Re: [gmx-users] Using thermostats to create temperature gradient in system

Hi Agnivo, Temperature gradient means non-equilibrium MD (NEMD) See notes from Prof. Martini: https://nanohub.org/resources/7582/download/Martini_L10_NonequilibruimMD.pdf What observable would you like to measure? Lets say you want to measure observable A. One procedure I can think of: 1.

Re: [gmx-users] Using thermostats to create temperature gradient in system

Hi Agnivo; Yes, the idea of freezing the solvent or the protein in many times is to sample the non-equilibrium thermal process. It will remain in the target temperature on average, over many fixed configurations obtained by different NVT runs (equilibrium runs). But you may need to run this many

Re: [gmx-users] Using thermostats to create temperature gradient in system

Hello Users, This is in relation to my previous posts. I am looking to replicate the figure below : ​ tempgradient.png https://docs.google.com/file/d/0B-U8uULVZjfRQWlHeHVJdDJjcms/edit?usp=drive_web ​ Basically I am following this paper for my work : ​ Lervik_ProtWatInterHT_2009.pdf

Re: [gmx-users] Using thermostats to create temperature gradient in system

Hello all, Thanks to Dr. Lemkul for asking. This is what I did to reach my present state : (a) Prepared the topology of the system using GROMOS96 43a2 ff and energy minimized the system after solvation using steepest descent algorithm. (b) Did a position restrained ( protein ) 5 ns Fatal

Re: [gmx-users] Using thermostats to create temperature gradient in system

Hello all, Thanks to Dr. Lemkul for asking. This is what I did to reach my present state : (a) Prepared the topology of the system using GROMOS96 43a2 ff and energy minimized the system after solvation using steepest descent algorithm. (b) Did a position restrained ( protein restrained ) 5 ns

Re: [gmx-users] Using thermostats to create temperature gradient in system

On 4/26/15 7:07 PM, Agnivo Gosai wrote: Hello Users, This is in relation to my previous posts. I am looking to replicate the figure below : ​ tempgradient.png https://docs.google.com/file/d/0B-U8uULVZjfRQWlHeHVJdDJjcms/edit?usp=drive_web ​ Basically I am following this paper for my work :

Re: [gmx-users] Using thermostats to create temperature gradient in system

On 4/26/15 8:14 PM, Agnivo Gosai wrote: Hello all, Thanks to Dr. Lemkul for asking. This is what I did to reach my present state : (a) Prepared the topology of the system using GROMOS96 43a2 ff and energy minimized the system after solvation using steepest descent algorithm. (b) Did a

Re: [gmx-users] Using thermostats to create temperature gradient in system

Hello, I am copy pasting my mdp file for the last step of my procedure : Here I am not using any freeze group. ; Run parameters integrator = md; leap-frog integrator nsteps = 5; 100 ps dt = 0.002 ; 2 fs energygrps = Protein

Re: [gmx-users] Using thermostats to create temperature gradient in system

Dr. Lemkul Thanks for such an easy fix to my problem. I guess I have been doing all sort of weird stuff since last night instead of thinking logically and reading the relevant portion of the manual. Thanks Regards Agnivo Gosai Grad Student, Iowa State University. -- Gromacs Users mailing list

Re: [gmx-users] Using thermostats to create temperature gradient in system

Hello users, Thanks a lot Suzen for an insightful suggestion. My protein and solvent have been equilibrated at 300 K in an NVT ensemble. I raised the temperature of protein gradually by using simulated annealing to 400 K and the solvent has been kept at 300 K. Now I wish to get a temperature

[gmx-users] Using thermostats to create temperature gradient in system

Hello Users I have equilibrated a protein solvent system using NVT ensemble and V - rescale thermostat. Target temperature was 300 K. Now I want to establish a temperature gradient in my system as follows : 1. Use Two Berendsen thermostats separately for Protein and Non Protein grps. Protein