Yes - when you minimize in section the velocities are lost. The heating
back to 300K is effectively in the stage termed equilibration. Note the
initial temp tempi=0.0 and the target temperature temp0=300.0. Note the
simulation here is Alanine dipeptide which is very small so one can be
quite aggressive when it comes to section 2 and heating things up again.
Plus the density etc was already equilibrated in the previous step so it
is not critical to split out heating and equilibration as one would
normally. However, for a larger system, or to just be more conservative it
would probably be a good idea to heat things up again slowly for each of
the different angles.
Hope that helps.
All the best
Ross
On 9/23/13 8:49 PM, "Sourav Purohit" <sour000.gmail.com> wrote:
>So do you mean that in the tutorial, when minimization is done with
>dihedral restrained at 120 deg, the velocity information is lost? If so,
>should we not heat the syatem again ?
>
>
>On Tue, Sep 24, 2013 at 9:06 AM, Ross Walker <ross.rosswalker.co.uk>
>wrote:
>
>> Minimization is simply optimization of coordinates on the potential
>>energy
>> surface such that the overall potential energy is reduced. There is no
>> integration step and thus no concept of temperature.
>>
>>
>> On 9/23/13 8:03 PM, "Sourav Purohit" <sour000.gmail.com> wrote:
>>
>> >Hi all,
>> >
>> > In AMBER ADVANCED TUTORIAL 17 on finding PMF using Umbrella
>>Sampling,
>> >The system has been first minimized, then heated to 300K and then
>> >equilibriated. Then, after setting the restraint on the dihedral to a
>> >value
>> >of 120 deg, the system has been minimized and then equilibriated. I
>>had a
>> >doubt on what keeps the temperature maintained at 300K during the
>> >minimization step.
>> >Thanks.
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>>
>>
>>
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Received on Mon Sep 23 2013 - 21:30:03 PDT
