One last question!
1- So what are the 12 energy terms I get by passing index file onto step 2
below? I ignored rerun! what does rerun does?
2- So I dont have to include index file in mdrun initially..In brief what I
need is:
step 1 grompp .....(no index)
step 2 mdrun -s old.tpr -o old.trr -c *.gro
(grompp and mdrun as usual) then:
grompp -f energygroups.mdp -c .top -o new.tpr
*-n index.ndx
*
mdrun *-s new.tpr -rerun old.trr...*
Please confirm. Many thanks for your help.
On 22 February 2011 17:35, Justin A. Lemkul <jalem...@vt.edu> wrote:
>
>
> Nick wrote:
>
>>
>> Dear Justin,
>>
>> Thanks for your reply and Sorry for asking naive questions...
>>
>
>> 1- I am looking at all possible interaction energies between components A
>> and B. that is A-A AB and BB. So interaction between single chains is not
>> what I want. With this I think my initial approach was right. That is
>> putting all atoms of 3 A chains under [A] and the same all solvent atoms
>> under [B] and setting A and B as energy groups in mdp. Am I right?
>>
>>
> If you don't want your energies on a per-chain basis, then yes.
>
>
> 2- One more thing bout question 3: I am passing on index.ndx to mdrun
>> command.
>>
>> with the index file I talked about I am getting the follwoing for AA AB
>> and BB: LJ SR, LJ 1-4 coulomb SR and 1-4. (i.e 12 energy terms).
>>
>> I think you say I need rerun since you assumed I did not pass it onto
>> mdrun. right?
>>
>>
> You need to create a new .tpr file that has the desired groups specified in
> it. You pass the new .tpr file to mdrun, in conjunction with your old
> trajectory (i.e., mdrun -s new.tpr -rerun old.trr).
>
>
> 3- to get intermolecular interaction energies say for AA I need to add up
>> LJ SR+coulomb SR? say +123-50=73 ? or just take absolute values : 123+50=173
>> ?
>>
>>
> Sign matters a lot. Positive is repulsive, negative is attractive. You
> can't just switch them arbitrarily.
>
> -Justin
>
> Thanks,
>>
>>
>>
>> Nick wrote:
>>
>> Dear experts,
>>
>> 1- I am trying to get interaction energies between solute (3
>> chains A) and solvent 50 molecules B. In the index file I
>> created two groups: one for all atoms of [A] and and [B] for all
>> solvent molecules. and by setting A and B as energy groups in
>> mdp file I am getting break down as A-A, A-B and B-B with g_energy.
>>
>> I am a little confused as I dont know if I need to create
>> different groups for my solute to get interaction energies A-A,
>> A-B and B-B. I mean do I need to have [A1] for solute chain 1
>> ...[A3] for chain 3?
>>
>>
>> If you want a breakdown of per-chain energetics, then yes, specify
>> each chain as a group. The programs will only do what you tell
>> them, nothing more, nothing less.
>>
>>
>>
>>
>> and then sent A1, A2, A3 in mdp file and run g_energy? if I need
>> to specify different chains, then to get say A-A should I
>> average over all possible A1-A2, A1A3, A2-A3, A1-B, A2,B...? I
>> am really confused ..
>>
>>
>> Theoretically, the short-range terms should sum, not average.
>>
>>
>> 2- I know it is naive question but What does A1-A1 mean? How can
>> one chain interact with itself?
>>
>>
>> Without knowing what the chain is, no one can answer this.
>> Generally, any atoms that are within the short-range cutoff and
>> further away than nrexcl bonds contribute to short-range
>> interactions. Long-range interactions (i.e., PME terms) happen too,
>> but you can't decompose that term with energygrps.
>>
>>
>> 3- Do I need to use mdrun - rerun option to get beakdown or just
>> g_energy gives what I need?
>>
>>
>> You need to -rerun. g_energy does not take an index file, and it
>> only analyzes existing groups, it cannot derive new ones.
>>
>> -Justin
>>
>>
>> Thanks for your help
>> Paniz
>>
>>
>> -- ========================================
>>
>> Justin A. Lemkul
>> Ph.D. Candidate
>> ICTAS Doctoral Scholar
>> MILES-IGERT Trainee
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>>
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>> ========================================
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>>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
> --
> gmx-users mailing list gmx-users@gromacs.org
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