Golnaz, I think you're creating a bit of a mess by replying to the digest. If you don't mind, please see my answer directly to your specific question, where I will also quote your message from below.
Alex GR> Thank you Alex GR> First of all it is better to say that I am a beginner. I follow two papers GR> for my project. The authers are ''Tumala'' and ''Samalkorpi'' . GR> My surfactants are mixture of CTAB and SDS. In these two papers surfactants GR> were put perpendicular on the graphene sheet. because if I put surfactants GR> random in the box it will take a alot of time for surfactants to transfer GR> to the graphene sheet. The simulation method in the papers is GROMACS but GR> authors did not mention how they loacted surfactants on the graphene sheet. GR> I have written the link of the papers. I knew that it is not specifically GR> Gromacs but I would like to know with which software I can make this GR> change on configuration. GR> http://pubs.acs.org/doi/abs/10.1021/jp077636y GR> http://pubs.acs.org/doi/abs/10.1021/jp077678m GR> On Fri, May 15, 2015 at 7:14 PM, < GR> gromacs.org_gmx-users-requ...@maillist.sys.kth.se> wrote: >> Send gromacs.org_gmx-users mailing list submissions to >> gromacs.org_gmx-users@maillist.sys.kth.se >> >> To subscribe or unsubscribe via the World Wide Web, visit >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users >> or, via email, send a message with subject or body 'help' to >> gromacs.org_gmx-users-requ...@maillist.sys.kth.se >> >> You can reach the person managing the list at >> gromacs.org_gmx-users-ow...@maillist.sys.kth.se >> >> When replying, please edit your Subject line so it is more specific >> than "Re: Contents of gromacs.org_gmx-users digest..." >> >> >> Today's Topics: >> >> 1. Re: energy minimization problem (Ming Tang) >> 2. Re: energy minimization problem (Justin Lemkul) >> 3. question (Golnaz Roudsari) >> 4. Re: question (Alex) >> 5. Re: question (abhijit Kayal) >> >> >> ---------------------------------------------------------------------- >> >> Message: 1 >> Date: Fri, 15 May 2015 13:32:04 +0000 >> From: Ming Tang <m21.t...@qut.edu.au> >> To: "gmx-us...@gromacs.org" <gmx-us...@gromacs.org> >> Subject: Re: [gmx-users] energy minimization problem >> Message-ID: <dv888t2enjj742h6jn4fglmx.1431696517...@email.android.com> >> Content-Type: text/plain; charset="us-ascii" >> >> Reducing time helps it run longer. But 0.02ps-0.04ps is believed to be >> reasonable according to gromacs website. So ijust kept trying 0.02ps >> >> Sent from my Huawei Mobile >> >> Justin Lemkul <jalem...@vt.edu> wrote: >> >> >> >> On 5/14/15 10:02 PM, Ming Tang wrote: >> > Hi Justin >> > >> > Here is the .mdp file with position restraints, which I downloaded from >> the martini tutorial website. It works well with the tutorial and my small >> triple helix, and the grompp process does not give any warnings. Please >> help to have a look. Many thanks to you. >> > >> > define = -DPOSRES >> > integrator = md >> > dt = 0.02 >> >> Have you tried simply reducing the time step? 20 fs may be reasonable for >> a >> well equilibrated system, but if the run is dying early, then this is the >> first >> thing I would look at. >> >> -Justin >> >> > nsteps = 50000 >> > nstxout = 0 >> > nstvout = 0 >> > nstlog = 1000 >> > nstxtcout = 1000 >> > xtc-precision = 10 >> > cutoff-scheme =verlet >> > coulombtype = reaction-field-zero >> > coulomb-modifier = potential-shift-verlet >> > rcoulomb-switch = 0.9 >> > rcoulomb = 1.4 >> > epsilon_r = 15 >> > vdw-modifier = force-switch >> > rvdw-switch = 0.9 >> > rvdw = 1.4 >> > tcoupl = v-rescale >> > tc-grps = Protein W >> > tau-t = 1.0 1.0 >> > ref-t = 310 310 >> > compressibility = 3e-4 >> > ref-p = 1.0 >> > refcoord_scaling = all >> > pbc = xyz >> > >> > -----Original Message----- >> > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto: >> gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Justin >> Lemkul >> > Sent: Friday, 15 May 2015 11:50 AM >> > To: gmx-us...