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AMBER Archive (2007)Subject: Re: AMBER: How to extract energy of molecule from the system with explicit water molecules
From: priya priya (priyaanand_27_at_yahoo.co.in)
Dear Sir,
I am running my simulations in explicit solvent, if i want the energy of peptide , i can strip water molecules for it. But that will not include the interactions of the water molecules with it. so after excluding the water molecules from the trajectory and in calculating the energy can i add the implicit solvent by using igb=1.
Carlos Simmerling <carlos.simmerling_at_gmail.com> wrote:
On 7/5/07, priya priya <priyaanand_27_at_yahoo.co.in> wrote: I am not able to understand what exactly you are saying.
trajin mdcrd
for the energy analysis, there is an example in test/trajene that you can follow.
then how can i write a new mdcrd file from this and how to use sander command.
Carlos Simmerling < carlos.simmerling_at_gmail.com> wrote: the easiest way is to do what I suggested, make a new prmtop in
On 7/5/07, priya priya < priyaanand_27_at_yahoo.co.in> wrote:Hi,
Carlos Simmerling < carlos.simmerling_at_gmail.com> wrote: do you mean just the internal energy, or also the interaction with
On 7/5/07, priya priya < priyaanand_27_at_yahoo.co.in> wrote: Dear All
I am interested in extracting the energy of the molecule i.e peptide only from the output file that i obtained from running MD of that peptode in explicit solvent (water).
Please suggest me something!
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