RE: AMBER: restart a MD after replacing molecules

From: Ross Walker <>
Date: Wed, 25 Aug 2004 10:29:13 -0700

Dear Fabien,

> I think I can just take the last line of the last restart file of my
> previous MD and put it at the end
> of the crd file but I am not sure this is correct to do this.
> Is this the correct way to do what I want ? Or is there any
> better way
> to do it ?

Since you are not doing a restrt (no velocity info in the crd file) you have
two options. One option would be to do as you say and cut and paste the box
info - be very careful with the format. The other option, and something you
might want to do anyway to remove any VDW clashes with your 3 added waters
is to run a 100 steps of minimisation or so. If you just want to save
yourself time equilibrating the water box then this will probably be fine.
You will then get a rstrt file that has box info without having changed your
structure too much. Simply removed the largest strains...

I hope this helps

|\oss Walker

| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
| Tel:- +1 858 784 8889 | EMail:- |
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Received on Thu Sep 02 2004 - 01:15:11 PDT
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