On Thu, Feb 14, 2013 at 6:13 AM, 라지브간디 <ra...@kaist.ac.kr> wrote:
> Dear gmx, > > I've used -pbc nojump options but still the protein goes all around the > box within 4ns. Any specific command to avoid this ? It's a myoglobin > protein! > The usual approach is here: http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions Mark > --------------------- orig.Message --------------------- > From : gmx-users-requ...@gromacs.org > To : gmx-users@gromacs.org > Sent date : 2013-02-14 07:24 > Subject : gmx-users Digest, Vol 106, Issue 69 > Send gmx-users mailing list submissions to > gmx-users@gromacs.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://lists.gromacs.org/mailman/listinfo/gmx-users > or, via email, send a message with subject or body 'help' to > gmx-users-requ...@gromacs.org > > You can reach the person managing the list at > gmx-users-ow...@gromacs.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of gmx-users digest..." > > > Today's Topics: > > 1. Stopping protein jumping inside box (?????) > 2. Re: Stopping protein jumping inside box (Naga Sundar) > 3. Re: Stopping protein jumping inside box (Justin Lemkul) > 4. RE: on the ussage of SD1 integrator (Berk Hess) > 5. Chandler autcorrelation function fitting (KARAKAS Esra) > 6. Bond potential of atom groups (Steven Neumann) > 7. Join my network on LinkedIn (Gideon Lapidoth via LinkedIn) > 8. GROMOS54A8 parameters in GROMACS format (ABEL Stephane 175950) > 9. Re: different springs - WHAM (Steven Neumann) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 13 Feb 2013 22:29:05 +0900 (KST) > From: ????? <ra...@kaist.ac.kr> > Subject: [gmx-users] Stopping protein jumping inside box > To: gmx-users@gromacs.org > Message-ID: <511b98243fa7_@_imoxion.com> > Content-Type: text/plain; charset="utf-8" > > Dear gmx users, > > > I need to stop my protein jumping inside box. I have used -pbc mol -ur > compact -center command too but still the protein gets moving from one > place to other. > > > Could you please suggest me how to make the protein to stop in one place ? > Moreover, its protein with their ligand. > > > > > Thnx. > > > > ------------------------------ > > Message: 2 > Date: Wed, 13 Feb 2013 05:47:07 -0800 > From: Naga Sundar <naga25sun...@gmail.com> > Subject: Re: [gmx-users] Stopping protein jumping inside box > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: > < > calobx4n_6huojhv-aecjgj9uctvivv2h5u-+izyvizmr0ec...@mail.gmail.com> > Content-Type: text/plain; charset=EUC-KR > > Hi > Plz try -pbc nojump option...It may work > > On Wed, Feb 13, 2013 at 5:29 AM, ���������� <ra...@kaist.ac.kr> wrote: > > > Dear gmx users, > > > > > > I need to stop my protein jumping inside box. I have used -pbc mol -ur > > compact -center command too but still the protein gets moving from one > > place to other. > > > > > > Could you please suggest me how to make the protein to stop in one place > ? > > Moreover, its protein with their ligand. > > > > > > > > > > Thnx. > > > > > > > > -- > > gmx-users mailing list gmx-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! > > * 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/Mailing_Lists > > > > > > -- > Regards > N.NagaSundaram > > > ------------------------------ > > Message: 3 > Date: Wed, 13 Feb 2013 08:50:04 -0500 > From: Justin Lemkul <jalem...@vt.edu> > Subject: Re: [gmx-users] Stopping protein jumping inside box > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: <511b9a0...@vt.edu> > Content-Type: text/plain; charset=UTF-8; format=flowed > > > > On 2/13/13 8:47 AM, Naga Sundar wrote: > > Hi > > Plz try -pbc nojump option...It may work > > > > Several iterations of trjconv are often needed to achieve the desired > representation. Indeed, the first step to removing jumps should be -pbc > nojump...which removes jumps ;) > > -Justin > > > On Wed, Feb 13, 2013 at 5:29 AM, ��������������� <ra...@kaist.ac.kr> > wrote: > > > >> Dear gmx users, > >> > >> > >> I need to stop my protein jumping inside box. I have used -pbc mol -ur > >> compact -center command too but still the protein gets moving from one > >> place to other. > >> > >> > >> Could you please suggest me how to make the protein to stop in one > place ? > >> Moreover, its protein with their ligand. > >> > >> > >> > >> > >> Thnx. > >> > >> > >> > >> -- > >> gmx-users mailing list gmx-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! > >> * 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/Mailing_Lists > >> > > > > > > > > -- > ======================================== > > Justin A. Lemkul, Ph.D. > Research Scientist > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > > > ------------------------------ > > Message: 4 > Date: Wed, 13 Feb 2013 15:57:34 +0100 > From: Berk Hess <g...