Re: [AMBER] constant pH equilibration confusion

From: Sangita Kachhap <>
Date: Sun, 20 Jun 2010 01:39:27 +0530 (IST)

> Hello,
> The restraints for the constant pH simulations should not be any different
> than restraints for any other simulations. What I normally do is just
> restrain the backbone atoms (CA, N, C, and O). Since you should be using
> SHAKE anyway, there's really no point in restraining hydrogen atoms I
> wouldn't think. I've noticed that heating and equilibration has to be done

is heating and equlibration is required for implicit simulation ?

Because in tutorial for simulation of DNA in implicit condition there is only
relaxing the
molecule then molecular dynamics run at tempi = 300.0, temp0 = 300.0

so should I directly run molecular dynamics at constant pH after minimization?

> more carefully with constant pH simulations as opposed to other types of
> simulations, so you should keep relatively strong restraints for heating (if
> you're using ntr, use restraint_wt=5 or something to that effect). You can
> then reduce these to ~1 for your equilibration (which is run AFTER heating,
> it's not a part of heating).
> If one of your steps generates a cprestrt file, you should use that as the
> cpin file for the next simulation. The only real differences between the
> cprestrt and cpin will be the resstate array. All other variables will be
> the same, although the formatting will look drastically different.
> The cprestrt file will hold the protonation states (resstate) for each of
> your titratable residues that correspond to the conformation defined in your
> restrt file.
> Hope this helps,
> Jason
> On Sat, Jun 19, 2010 at 3:55 AM, Sangita Kachhap <>wrote:
>> Hello all
>> I am doing constant pH simulation using amber10.
>> I have minimized it using restriant on all hydrogen and generated restrt
>> file.
>> Now I have to euqilibrat it with heating 0 - 300K.
>> Should I use restraint at this time if yes then what I should consider for
>> it ?
>> Should I make restrt and cprestrt file during equilibration?
>> As cprestrt contains protonation state definitions, final protonation states
>> for restart (same format as cpin).
>> Anybody please suggest me.
>> With regard
>> Sangita Kachhap
>> JRF
>> _____________________________________

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Received on Sat Jun 19 2010 - 13:30:04 PDT
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