[AMBER] Umbrella Sampling Collective Variable

From: Volkan Findik <volkan.findik.univ-lorraine.fr>
Date: Thu, 27 Jan 2022 08:25:09 +0100 (CET)

Dear Amber users,

I am trying to do QMMM MD Simulation, I have a zwitterionic molecule and my purpose is pulling it from the gas to water phase. I want to constraint the distance between the center of mass of all water and COM of my molecule only for one direction. For this purpose, I used this [ https://github.com/callumjd/AMBER-Umbrella_COM_restraint_tutorial | https://github.com/callumjd/AMBER-Umbrella_COM_restraint_tutorial ] tutorial. However, in " &rst iat=-1,-1, r1=-99.0, r2=0.0, r3=0.0, r4=99.0, rk2=2.5, rk3=2.5, iresid=0, fxyz=0,0,1, outxyz=1, igr1=1,2,3,4,5,6, igr2=7,8,9, " option I cannot choose COM of more than 200 atoms. That's why I used the NFE option [ http://ambermd.org/tutorials/advanced/tutorial31/custom_cv/index.html | http://ambermd.org/tutorials/advanced/tutorial31/custom_cv/index.html ] , in this case, I cannot apply the force constant only for the Z direction. Do you have any solution for my case?

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Received on Wed Jan 26 2022 - 23:30:02 PST
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