@hotmail.com> > Subject: RE: [gmx-users] on the ussage of SD1 integrator > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: <dub124-w136490404914302a83f9b68e...@phx.gbl> > Content-Type: text/plain; charset="iso-8859-1" > > > Hi, > > With tau_t=2 the sd1 integrator should be ok. > But in 4.6.1, which will be released this week, the performance issues > with the sd integrator are fixed. > > Cheers, > > Berk > > > Date: Wed, 13 Feb 2013 09:19:46 +0300 > > From: jmsstarli...@gmail.com > > To: gmx-users@gromacs.org > > Subject: [gmx-users] on the ussage of SD1 integrator > > > > Dear Gromacs users! > > > > > > Commonly I'm using langevin's dynamics for thermostat modelling in my > > simulations of the membrane proteins > > (sd integrator without t_coupl with tau_t=2.0) > > > > Recently I've found that with sd1 integrator I can obtain better > > performance ( up to 50% in comparison to sd integrator). Could I use > > that integrator for modelling of stochastic thermostat with the same > > tau_t which I've used with SD ? > > Also during ussage of that thermostat I obtain notions from grommp like > > > > NOTE 4 [file ./mdps_cuda/md_sd.mdp]: > > With constraints integrator sd1 is less accurate, consider using sd > > instead > > > > What should I do to reduce such degree of inacuracy of SD1? > > > > Thanks for help, > > > > James > > -- > > gmx-users mailing list gmx-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! > > * 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/Mailing_Lists > > > ------------------------------ > > Message: 5 > Date: Wed, 13 Feb 2013 15:36:48 +0000 > From: KARAKAS Esra <esra.kara...@cea.fr> > Subject: [gmx-users] Chandler autcorrelation function fitting > To: "gmx-users@gromacs.org" <gmx-users@gromacs.org> > Message-ID: > <981823adf8938344ae9de8f0922f6494ad4...@e-exdage-a0.extra.cea.fr> > Content-Type: text/plain; charset="iso-8859-1" > > Dear gromacs users, > > I would like to compute the transition time gauche-trans for dihedral > angles. > For that, I used this command : > g_angle_mpi -f myfile.xtc -n dihedral.ndx -b 25000 -e 30000 -type dihedral > -chandler -avercorr -oc myoutput.xvg > > I have dihedral autocorrelation function C(t) but I can't manage to fit > this curve with a function. > > Anybody know how this autocorrelation function is computed and with what > kind of function I can fit it ? > > Thanks for help, > > Esra > > > ------------------------------ > > Message: 6 > Date: Wed, 13 Feb 2013 16:07:53 +0000 > From: Steven Neumann <s.neuman...@gmail.com> > Subject: [gmx-users] Bond potential of atom groups > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: > <CAKZJqQEztzuGqm0t4= > f37v+w-jioire0pz1tvdpj6cv7cyg...@mail.gmail.com> > Content-Type: text/plain; charset=ISO-8859-1 > > Dear Gmx Users, > > I want to create coarse grained model. I need bond constant and > equilibrium distance according to the equation > > V(r) =K (R - Req)^2 > > I wish to extract bonded potential between beads made out 3 atoms. I > need Req and K. Equilibrium distance is straight forward - g_dist > between COM or COG with index file conatining those 3 atoms. To match > force constant K I need to extract bonded potential and try to fit to > my parabolic curve. > > My question: > > How can I get bonded potential between beads of 3 atoms from AA > simulation? Do I have to specify energy groups (energgrps) before the > run in my mdp and then use g_energy? > > Thank you > > Steven > > > ------------------------------ > > Message: 7 > Date: Wed, 13 Feb 2013 16:36:35 +0000 (UTC) > From: Gideon Lapidoth via LinkedIn <mem...@linkedin.com> > Subject: [gmx-users] Join my network on LinkedIn > To: "Chinmay D." <gmx-users@gromacs.org> > Message-ID: > <1132639804.8784666.1360773395306.javamail....