Re: [gmx-users] charge changes in free energy calculations

Hi David, Thanks for clarification. Yes, you are right. I am morphing only parts of the sidechain. Qiang David Mobley wrote: Hi, As long as you end up with the same charge in the initial and final states, you should be OK. It's only if your total transformation involves a change of net

Re: [gmx-users] least squares fit

Hi Ram, Yes. Tsjerk PS. Do mind that the PBC are not preserved in that case. On Thu, Oct 2, 2008 at 7:54 PM, rams rams [EMAIL PROTECTED] wrote: Dear users, While doing the least squares fit, if I choose the protein as input group and system as output group, does it mean that the protein

[gmx-users] different g_hbond result for two run

hi all, I was trying to analyze some h_bond interaction for a protein with one ligand. I tried two runs for the same one for 5 nsec and another for 10 nsec. What I found here is that, the h-bonds present in the 5 nsec trajectory are more than that in 10 nsec trajectory, h-bonds in 10 nsec run

[gmx-users] Howto output from bondfree.c

Hi all, I am trying to modify the functional form of a bonding interaction in bondfree.c and how to output from this source file if I want to check the value of some variable? I tried printf or fprintf following fopen, neither works. Any suggestion is highly appreciated. Regards, Jian

[gmx-users] The Warning: you should increase table-extension in your mdp file

Hi I put a +1 charge molecule in gas phase and run MD without adding the Counter ions. And, I got the following warning: Although I checked the manual, I don't know how to increase the Table-extension. Thank you Lin Warning: 1-4 interaction between 12 and 19 at distance 1.469 which is larger

[gmx-users] tip3p water model

Hi gmx-users, I want to use tip3p water model when I mention this model with flag -cs by genbox command it showed that no program for tip3p.gro, from this link http://www.gromacs.org/pipermail/gmx-users/2007-February/025712.html I understood that mention -spc water model in genbox command but in

Re: [gmx-users] The Warning: you should increase table-extension in your mdp file

Chih-Ying Lin wrote: Hi I put a +1 charge molecule in gas phase and run MD without adding the Counter ions. And, I got the following warning: Although I checked the manual, I don't know how to increase the Table-extension. It is an option in the .mdp file, however it is not recommended to

Re: [gmx-users] tip3p water model

Justin A. Lemkul wrote: The angle of TIP3P should be 104.5, also. Where have you seen 109.4? Oops, read that backwards, sorry! Indeed, SPC has an angle of 109.4, but using tip3p.itp from the spc.gro file should fix the angles after a bit of EM and equilibration. -Justin Can clear

Re: [gmx-users] Heat Flux and Lambda

Andy Shelley wrote: David, I looked up the euqation for the Nose-Hoover thermostat and don't understand where lambda comes from and how to use the number of degreees of freedom to determine the heat flux of a group. Could you explain some more? Aha, this only works for Berendsen I would

[gmx-users] (no subject)

Hello all, I am using the pull code and was wondering if there was a way to permanently fix the position of only a single atom of a polypeptide throughout the simulation? Thank you. __ Venkatesh Hariharan Pennsylvania State University Schreyer Honors College