cnt in tip4p water using oplsaa force field. first i used *g_x2top -f carbon.pdb -o carbon.top* ( successfully created the topology) * editconf -f carbon.pdb -o carbon_newbox.gro -c

Re: [gmx-users] Atoms in the .top are not numbered consecutively from 1

sreelakshmi ramesh wrote: Dear all, when i run energy minimization i get the following error. the topology file was created from the starting pdb file using g_x2top *grompp -f em.mdp -c out.gro -p carbon.top -o o.tpr -maxwarn 3* In general, the use of -maxwarn is

[gmx-users] Calculation of unsaturated deuterium order parameters for POPC

I have patched g_order version 4.5.4 to compute the order parameters in a different way. Despite trying, I don't understand the original g_order implementation. In the version that I am providing, the hydrogens are explicitly built and the coordinates of these hydrogens are output to

Re: [gmx-users] Lennard Jones interactions

You can calculate that by hand on a calculator in a few seconds. There is no need to use Gromacs. On Jun 10, 2011, at 2:27 PM, Nilesh Dhumal wrote: Hello, How can I calculate Lennard Jones interaction for two selected atoms with a specific distance? I am using Gromacs 4.0.7 version.

Re: [gmx-users] Lennard Jones interactions

If eplilon of hydrogen atom is zero then the lennard jones interaction of OH bond (at 0.22nm)is also zero. Is it correct? I used equation 4.5 to calculate LJ energy. Nilesh On Fri, June 10, 2011 2:47 pm, Justin A. Lemkul wrote: Nilesh Dhumal wrote: Hello, How can I calculate Lennard

Re: [gmx-users] Lennard Jones interactions

The LJ interaction is 0. But you're asking about a bond. 1-2 interactions are typically modeled with a harmonic potential. This is most definitely not zero. On Jun 10, 2011, at 2:54 PM, Nilesh Dhumal wrote: If eplilon of hydrogen atom is zero then the lennard jones interaction of OH

Re: [gmx-users] Lennard Jones interactions

Basically I want to calculate LJ interaction for OH bond. If I use eq. 4.5 in manual to calculate LJ interaction then zero. How can I calculate LJ interaction of a bond? Nilesh On Fri, June 10, 2011 3:00 pm, Andrew Paluch wrote: The LJ interaction is 0. But you're asking about a bond. 1-2

Re: [gmx-users] Lennard Jones interactions

Nilesh Dhumal wrote: Basically I want to calculate LJ interaction for OH bond. If I use eq. 4.5 in manual to calculate LJ interaction then zero. How can I calculate LJ interaction of a bond? This type of measurement doesn't make any sense. Bonded interactions up to 3 bonds away are

[gmx-users] http gromacs.org down?

I get this error when trying to http://www.gromacs.org/* Site settings could not be loaded We were unable to locate the API to request site settings. Please see below for debugging information. If this is a new install, try refreshing - the API is simply taking its time loading up! HTTP

[gmx-users] Largest charge group radii for Van der Waals; Largest charge group radii for Coulomb

Dear Gromacs Users, My file has no problem when i grompp with verison of 4.0.7 When i swith to Gromacs 4.5.3 and grompp my file, it gives this reports: NOTE 3 [file grompp.mdp]: You are using a plain Coulomb cut-off, which

[gmx-users] reg SA cum SMD

Dear justin., Thank you tfor your reply   Can i combine Simulated annealing protocol with SMD . if possible what Time factor should i  consider to avoid Clashes in Md simulation i am asking whether any relation between time of pulling and time of annealing should i have