[gmx-users] non-native contatcs
jalemkul at vt.edu
Wed Jan 15 15:10:09 CET 2014
On 1/15/14, 7:11 AM, bipin singh wrote:
> First define and calculate the native contacts (contacts which were present
> in native reference structure and exist for significant amount of time
> during simulation). Then you can identify the contacts which exist for
> significant amount of time but were not present in native reference
> structure (which may correspond to non-native contacts).
Can you actually do this within Gromacs, or outside software? I'd be curious to
> On Wed, Jan 15, 2014 at 1:05 PM, suhani nagpal <suhani.nagpal at gmail.com>wrote:
>> I'm studying protein unfolding by CTMD and REMD simulations to capture the
>> intermediate states.
>> I want to calculate the non-native contacts formed during the intermediate
>> Suggestions please
>> Proteomics and Structural biology Lab
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Justin A. Lemkul, Ph.D.
Department of Pharmaceutical Sciences
School of Pharmacy
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University of Maryland, Baltimore
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jalemkul at outerbanks.umaryland.edu | (410) 706-7441
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