[gmx-users] energy corresponding to H-bond

Dear All, Can anybody please tell me that if I would want to find out the change in related to Hydrogen bond formation between two simulations, which of the energy terms ( when calculated through g_energy) should be used? The potential energy term does not include contribution from hydrogen bonding

[gmx-users] about g_sas analysis

Dear gromacs users, I have some doubts regarding the options to be selected in g_sas program. g_sas asks for two groups, first one for calculation and second one for output. As I have understood from the manual that first group should contain all non solvent groups and second one the whole or part

[gmx-users] Required help in topology making

Dear All I have a protein where one residue ( Lysine ) is making a covalent bond with the cofactor Pyridoxal phosphate. I have created other parameters of heteroatom PLP through PRODRG and manual checking. But I am not sure how to include the parameters for the "imine" bond ( C=N bond

[gmx-users] Reminder: Please Respond to supti's Invitation

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[gmx-users] mdrun error

Dear all, I am doing a protein simulation for 20ns in single processor machine. after 11.1ns when I am trying to rerun mdrun its coming out with the following error. -- Inner product between old and new vector <= 0.0! constraint #0 atoms 1 and 2 Warning: 1-4 inte

[gmx-users] grompp error

Dear all I am facing a problem in gromacs-4.0 during grompp. 1. After Genbox command , when I am giving Grompp command,the coordinates of top file and gro file are not matching. 2. I have tried following the same protocol in gromacs-3.3.3D. It went on fine without any error. 3. Both the top file

[gmx-users] Re: gmx-users Digest, Vol 54, Issue 138

Dear all What is the command to run grompp in multiple processors in Gromacs version 4.0? It seems -np option does not work in Gromacs-4.0. Can anybody please help me out? Thanks in advance Supti mukhopadhyay Phd student NIMHANS Bangalore 2008/10/30 <[EMAIL PROTECTED]> > Send gmx-users mailing l

[gmx-users] Energy Minimisation problem

Dear all, I was minimising a protein structure. I added polar hydrogens to the protein by some program and then proceeded for the energy minimisation. I chose Conjugate Gradient of 1000 steps with emtol as 100. The mdrun came out with the following error. " During neighborsearching, we assign each