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CHARMM Development Project Forums User Discussion & Questions Energy terms, Constraints, Restraints, and Solvation GB methods compatible with BLOCK module

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GB methods compatible with BLOCK module #22173 09/22/09 06:44 PM
Joined: Oct 2008 Posts: 55 Baltimore, MD 21218, USA Zhiguo OP Forum Member
OP Zhiguo Forum Member Joined: Oct 2008 Posts: 55 Baltimore, MD 21218, USA	Hi, I'd like to estimate the solvation free energy of a few DNA double strands (10~20 base pairs long) fastly. The GBMV module looks like the best choice for this task. Unfortunately, it doesn't work with BLOCK. Any other option to do the same job? Thanks! Last edited by Zhiguo; 09/22/09 06:45 PM. --------------------------- CHARMM c32b1 driven by RHEL 2.6.9-22.0.2 on PPC64

Re: GB methods compatible with BLOCK module Zhiguo #22175 09/22/09 06:52 PM
Joined: Sep 2003 Posts: 8,658 Likes: 26 39 59 56 N, 77 06 07 W rmv Forum Member
rmv Forum Member Joined: Sep 2003 Posts: 8,658 Likes: 26 39 59 56 N, 77 06 07 W	The P-B code in CHARMM (pbeq.doc) has been used for that. Rick Venable computational chemist

Re: GB methods compatible with BLOCK module rmv #22177 09/22/09 07:12 PM
Joined: Oct 2008 Posts: 55 Baltimore, MD 21218, USA Zhiguo OP Forum Member
OP Zhiguo Forum Member Joined: Oct 2008 Posts: 55 Baltimore, MD 21218, USA	Originally Posted By: rmv The P-B code in CHARMM (pbeq.doc) has been used for that. Thanks! Is it compatible with BLOCK module? --------------------------- CHARMM c32b1 driven by RHEL 2.6.9-22.0.2 on PPC64

Re: GB methods compatible with BLOCK module Zhiguo #22179 09/22/09 07:50 PM
Joined: Sep 2003 Posts: 8,658 Likes: 26 39 59 56 N, 77 06 07 W rmv Forum Member
rmv Forum Member Joined: Sep 2003 Posts: 8,658 Likes: 26 39 59 56 N, 77 06 07 W	I believe the solvation free energy can be estimated directly from P-B calculations at eps=1 and eps=80, without the need for BLOCK. Rick Venable computational chemist

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