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
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
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
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,
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
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
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
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.
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
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
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
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