AMBER Archive (2007)

Subject: AMBER: how much restraint ?

From: AYTUG TUNCEL (ATUNCEL_at_ku.edu.tr)
Date: Mon Jan 22 2007 - 16:09:12 CST

Dear all,

I am trying to heat up my system (two protein chains + explicit water + counter ions + PBC) from 0K to 300K, after minimization, by an NVT simulation. The time period for this protocol is 300 ps with an 10K increment at every 10 ps. I know that, we can use restraint_wt (kcal/(mol A^2)) option to restrain the atoms during heating. About this I have two questions,

1) Should we restrain all the backbone atoms or just the CA atoms are enough?

2)What should be the amount of this "restraint_wt", is there a consensus value? I looked some of the papers and found that some use 2 or 5. I mean, in order to compansate the repositioning of an atom as a result of a 10K increment in temperature what should I use?

Thanks in advance.

Aytug

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