[gmx-users] Varying results due to parallel processing (1 node versus 2 nodes)

Dear Gromacs users I am trying to simulate peptide in 30% TFE/water complex. Using parallel processing, I ran this system for 100ns using 2 nodes. The peptide is known to obtain helical conformation in this system. After 100ns, the peptide was found to be 37% helical. I ran the same system again o

[gmx-users] Varying results due to parallel processing (1 node versus 2 nodes)

Dear Gromacs users I am trying to simulate peptide in 30% TFE/water complex. Using parallel processing, I ran this system for 100ns using 2 nodes. The peptide is known to obtain helical conformation in this system. After 100ns, the peptide was found to be 37% helical. I ran the same system again o

Re: [gmx-users] Varying results due to parallel processing (1 node versus 2 nodes)

Hi, This is normal. mdrun trajectories are not reproducible by default, and reproducing any single trajectory is not generally useful. For example, you will see similar variation if you run each of those again with different starting velocities. Any single trajectory is questionable, and you now h

Re: [gmx-users] Unknown bond_atomtype CAY

On 9/18/16 10:14 PM, Sameer Edirisinghe wrote: Dear Dr. Justin, If the bond types have not added, following errors occuring with grompp, 1) ERROR 1 [file topol.top, line 108]: No default Bond types 2) ERROR 2 [file topol.top, line 168]: No default Angle types 3) ERROR 3 [file topol.top,

Re: [gmx-users] Do I need position restraint for umbrella sampling?

On 9/18/16 11:35 PM, Yoo Chan Myung wrote: Dear gmx users, I'm trying to simulate membrane penetration with peptide(octamer) using GROMACS-5.1.2. and I referred the Umbrella Sampling tutorial by Dr. Justin Lemkul. After 100 ps umbrella_NPT run, peptides confirmations are still kept in their i

Re: [gmx-users] parameters of GppNHp

Hi everyone, I am also working on simulation a protein-protein complex which has the ligand GppNHp molecule and an analogue of GTP. I tried to build the topology using GAFF and antechamber. but it was not working. Please provide the details for obtaining the same Dading Huang- if you are able t

Re: [gmx-users] Do I need position restraint for umbrella sampling?

Dear Justin, Thank you for your advice. I tried to restraint the wandering peptides, because umbrella MD results showed 'missing z=0.? ‘ errors when I run WHAM analysis. If I narrow the sampling space from 0.2nm to 0.1nm for umbrella MD simulation, could it be a better way to solve the ‘missin

Re: [gmx-users] How to make a program run on the trajectory

Dear João and Dan Thank you for the response and I am sorry for the confusion. I will try explaining my query with one example: In GROMACS, there are many programs available for the analyses of the trajectory. One of them is "do_dssp". For this purpose, one need to have dssp installed locally.

[gmx-users] How to calculate the diffusion coefficient.

Dear all, I want to calculate the diffusion coefficient of a single coarse-grained polymer adsorbed on a wall with Gromacs 5.0.7, where the wall's type is 9-3 and the density is set as 1. Firstly, I use the "gmx msd" command to calculate the diffusion coefficient. The calculation error i

[gmx-users] RMSD of interested region?

Dear gromcas users, I have done simulations for 100ns for protein of my interest. The protein length is 197 residues and I fixed the positions one n-terminal residue and from 28th residue to 197 residues also fixed. My interest of area in protein is from 2 to 27 residues. Although I have done simu

Re: [gmx-users] RMSD of interested region?

Create two index groups. One with 28-197 residues and second group with 2-27. Supply this index file to gmx rms (if using 5.1) with -n option and select 28-197 as fit group and 2-27 for RMSD analysis. Regards, Sarath On 20 September 2016 at 12:05, Seera Suryanarayana wrote: > Dear gromcas use