Hi,
Best practice is to read and learn others practice from publications that
are similar to what you want to do, rather than making ad-hoc changes. In
this case, the GROMACS defaults are pretty close to the de facto standard,
and supported by analysis work done by other members of the community.
Dear Justin,
Thanks a lot for pointing out the issues. I now understand why there were
such high oscillations.
Could you please also tell me if there are any ideal values for pme_order
and fourier spacing with respect to the cut offs' value of 1.4.
Does the following Note imply I can raise the
On 6/30/16 9:16 AM, NISHA Prakash wrote:
Dear Justin,
Thank you for your reply.
It is a protein carbohydrate system. Including the solvent, the number of
atoms is 43499.
I have minimized the system for 200 ps followed by NPT and NVT simulations
for 200 ps respectively
Given that your
Dear Justin,
Thank you for your reply.
It is a protein carbohydrate system. Including the solvent, the number of
atoms is 43499.
I have minimized the system for 200 ps followed by NPT and NVT simulations
for 200 ps respectively
Below is the .mdp file.
; VARIOUS PREPROCESSING OPTIONS
title
On 6/30/16 8:46 AM, NISHA Prakash wrote:
Dear all,
I have conducted a 10ns REMD simulation for a protein ligand complex with
the temperature range - 270 to 350 K, however the temperature distribution
plot of the replicas show that the sampling has occurred at higher
temperatures as well that
Dear all,
I have conducted a 10ns REMD simulation for a protein ligand complex with
the temperature range - 270 to 350 K, however the temperature distribution
plot of the replicas show that the sampling has occurred at higher
temperatures as well that is beyond 350K -
Below is an excerpt from the
