Hi, I am running essential dynamics for a protein in water system (charmm-nocmap and tip3p). I use the first 25 eigenvectors and targeted ED. It stops after 630ps when settle and lincs start giving warnings.
Step 315573, time 631.146 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.000121, max 0.003164 (between atoms 144 and 145) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 148 151 36.2 0.1112 0.1111 0.1111 144 145 45.7 0.1109 0.1107 0.1111 I am also running the same simulation with the first 12 eigenvectors and face no such problems. I understand that targeted ED may lead to some unphysical trajectory which may be the cause of this error. However, is there a way to override this and in that case an alternative check which may be used instead of lincs rotation constraint to make sure that the contacts arent unphysical? Pooja -- Quaerendo Invenietis-Seek and you shall discover.
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