@ela4-app2322.prod> > Content-Type: text/plain; charset=UTF-8 > > LinkedIn > ------------ > > > > > Gideon Lapidoth requested to add you as a connection on LinkedIn: > > > ------------------------------------------ > > Chinmay, > > I'd like to add you to my professional network on LinkedIn. > > - Gideon > > Accept invitation from Gideon Lapidoth > > http://www.linkedin.com/e/-85v1n9-hd4pcfob-2u/Xl9gjr6GAOlB4vIjeR9gqTUPRTlBoITTu0/blk/I446675742_16/0UcDpKqiRzolZKqiRybmRSrCBvrmRLoORIrmkZt5YCpnlOt3RApnhMpmdzgmhxrSNBszYSclYOd3sRdPoSd3h9bQtDtD9jbmJfbP4PejkNdzwQczcLrCBxbOYWrSlI/eml-comm_invm-b-in_ac-inv28/?hs=false&tok=3qxljZfqg445E1 > > View profile of Gideon Lapidoth > > http://www.linkedin.com/e/-85v1n9-hd4pcfob-2u/rso/124852802/3yE9/name/15686615_I446675742_16/?hs=false&tok=0-QNCQqiI445E1 > ------------------------------------------ > You are receiving Invitation emails. > > > This email was intended for Chinmay Das. > Learn why this is included: > http://www.linkedin.com/e/-85v1n9-hd4pcfob-2u/plh/http%3A%2F%2Fhelp%2Elinkedin%2Ecom%2Fapp%2Fanswers%2Fdetail%2Fa_id%2F4788/-GXI/?hs=false&tok=1TX0BfxFI445E1 > > (c) 2012, LinkedIn Corporation. 2029 Stierlin Ct, Mountain View, CA 94043, > USA. > > > > > > ------------------------------ > > Message: 8 > Date: Wed, 13 Feb 2013 21:25:33 +0000 > From: ABEL Stephane 175950 <stephane.a...@cea.fr> > Subject: [gmx-users] GROMOS54A8 parameters in GROMACS format > To: "gmx-users@gromacs.org" <gmx-users@gromacs.org> > Message-ID: > <3e39b768bb199548ab18f7289e7534af02d60...@exdag0-b0.intra.cea.fr> > Content-Type: text/plain; charset="utf-8" > > Hello all, > > Does somebody know where i can find the latest GROMOS force field (i.e. > GROMOS54A8) described in [1] in the GROMACS format (gromos54a7.ff) ? > > [1] Reif et al. J. Chem. Theory Comput. 2013, 9, 1247���1264 doi: > http://pubs.acs.org/doi/citedby/10.1021/ct300156h > > Thank you > > Stephane > > ------------------------------ > > Message: 9 > Date: Wed, 13 Feb 2013 22:23:41 +0000 > From: Steven Neumann <s.neuman...@gmail.com> > Subject: Re: [gmx-users] different springs - WHAM > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: > < > cakzjqqhoyd21hg003dhuufbtdzsaci8uhf78_top79yz7ya...@mail.gmail.com> > Content-Type: text/plain; charset=ISO-8859-1 > > On Tue, Feb 12, 2013 at 5:01 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > > > > On 2/12/13 9:57 AM, Steven Neumann wrote: > >> > >> On Tue, Feb 12, 2013 at 2:53 PM, Justin Lemkul <jalem...@vt.edu> wrote: > >>> > >>> > >>> > >>> On 2/12/13 9:40 AM, Steven Neumann wrote: > >>>> > >>>> > >>>> Dear Gmx Users, > >>>> > >>>> I know it is possible to combine windows with different spring > >>>> constants into the one PMF curve using g_wham. > >>>> > >>>> Do I have to somehow tell g_wham that one or two windows have > >>>> different spring constants? > >>>> > >>> > >>> No, they are read from the .tpr files. > >>> > >>> > >>>> For instance - I got the better histogram overlap with lower force > >>>> constant in one window. When I replace this window into the window > >>>> with the sring constant like all windwos (worse overlap) both PMF > >>>> curves differ app. 2kcal/mol which is around 30% of the overall > >>>> deltaG. > >>>> > >>>> Is there any error I should inroduce when one window differ in terms > of > >>>> k1? > >>>> > >>> > >>> What does g_wham's error analysis suggest? > >>> > >>> -Justin > >> > >> > >> In both PMF error estimate with bayesian bootstraping is app. 0.2 > kcal/mol > >> > > > > Seems like a good result, so what's the problem? > > > > -Justin > > That the better overlap of histograms produce worse deltaG comparing > to experiment. With all the same spring constants I get the > experimental value of deltaG but there is a poor overlap. There must > be (somehow) a correction added to deltaG when introdcuing windows > with different spring constants. > > > Steven > > > > > > > -- > > ======================================== > > > > Justin A. Lemkul, Ph.D. > > Research Scientist > > 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 > > 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-requ...@gromacs.org. > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > ------------------------------ > > -- > gmx-users mailing list > gmx-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! > > End of gmx-users Digest, Vol 106, Issue 69 > ****************************************** > > > -- > gmx-users mailing list gmx-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! > * 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/Mailing_Lists > -- gmx-users mailing list gmx-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! * 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/Mailing_Lists
