Re: [AMBER] pmemd.cuda with CoM restraints

From: Charles Lin <>
Date: Thu, 3 Dec 2015 17:22:33 +0000

Try changing it from iat(3) in your call to just iat=-1,-1,r1=...

I don't believe iat(3) is part of the namelist.

From: Dhananjay (達南杰) []
Sent: Thursday, December 03, 2015 6:56 AM
Subject: [AMBER] pmemd.cuda with CoM restraints

Dear users,

 I successfully run the MD with restraints applied on two atoms (in cpu) using disangle specifier as follows:

#Disrance restraint
  iat=1220,18, r1=0.0, r2=50.0, r3=50.0, r4=55.0, rk2=10.0, rk3=10.0,

Now, I wish to extend this to protein and a peptide system and want to keep them at certain distance by applying distance restraints on centre of mass/geometry of two groups of atoms. Therefore, I used igr1 and igr2 as follows:

#Disrance restraint
  iat(3)=-1,-1, r1=0.0, r2=15.0, r3=15.0, r4=20.0, rk2=10.0, rk3=10.0,

I used pmemd.cuda(GPU) and got following error:

CUDA (GPU): Implementation does not currently support the use of COM simulations for angle or dihedral restraints.
            Require iat(3) >= 0.

I do not want to apply angle or dihedral restraints but distance only.
What is wrong here ?
Any help in this regard will be appreciated !!
Thanks in advance,

-- Joshi

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Received on Thu Dec 03 2015 - 09:30:02 PST
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