How to perform gromacs MD simulations of a protein to get the atomistic details of its unfolding at different temperatures?

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Pruthvi Raj Bejugam

Dear Dhaval, This kind of MD simulations are called as the Replica Exchange Molecular Dynamics (REMD). where if you prepare a system i.e. protein in solvent which is equilibrated with required constraints, then this REMD will make multiple copies of this systems and performs the parallel MD calculations at various required (user defined) conditions. you can find the more info in trhe GROMACS site but you can learn more about these REMD simulations from the link attached to this answer and this link has thesis entirely based on REMD theory and practice.

If you are familiar with GROMACS then it is very easy to perform the REMD, but if you are new to this then i suggest you to use the Desmond software provided by D.E.Shaw research and this software is GUI based and it is easy to use and it has special module for Replica exchange molecular dynamics

http://dukespace.lib.duke.edu/dspace/bitstream/handle/10161/923/D_Cooke_Benjamin_a_200812.pdf?sequence=1

Dhaval Patel

Thanks pruthvi for your advice i will go through the paper and try to run REMD for my problem. Can we just change ref_t = 300 (in .mdp file) to our desired value and run the system at desired temp???

hey pruthvi i dont know you remember me or not but we met at NCCS workshop in this march..hope you rememeber i came to your lab for the autodock session....

Hai Dhaval, sorry did not remember you. Nice to meet you in Research gate. yeah you can change that ref_t=300 or any thing and then you can run it. but if you wanted to check its thermal denaturation effects then you have to repeat the same by changing the ref_t value every time and then it will take quite a lot of time. where as if you use REMD comparatively it will be finished in faster time.

Any how its up to you to decide in which method you will go for to perform your simulations and all the best for your MD

Hi Pruthvi

If i want to run MD at 310K then changing ref_t=310 will take effect. But should i need to change in npt.mdp, nvt.mdp or only in md.mdp?? Only final MD needs to be change or equilibration ref_t should also be change?