[gmx-users] tpic run option - potential energy meaning

3e+08 (for my test) vs. 182452256.00 (of epot dumped from tpic), a difference of 4.14074e+06 kJ/mol. Thanks in advance. Regards, João -- João M. Damas PhD Student Protein Modelling Group ITQB-UNL, Oeiras, Portugal Tel:+351-214469613 -- gmx-users mailing listgmx-users@gromacs.org http://list

Re: [gmx-users] Re: Test particle insertion extra coordinate

he > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- João M. Damas PhD Student Protein Modelling Group ITQB-UNL, Oeiras, Portugal Tel:+351-214469613 -- gmx-users mailing listgmx-users@gromacs.org http://l

Re: [gmx-users] Re: Test particle insertion extra coordinate

gt; 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-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/

Re: [gmx-users] Charge groups for particle insertion

sts to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- João M. Damas PhD Student Protein Modelling Group ITQB-UNL, Oeiras, Portugal Tel:+351-214469613 -- gmx-users mailing listgmx-

Re: [gmx-users] ATP/Mg+2 parameters

o the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- João M. Damas PhD Student Protein Modelling Group ITQB-UNL, Oeiras, Portugal Tel:+351-214469613 -- gmx-users mailing list

Re: [gmx-users] ATP/ADP+Pi

org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- João M. Damas PhD Student Protein Modelling Group ITQB-UNL, Oeiras, Portugal Tel:+351-214469613 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please

Re: 回复： 回复： [gmx-users] ATP/ADP+Pi

with this. > > > > Thank you very much . > > -- > > gmx-users mailing listgmx-users@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!

Re: [gmx-users] constant PH simulations

x-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-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Su

Re: Re: [gmx-users] constant PH simulations

uni-regensburg.de> wrote: > Could you just tell me smth. ! > No forcefield on whole earth is able to reproduce the pH realistically > by H+. > You just can apply pH of your system through the protonation states > of each part in your system. > > monkey. > > > >

Re: [gmx-users] Re: Folding rate

tp://www.gromacs.org/** >> Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before >> posting! >> Please don't post (un)subscribe requests to the list. Use thewww >> interface or send it to gmx-users-requ...@gromacs.org. >> &g

Re: [gmx-users] Test Particle Insertion

requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- João M. Damas PhD Student Protein Modelling Group ITQB-UNL, Oeiras, Portugal Tel:+351-214469613 -- gmx-users mailing li

Re: [gmx-users] TPI Results differ in v4.5.7 and v4.6.1

= 100 > > ; Free energy control stuff > free-energy = no > init-lambda = 0 > delta-lambda = 0 > sc-alpha = 0 > sc-sigma = 0.3 > > ; Non-equilibrium MD stuff > acc-grps = > acc

Re: [gmx-users] TPI Results differ in v4.5.7 and v4.6.1

PM, Niels Müller wrote: > Hi João, > > Indeed your instinct seems to be good! When switching the Coulomb-Type to > Cut-Off, there doesn't seem to be a difference between 4.6 and 4.5. > Apparently its an issue with the PME sum. We will investigate further. > > > Am 24

Re: [gmx-users] TPI Results differ in v4.5.7 and v4.6.1

th charged particles? And are you going to file an issue like Szilárd suggested? Best, João On Sat, Jun 29, 2013 at 5:21 PM, João M. Damas wrote: > Niels, > > Which force-field did you use? I guess an uncharged CH4 shouldn't be > giving different results for TPI when c

Re: [gmx-users] TPIC and GMX_TPI_DUMP

(un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- João M. Damas PhD Student Protein Modelling Group ITQB-UNL, Oeiras, Portugal Tel:+351-214469613 -- gmx-u

Re: [gmx-users] TPIC and GMX_TPI_DUMP

/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-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.

Re: [gmx-users] TPIC and GMX_TPI_DUMP

> -1445436.00 0 -nan > -1445435.90 0 -nan > -1445435.80 0 -nan > -1445435.70 0 -nan > -1445435.60 0 -nan > -1445435.50 0 -nan > -1445435.40 0 -nan > -1445435.30

Re: [gmx-users] TPIC and GMX_TPI_DUMP

Sorry, where I said "put it as the last coordinate on the .tpr file you're building" it should be "put it as the last coordinate of each frame of the .trr file". You'll need to do some trajectory "hand-editing". João On Sat, Aug 31, 2013 at 2:41 AM, João

Re: [gmx-users] is there any tool for flexibility?

