[gmx-users] Pdb files generated on Lincs warning

[Justin Lemkul]

On 11/27/17 1:04 AM, atb files wrote:
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>              Dear Users,When there is a Lincs warning (sometimes because of exceeding warnangle etc) the gromacs generates pdb files. My questions is:What is purpose of generating pdb files? What information they give? Which information we need to look for to analyse those pdbs. ThanksYogi Sent using Zoho Mail
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These are the coordinates before and after applying constraints for each 
domain of the system. They are not PBC-corrected so they can be really 
hard to interpret. mdrun prints which atoms are having issues, which is 
usually sufficient to begin diagnosing what is going on.

-Justin

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Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

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jalemkul at vt.edu | (540) 231-3129
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