[gmx-users] How to modify the code g_hbond to analyze the non-traditional hydrogen bonds like C-H...O

2013-06-30 Thread Wu Chaofu
Dear gmxers, I want to analyze the non-traditional hydrogen bonds like C-H...O. To my best knowledge, the g_hbond code can be used for traditional hydrogen bonds but not for our case. One possible solution is to modify the g_hbond code to include the non-traditional hydrogen bonds. However, the

Re: [gmx-users] How to modify the code g_hbond to analyze the non-traditional hydrogen bonds like C-H...O

2013-06-30 Thread David van der Spoel
On 2013-06-30 11:34, Wu Chaofu wrote: Dear gmxers, I want to analyze the non-traditional hydrogen bonds like C-H...O. To my best knowledge, the g_hbond code can be used for traditional hydrogen bonds but not for our case. One possible solution is to modify the g_hbond code to include the

[gmx-users] Re: Pulling

2013-06-30 Thread Thomas Schlesier
If you use periodic boundary conditions, there is no need that the protein stays at one side of the box. For the pulling simulation: Read the chapters 6.4 (explains the pull-code) and 7.3.21 (explains the mdp-paramters). Additional information you an also get from Justin Tutorial for Umbrella

[gmx-users] unit conversion

2013-06-30 Thread Hyunjin Kim
Hi, When I convert FF parameters from OPLS (in Gromacs) to Charmm, I divide bond and angle force constants, i.e., Kb and Ktheta, by 836.8 and 8.368. However, parameters for tip3p water do not convert properly in this ways. For example, Kb = 502416.0 kJ/mol/nm^2 for OW-HW in Gromacs and 450.0

Re: [gmx-users] unit conversion

2013-06-30 Thread Justin Lemkul
On 6/30/13 12:11 PM, Hyunjin Kim wrote: Hi, When I convert FF parameters from OPLS (in Gromacs) to Charmm, I divide bond and angle force constants, i.e., Kb and Ktheta, by 836.8 and 8.368. However, parameters for tip3p water do not convert properly in this ways. For example, Kb = 502416.0

Re: [gmx-users] Covariance file format

2013-06-30 Thread Tsjerk Wassenaar
Hi Ankita, The fie contains the eigenvectors as x1 y1 z1 x2 y2 z2 ... xN yN zN Hope it helps, Tsjerk On Mon, Jul 1, 2013 at 1:38 AM, Ankita naithani ankitanaith...@gmail.comwrote: Hi, I wanted to know the exact format of covariance.dat file as generated by g_covar during covariance