AMBER Archive (2003)

Subject: AMBER: re: MD problem!!

From: Pradipta Bandyopadhyay (pradipta_at_cgl.ucsf.edu)
Date: Thu Sep 18 2003 - 12:36:59 CDT

 Dear Dr. Darden,

 Thanks for your mail. I am working on it.

 Meanwhile I tried to do a simulation with ONLY the WATBOX216.
 I am getting the error message

   parameter skinnb+cutoffnb has value 0.10+02
   the legal range is 0 to 0.98667E+01

 Which is the similar message I got when I tried to use 32 water
 molecules.

 I don't want to play with ewald parameters without knowing. Could you
 please tell me how to change those?

 Also, a general question- how to generate box of waters (and only
 waters) of different numbers (32,256,512,1024 so on) in AMBER? I was
 using one water molecule as solute and then WATBOX216 but the structures
 are taking very long time to equilibrate. Is there a better way?

 thanks.

          Pradipta

 ----- Original Message -----
 From: darden <darden_at_gamera.niehs.nih.gov>
 Date: Wednesday, September 17, 2003 8:29 am
 Subject: Re: AMBER: MD problem!

> Dear Pradipta
> Its hard to tell without more info. However as a general policy,
> its best
> to first minimize to relieve bumps (with a new box you can have
> collisions
> across the box boundary), then run constant temperature to get up
> to 300K,
> then run (using a restart from the constant temp run) constant
> pressure to
> get up to correct density. You could for example run ~100 steps
> conjugate gradient minimization (keep shake on if you like although
> this
> will prevent minimization to a tight minimum--its ok you just want
> to
> relieve bumps). Next run NVT for ~10-20ps with default temperature
> control, this will get you to room temperature and listtot will not
> change
> much. Finally turn on NPT and run for ~10-20ps to get density
> right.

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