Re: [AMBER] Number of water molecule to solvate 2.5KDa peptide in TIP3PBOX

From: V. Kumar <>
Date: Wed, 18 Nov 2015 15:39:49 +0100

Dear David,

thanks a lot for your suggestions.

For simulated annealing (200ps) I am using following steps for heating and
cooling (below). Then I have a script to loop it until 200ps simulation
until to 10ns.
I am using 600K has high temperature as reported for many cases in the
literature. I actually heat to high temperature
much faster followed by slow cooling. Could you please suggest me is this
flow chart is fine for simulated annealing in explicit solvent.

Is there any advantage to perform regular MD production (for complete 10ns)
over multiples of simulated annealing?
I have selected block of 200ps instead of whole 10ns. so that I can check

#Simple simulated annealing

#from steps 0 to 10000: heat the system to 600K
#from steps 5001-180000: re-cool to low temperatures with long tautp
#from steps 18001-200000: final cooling with short tautp

 &wt type='TEMP0', istep1=0,istep2=10000,value1=600.,
            value2=600., /
 &wt type='TEMP0', istep1=10001, istep2=180000, value1=600.0,
            value2=100.0, /
 &wt type='TEMP0', istep1=180001, istep2=200000, value1=0.0,
            value2=0.0, /

 &wt type='TAUTP', istep1=0,istep2=10000,value1=0.4,
            value2=0.4, /
 &wt type='TAUTP', istep1=10001,istep2=180000,value1=4.0,
            value2=4.0, /
 &wt type='TAUTP', istep1=180001,istep2=190000,value1=1.0,
            value2=1.0, /
 &wt type='TAUTP', istep1=190001,istep2=200000,value1=0.1,
            value2=0.05, /

 &wt type='REST',
            value2=1.0, /
 &wt type='REST',
            value2=1.0, /

thanks a lot

Best wishes

On 18 November 2015 at 15:22, David A Case <> wrote:

> On Wed, Nov 18, 2015, V. Kumar wrote:
> >
> > I am trying to perform simulated annealing in WATER.(TIP3PBOX) in the
> > presence of NMR restraints. When I solvated my peptide in a TIP3PBOX
> 10A°,
> > leap added 10000 water molecules.
> > Because of that my simulation is running slow.
> There's not an easy way around this. You already have a minimal (or even
> less
> than minimal) buffer (10 Ang.). Use solvateOct rather than solvateBox (if
> you
> have not already done this.)
> Generally, NMR refinement in explicit solvent is done at the final stages
> of
> refinement, so you can hope to already have a "pretty good" (tm) structure.
> Be careful about how high an annealing temperature you use with explicit
> solvent.
> It is possible that the poor performance you report is caused by a poor
> choice
> of input parameters: be sure to compare what you are doing to examples
> in the tutorials (doesn't have to be simulated annealing).
> ...dac
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Received on Wed Nov 18 2015 - 07:00:03 PST
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