[gmx-users] deltaG is positive after FEP

Dear all, I did a transformation of aa H->A using hybrid topology and performed FEP calculations. At the end im getting the positive value of DG (47.99 +/- 0.56). 1. it depicts that the mutation of H->A is not favourable to the protein? I have provided a link to the Free energy differences

[gmx-users] Symmetry corrections in FEP

Dear gmx-users, I'm analysing set of FEP simulations where a water molecule is decoupled from a protein. I’m using the orientational restraints as suggested by Boresch et al (doi 10.1021/jp0217839). In my simulations, the water molecule interconverts between two equivalent orientations at the

Re: [gmx-users] Bug?! Lost particles while sorting

Hi Mark, Thanks for your reply. I tried but I was not sure how to do so. May I send the corresponding files to your personal email, instead? Cheers, Mohsen On Wed, Aug 30, 2017 at 6:25 PM, Mark Abraham wrote: > Hi, > > That particular output indicates that the code

Re: [gmx-users] Fwd: Segmentation fault (core dumped) in g_mmpbsa

Hi, I tried to compile g_mmpbsa with APBS but no success. I am facing the following error while cmake: -- Found z library: /usr/lib/x86_64-linux-gnu/libz.so CMake Error at cmake/FindGROMACS.cmake:203 (list): list index: 2 out of range (-2, 1) Call Stack (most recent call first):

Re: [gmx-users] Gromacs simulation of two or more peptide chain

Generally that means you starting system is seriously wrong. Investigate atom 218 and surrounding area. Another atom really close or sth like that. On Thursday, August 24, 2017, 9:36:37 PM GMT+3, Kalyanashis Jana wrote: Dear all, I would like to run an MD simulation

[gmx-users] Fwd: Potential gradient in NVE simulation

Dear Users, Whenever I try to run an NVE simulation in GROMACS, I end up with a gradient in the potential ​, which is undesirable in NVE conditions. Following is my mdp script: integrator = md nsteps = 100 dt = 0.001 nstxout= 100 nstvout= 100 nstenergy = 100 nstlog

Re: [gmx-users] Difference in hydrogen bond lifetimes with and without pbc

Dear Apramita, What version are you using? There might have been some PBC-related bugs that were fixed if memory serves me right. Kind regards Erik __ Erik Marklund, PhD, Marie Skłodowska Curie INCA Fellow Department of Chemistry – BMC, Uppsala

[gmx-users] RMSD

Dear All, If I want to show difference in RMSD of peptide conformations in different solution compositions, what should I choose as reference structure so that more representative figure is formed? The .tpr file that I should choose for reference structure should be the file after equilibration

[gmx-users] gmx mindist

Hi, Which distance does the gmx mindist command compute? Is it the minimum distance between the center of mass of the first group due to the other group? Thanks,Mohammad -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List