[gmx-users] Relative constraint deviation after LINCS:

Hi all, I am running a simulation of peptide and during the course of the simulation after some steps, the simulation gets canceled stating the following message: Step 1848418, time 3696.84 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.08, max 0.000547 (between atoms

Re: [gmx-users] gmx gangle : How to calculate the angle between a vector and Z axis?

*Now use gmx gangle command without “-seltype res_com -selrpos -res_com” command. Obviously now your index.ndx file have indexes of [1] and [2] generated from mapped trajectory.Sent using Zoho Mail On Wed, 03 Jul 2019 13:59:39 +0530 Vikas Dubey wrote

Re: [gmx-users] gmx gangle : How to calculate the angle between a vector and Z axis?

Hi Vikas,One way is transform your atomic trajectory to center of mass position trajectory. You can do it by first removing periodic breakages by running gmx trjconv -s gromos.tpr -f gromos.xtc -pbc whole -o whole.xtc Then run below command to get transform the

Re: [gmx-users] How to generate topology file of cyclodextrin for gromacs?

Hi,First decide on which force field you want to use. There are scripts and online servers for generating the topology.For example   https://atb.uq.edu.au/ For generating gromos54a7 forcefield.http://zarbi.chem.yale.edu/ligpargen/For OPLS/CM1A parameter

[gmx-users] How to generate topology file of cyclodextrin for gromacs?

I could downloaded pdb file of alpha cyclodextrin with coordination. But I have no idea how to generate topology file for that. Although I found a similar question and answers in the archive, I only could pdb file of only one a-D-glycan.