[gmx-users] (no subject)

[Nilesh Dhumal]

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.
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
>>> --
>>> gmx-users mailing list    gmx-users at gromacs.org
>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>> Please search the archive at
>>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>>> Please don't post (un)subscribe requests to the list. Use the
>>> www interface or send it to gmx-users-request at gromacs.org.
>> Can't post? Read
>>
>>> http://www.gromacs.org/Support/Mailing_Lists
>>>
>>>
>>>
>>>
>>
>>
>>
>> --
>> gmx-users mailing list    gmx-users at gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>> Please don't post (un)subscribe requests to the list. Use the
>> www interface or send it to gmx-users-request at gromacs.org. Can't post?
>> Read http://www.gromacs.org/Support/Mailing_Lists
>>
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org. Can't post? Read
> http://www.gromacs.org/Support/Mailing_Lists