[gmx-users] (no subject)

[Nilesh Dhumal]

Thanks a lot.
I made some changes in topology file for rerun simulation.
Still I am getting same potential energy.
If topology files are different then why the potential energy is same?
Nilesh

On Tue, October 26, 2010 4:29 pm, Mark Abraham wrote:
>

>
> ----- Original Message -----
> From: Nilesh Dhumal <ndhumal at andrew.cmu.edu>
> Date: Wednesday, October 27, 2010 1:04
> Subject: Re: [gmx-users] (no subject)
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>
>
>> I used the same .tpr file. I added  -dlb yes and  -
>> reprod yes during mdrun with rerun option. Still I am not geting why
>> energy, temp, pressure are changing since I have same topology file and
>> .trr file.
>>
>
> As I said last time, a parallel rerun cannot reproduce a run unless
> they're both run under the same conditions. Changing the options for the
> rerun cannot achieve this, because the original run probably had dynamic
> load balancing.
>
> Mark
>
>
>> Is there any bug in rerun option?
>> Nilesh
>>
>>
>> On Mon, October 25, 2010 8:50 pm, Mark Abraham wrote:
>>
>>>
>>
>>>
>>> ----- Original Message -----
>>> From: Nilesh Dhumal <ndhumal at andrew.cmu.edu>
>>> Date: Tuesday, October 26, 2010 10:50
>>> Subject: Re: [gmx-users] (no subject)
>>> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>>>
>>>
>>>
>>>> I run a test simulation for -rerun. I didn't change the
>>>>
>> topology file.
>>>>
>>>>
>>>> grompp -f md.mdp  -c  solvent-bmi-pf6-128.pdb
>> - p
>>
>>>> solvent-bmi-pf6-128.top -o 3.tpr mpirun -machinefile cp -np 8 mdrun
>>>> -s 3.tpr -o 3.trr -c
>>>> solvent-bmi-pf6-128.pdb -e 3.edr -g 3.log
>>>>
>>>> with -rerun grompp -f md.mdp  -c  solvent-bmi-pf6-
>> 128.pdb  - p
>>
>>>> solvent-bmi-pf6-128.top -o 6.tpr mpirun -machinefile cp -np 8 mdrun
>>>> -s 6.tpr -o 6.trr -rerun
>>>>
>> 3.trr  -c
>>
>>>> solvent-bmi-pf6-128.pdb -e 6.edr -g 6.log
>>>>
>>>> I calculate the total energy by
>>>> g_energy -f 3.edr -o 3.xvg g_energy -f 6.edr -o 6.xvg
>>>>
>>>> The total energy varies between +- 30.00 KJ/mol.
>>>> It should be constant since I using same topology file and
>>>>
>> trajectory.>> Why the total energy is not constant.
>>>>
>>>
>>> Those .tpr should be identical - but you can check that with
>>>
>> gmxcheck.> Reruns do neighbour-searching every step, whereas your normal
>> simulation
>>> followed the nstlist setting. That's part of why my earlier advice
>>> suggested doing reruns for each simulation you wish to
>> compare. You
>>> should be able to get good/better agreement for steps where nstlist
>>> directed neighbour-searching in the original run. Also,
>> whether or not
>>> constraints have been applied (and when!) could influence the
>> energies to
>>> about this degree. I don't recall the details here.
>>>
>>> Even once you've removed all algorithm-specific sources of
>>>
>> difference,> there are other sources of non-reproducibility, such as the
>> assignment of
>>> particles to DD cells. Your original mdrun probably used dynamic
>>> load-balancing, and that cannot be reproduced in the DD used
>> by the
>>> rerun. (Or indeed by a repeat of your original mdrun!) Setting
>> -dlb no in
>>
>>> the original simulation might be enough to get agreement here,
>> or maybe
>>> mdrun -reprod will be required.
>>>
>>> Mark
>>>
>>>
>>>
>>>> NIlesh
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> On Thu, October 21, 2010 10:24 am, Mark Abraham wrote:
>>>>
>>>>
>>>>> On 22/10/2010 1:17 AM, Nilesh Dhumal wrote:
>>>>>
>>>>>
>>>>>
>>>>>> I am doing solvation dynamics for my system.
>>>>>> I have system with diatomic (PA---NE)solute surrounded by water
>>>>>> molecules.
>>>>>>
>>>>>> I want to run simulation with two differcent cases.
>>>>>> 1. PA charge=0 and NE charge=0 : No charge on solute
>>>>>> 2. PA charge=+1 and NE charge=-1 : Charge on solute
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> I want to calculate the energy at each step keeping the solvent
>>>>>>  configration same.
>>>>>>
>>>>>> IF I start a simulation with no charge on solute (case1), I
>>>>>>
>>>>>>
>>>> have the
>>>>>> energy for 1 step. I want to calculate the energy with charge
>>>> on solute
>>>>>> (case 2) with same configration water molecules.
>>>>>> Each step  I want to calculate the energy with and
>>>>>>
>>>>>>
>>>> without charge on
>>>>>> solute since the configration of solvent will be same for
>>>> that step.
>>>>>>
>>>>>> I was thinking two make two topologies file with charge and
>>>>>>
>>>>>>
>>>> with out
>>>>>> charge on solute. I don't know how to use them simultaneously
>>>> during the
>>>>>> simulation.
>>>>>
>>>>> Well, you don't use them simultaneously. You run a
>>>>>
>> simulation on
>>>>> whatever you think will generate a relevant conformational
>>>> ensemble. Then
>>>>> you want to use mdrun -rerun twice on the resulting
>>>> trajectory, using .tpr
>>>>> files based on .top files corresponding to the two cases in
>>>> order to
>>>>> create your comparison.
>>>>>
>>>>> Mark
>>>>> --
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>>>>
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