[gmx-users] Energy minimisation goes to several values

[Kevin C Chan]

Thanks Justin for the reply. 

Honestly I thought minimizing a large and complex (usually biomolecular) system part by part instead of as a whole will effectively shorten the computational time cost while causing no effect on the final structure. When you say “impedes”, do you mean it causes a longer calculation time in total or it will give a bad final structure?

Thanks in advance,
Kevin

> On 26 Jun, 2015, at 22:21, <gromacs.org_gmx-users-request at maillist.sys.kth.se> <gromacs.org_gmx-users-request at maillist.sys.kth.se> wrote:
> 
> From: Justin Lemkul <jalemkul at vt.edu <mailto:jalemkul at vt.edu>>
> Subject: Re: [gmx-users] Energy minimisation goes to several values
> Date: 26 June, 2015 21:27:32 HKT
> To: <gmx-users at gromacs.org <mailto:gmx-users at gromacs.org>>
> Reply-To: <gmx-users at gromacs.org <mailto:gmx-users at gromacs.org>>
> 
> 
> 
> 
> On 6/25/15 9:45 PM, Kevin C Chan wrote:
>> Dear Users,
>> 
>> I am energy minimising a quite large solvated system containing protein and
>> lipids (~800,000 atoms). I used to fix components of the system in order to
>> speed-up energy minimisation and sometimes it is easier to debug such
>> processes. Here is my protocol:
>> 1. fix all except water and so to minimise water
>> 2. fix water and then minimise all the rest atoms
>> 3. fix nothin and then minimise the whole system
>> 
>> While monitoring the energy of the system thought minimisations, it goes
>> fine for step 1 and 2 and converged after just few hundred steps. However
>> it goes back to several higher values of energy (bouncing between the
>> values) and they started to increase very slowly for step 3. This makes no
>> sense to me and did anyone have a similar experience?
>> 
>> There are two unusual points:
>> 1. The system energy drops suddenly instead of decreased gradually during
>> step2 and then stays at a constant value.
>> 2. If I use the resulting structure from step3 to proceed a, say, heating
>> process, it simply blows up.
>> 
>> To be clear, my system was solvated and auto-ionized using VMD tools and
>> some water inside the membrane has been directly deleted. Backbone of the
>> protein and phosphorus atoms of the membrane are under a
>> position constraint during all the minimisations. I was choosing conjugate
>> gradient for minimization.
>> 
> 
> Does a "normal" minimization (just one overall minimization with nothing fixed) yield a stable starting point?  Fixing atoms (using freezegrps?) often actually impedes minimization.
> 
> -Justin
> 
> -- 
> ==================================================
> 
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
> 
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
> 
> jalemkul at outerbanks.umaryland.edu <mailto:jalemkul at outerbanks.umaryland.edu> | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul <http://mackerell.umaryland.edu/~jalemkul>
> 
> ==================================================