't post (un)subscribe requests to the list. Use the www > interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read > http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> > -- João M. Damas PhD Student Protein Mod

Re: [gmx-users] TPI Results differ in v4.5.7 and v4.6.1

, have found a solution to your problem, which probably has a different origin from what I initially thought... Best, João On Mon, Jul 1, 2013 at 1:29 PM, João M. Damas wrote: > I have run TPI using three versions (4.0.4, 4.5.4 and 4.6.1) and three > different insertions particles: CH4 (unc

[gmx-users] vdwradii.dat - where do the values come from?

e it would be difficult to introduce other element's van der waals radii consistent to the current ones, why keep using them? Regards, João -- João M. Damas PhD Student Protein Modelling Group ITQB-UNL, Oeiras, Portugal Tel:+351-214469613 ___ gm

[gmx-users] Distance Restraints: Inconsistent Shifts, LINCS Warnings, Number of grid cells is zero, XTC error

hoping anyone could give me some insight. By the way, I'm using GROMACS 4. Thanks in advance and sorry if I sounded confusing. Best regards, João -- João M. Damas PhD Student Protein Modelling Group ITQB-UNL, Oeiras, Portugal Tel:+351-214469613 __

Re: [gmx-users] Distance Restraints: Inconsistent Shifts, LINCS Warnings, Number of grid cells is zero, XTC error

nts... Thanks, João On Fri, Oct 9, 2009 at 12:51 AM, Mark Abraham wrote: > João M. Damas wrote: > >> Gromacs users, >> >> I have a small test system of about 2500 atoms which consists on a few >> organic molecules in a box of water. I'm trying to use distance re

Re: [gmx-users] g_rms (rmsd vs residue no)

e the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- João M. Damas PhD Student Protein Modelling Group ITQB-UNL, Oeiras, Portugal Tel:+351-214469613 -- gmx-users mailing listgmx-users@gromacs.org http:

[gmx-users] Nicelevel default 0 - mdrun_mpi of Gromacs 4.0.2

thing. Thanks in advance, João -- João M. Damas PhD Student Protein Modelling Group ITQB-UNL, Oeiras, Portugal Tel:+351-214469613 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the ar

Re: [gmx-users] Nicelevel default 0 - mdrun_mpi of Gromacs 4.0.2

ld like to know if there is any reason for mdrun_mpi to have a > nicelevel default of zero in Gromacs 4.0.2 instead of the default 19 of > mdrun of every version or mdrun_mpi of the other versions. I searched the > mailing list for any discussion related to this but I haven't fou

Re: [gmx-users] Nicelevel default 0 - mdrun_mpi of Gromacs 4.0.2

I would like to know if there is any reason for mdrun_mpi to have a > nicelevel default of zero in Gromacs 4.0.2 instead of the default 19 of > mdrun of every version or mdrun_mpi of the other versions. I searched the > mailing list for any discussion related to this but I haven't found >

Re: [gmx-users] Nicelevel default 0 - mdrun_mpi of Gromacs 4.0.2

jmda...@itqb.unl.pt > To: gmx-users@gromacs.org > Subject: [gmx-users] Nicelevel default 0 - mdrun_mpi of Gromacs 4.0.2 > > > Hello, > > I would like to know if there is any reason for mdrun_mpi to have a > nicelevel default of zero in Gromacs 4.0.2

Re: [gmx-users] Tabulated potentials and performance

to form, but nothing very clear. Hence, is there really this cache size problem? João M. Damas On Mon, Jul 19, 2010 at 11:18 PM, Lanyuan Lu wrote: > >From our group's experience, there is a critical point for dramatic > performance drop when one uses two many tables. The possibl

[gmx-users] Section 5.3.3 in manuals 3.3, 4.0, 4.5 - Old description of format of atomtyoes

ction 5.3.3) have the "new" format described. The format is quite intuitive, but maybe the manuals should be corrected to reflect the correct format? Regards, João -- João M. Damas PhD Student Protein Modelling Group ITQB-UNL, Oeiras, Portugal Tel:+351-214469613 -- gmx-users mailing li