Hi,<div><br></div><div>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. </div>
<div><br></div><div><span class="Apple-style-span" style="border-collapse: collapse; font-family: arial, sans-serif; font-size: 13px; ">Step 315573, time 631.146 (ps) LINCS WARNING<br>relative constraint deviation after LINCS:<br>
rms 0.000121, max 0.003164 (between atoms 144 and 145)<br>bonds that rotated more than 30 degrees:<br> atom 1 atom 2 angle previous, current, constraint length<br> 148 151 36.2 0.1112 0.1111 0.1111<br>
144 145 45.7 0.1109 0.1107 0.1111<br>
</span><br></div><div>I am also running the same simulation with the first 12 eigenvectors and face no such problems. </div><div><br></div><div>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?</div>
<div><br></div><div>Pooja</div><div><br>-- <br>Quaerendo Invenietis-Seek and you shall discover.<br>
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