<table cellspacing="0" cellpadding="0" border="0" ><tr><td valign="top" style="font: inherit;"><div>Justin,</div>Thanks for your reply. Then I wonder whether there is any other way out in gromacs to get the net interaction potential energy due to each of the components in a simulations. <div><br></div><div>I am asking this, many times people report the potential energy contribution due to solvent-solvent interaction in a simulation containing solute( say peptide) and solvents and that are also being done in gromacs. I wonder, for those cases, whether just adding the non-bonding interaction will be good enough ? or, there is any other way out ?<div>Jagannath<br><br>--- On <b>Fri, 22/10/10, Justin A. Lemkul <i><jalemkul@vt.edu></i></b> wrote:<br><blockquote style="border-left: 2px solid rgb(16, 16, 255); margin-left: 5px; padding-left: 5px;"><br>From: Justin A. Lemkul <jalemkul@vt.edu><br>Subject: Re: [gmx-users] problem
with energy groups and mdrun -rerun option<br>To: "Discussion list for GROMACS users" <gmx-users@gromacs.org><br>Date: Friday, 22 October, 2010, 2:56 AM<br><br><div class="plainMail"><br><br>jagannath mondal wrote:<br>> Hi,<br>> I have used gromacs 4.0.7 to do MD simulation of two solutes A & B in water ( solvent) . Initially, I had set "energy groups = system " and used mdrun to do the simulation.<br>> <br>> Now,I wanted to get the potential energy contribution from due to interaction of A-A, B-B,A-B A-solvent, B-solvent, solvent-solvent.<br>> For that I followed some discussions in mailing list regarding using mdrun -rerun option:<br>> This is what I did:<br>> I used make_ndx and created 3 groups: A, B and solvent. Now, I modified the grompp.mdp file so that I have now energy groups = A B solvent <br>> Then I used grompp -c conf -f grompp
-n index -o topol<br>> <br>> Then I used mdrun -s -rerun traj_old.xtc <br>> ( here traj_old.xtc is the old xtc file I obtained during the original mdrun)<br>> <br>> But, now, after using this -rerun option , if I try to use the g_energy on the resulting ener.edr file to obtain the individual potential energy of interaction for A-A, B-B , A-B, A-solvent<br>> I get following output <br>> <br>> Here is the output from g_energy -f ener.edr :<br>> <br>> Select the terms you want from the following list by<br>> selecting either (part of) the name or the number or a combination.<br>> End your selection with an empty line or a zero.<br>> -------------------------------------------------------------------<br>> 1 Bond 2 Angle 3 U-B 4
Ryckaert-Bell.<br>> 5 Improper-Dih. 6 LJ-14 7 Coulomb-14 8 LJ-(SR) 9 Coulomb-(SR) 10 Coul.-recip. 11 Potential 12 Kinetic-En. 13 Total-Energy 14 Conserved-En. 15 Temperature 16 Pressure-(bar)<br>> 17 Cons.-rmsd-() 18 Vir-XX 19 Vir-XY 20 Vir-XZ 21 Vir-YX 22 Vir-YY 23 Vir-YZ 24 Vir-ZX 25 Vir-ZY
26 Vir-ZZ 27 Pres-XX-(bar) 28 Pres-XY-(bar) 29 Pres-XZ-(bar) 30 Pres-YX-(bar) 31 Pres-YY-(bar) 32 Pres-YZ-(bar) 33 Pres-ZX-(bar) 34 Pres-ZY-(bar) 35 Pres-ZZ-(bar) 36 #Surf*SurfTen 37 Mu-X 38 Mu-Y 39 Mu-Z 40 Coul-SR:A-A 41 LJ-SR:A-A 42 Coul-14:A-A 43 LJ-14:A-A 44 Coul-SR:A-B 45 LJ-SR:A-B 46
Coul-14:A-B 47 LJ-14:A-B 48 Coul-SR:A-Solvent 49 LJ-SR:A-Solvent 50 Coul-14:A-Solvent 51 LJ-14:A-Solvent 52 Coul-SR:B-B 53 LJ-SR:B-B 54 Coul-14:B-B 55 LJ-14:B-B
56 Coul-SR:B-Solvent 57 LJ-SR:B-Solvent 58 Coul-14:B-Solvent 59 LJ-14:B-Solvent 60 Coul-SR:Solvent-Solvent 61 LJ-SR:Solvent-Solvent 62 Coul-14:Solvent-Solvent 63 LJ-14:Solvent-Solvent 64 T-System 65 Xi-System<br>> <br>> It
provides me contribution from each of the energy groups on nonbonding terms: LJ(SR),Coulomb(SR),Coulomb(14),LJ(14) . But, it does NOT provide me their contribution to Bonding term( i.e bond,angle, U-B,RB,improper-Dih) !! As a result, I am a not sure how to get the net potential energy from each of the 3 energy groups. Am I doing something wrong ? Do I need to use any other utilities ?<br><br>Using energygrps only allows you to decompose nonbonded interactions. You cannot decompose bonded interactions, potential, kinetic energy, etc.<br><br>-Justin<br><br>> Any help will be useful. <br>> Jagannath<br>> <br>> <br><br>-- ========================================<br><br>Justin A. Lemkul<br>Ph.D. Candidate<br>ICTAS Doctoral Scholar<br>MILES-IGERT Trainee<br>Department of Biochemistry<br>Virginia Tech<br>Blacksburg, VA<br>jalemkul[at]vt.edu | (540) 231-9080<br><a
href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br><br>========================================<br>-- gmx-users mailing list <a ymailto="mailto:gmx-users@gromacs.org" href="/mc/compose?to=gmx-users@gromacs.org">gmx-users@gromacs.org</a><br><a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>Please search the archive at <a href="http://www.gromacs.org/Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a> before posting!<br>Please don't post (un)subscribe requests to the list. Use the www interface or send it to <a ymailto="mailto:gmx-users-request@gromacs.org" href="/mc/compose?to=gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists"
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