@gromacs.org >> > Subject: Re: [gmx-users] energy minimization problem >> > >> > >> > >> > On 5/14/15 9:47 PM, Ming Tang wrote: >> >> Dear Justin, >> >> >> >> I saw it in the terminal. >> >> >> >> Potential Energy = -6.3682131e+05 >> >> Maximum force = 1.8876091e+02 on atom 1147 >> >> Norm of force = 3.1155257e+00 >> >> >> >> But, how can I further minimize my protein? >> >> >> > >> > Minimization is not your problem. Post a full .mdp file of the run that >> is failing. >> > >> > -Justin >> > >> > -- >> > ================================================== >> > >> > Justin A. Lemkul, Ph.D. >> > Ruth L. Kirschstein NRSA Postdoctoral Fellow >> > >> > Department of Pharmaceutical Sciences >> > School of Pharmacy >> > Health Sciences Facility II, Room 629 >> > University of Maryland, Baltimore >> > 20 Penn St. >> > Baltimore, MD 21201 >> > >> > jalem...@outerbanks.umaryland.edu | (410) 706-7441 >> http://mackerell.umaryland.edu/~jalemkul >> > >> > ================================================== >> > -- >> > Gromacs Users mailing list >> > >> > * Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >> posting! >> > >> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> > >> > * For (un)subscribe requests visit >> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >> send a mail to gmx-users-requ...@gromacs.org. >> > >> >> -- >> ================================================== >> >> Justin A. Lemkul, Ph.D. >> Ruth L. Kirschstein NRSA Postdoctoral Fellow >> >> Department of Pharmaceutical Sciences >> School of Pharmacy >> Health Sciences Facility II, Room 629 >> University of Maryland, Baltimore >> 20 Penn St. >> Baltimore, MD 21201 >> >> jalem...@outerbanks.umaryland.edu | (410) 706-7441 >> http://mackerell.umaryland.edu/~jalemkul >> >> ================================================== >> -- >> Gromacs Users mailing list >> >> * Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >> posting! >> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> * For (un)subscribe requests visit >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >> send a mail to gmx-users-requ...@gromacs.org. >> >> >> ------------------------------ >> >> Message: 2 >> Date: Fri, 15 May 2015 09:37:44 -0400 >> From: Justin Lemkul <jalem...@vt.edu> >> To: gmx-us...@gromacs.org >> Subject: Re: [gmx-users] energy minimization problem >> Message-ID: <5555f6a8.7080...@vt.edu> >> Content-Type: text/plain; charset=windows-1252; format=flowed >> >> >> >> On 5/15/15 9:32 AM, Ming Tang wrote: >> > Reducing time helps it run longer. But 0.02ps-0.04ps is believed to be >> reasonable according to gromacs website. So ijust kept trying 0.02ps >> > >> >> The time step will depend on the stability of the system, which in turn >> depends >> on how well equilibrated it is. If reducing the time step promotes >> stability >> during equilibration, that is the most obvious solution. After >> equilibrating >> for a while, try increasing the time step. >> >> -Justin >> >> > Sent from my Huawei Mobile >> > >> > Justin Lemkul <jalem...@vt.edu> wrote: >> > >> > >> > >> > On 5/14/15 10:02 PM, Ming Tang wrote: >> >> Hi Justin >> >> >> >> Here is the .mdp file with position restraints, which I downloaded from >> the martini tutorial website. It works well with the tutorial and my small >> triple helix, and the grompp process does not give any warnings. Please >> help to have a look. Many thanks to you. >> >> >> >> define = -DPOSRES >> >> integrator = md >> >> dt = 0.02 >> > >> > Have you tried simply reducing the time step? 20 fs may be reasonable >> for a >> > well equilibrated system, but if the run is dying early, then this is >> the first >> > thing I would look at. >> > >> > -Justin >> > >> >> nsteps = 50000 >> >> nstxout = 0 >> >> nstvout = 0 >> >> nstlog = 1000 >> >> nstxtcout = 1000 >> >> xtc-precision = 10 >> >> cutoff-scheme =verlet >> >> coulombtype = reaction-field-zero >> >> coulomb-modifier = potential-shift-verlet >> >> rcoulomb-switch = 0.9 >> >> rcoulomb = 1.4 >> >> epsilon_r = 15 >> >> vdw-modifier = force-switch >> >> rvdw-switch = 0.9 >> >> rvdw = 1.4 >> >> tcoupl = v-rescale >> >> tc-grps = Protein W >> >> tau-t = 1.0 1.0 >> >> ref-t = 310 310 >> >> compressibility = 3e-4 >> >> ref-p = 1.0 >> >> refcoord_scaling = all >> >> pbc = xyz >> >> >> >> -----Original Message----- >> >> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto: >> gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Justin >> Lemkul >> >> Sent: Friday, 15 May 2015 11:50 AM >> >> To: gmx-us...@gromacs.org >> >> Subject: Re: [gmx-users] energy minimization problem >> >> >> >> >> >> >> >> On 5/14/15 9:47 PM, Ming Tang wrote: >> >>> Dear Justin, >> >>> >> >>> I saw it in the terminal. >> >>> >> >>> Potential Energy = -6.3682131e+05 >> >>> Maximum force = 1.8876091e+02 on atom 1147 >> >>> Norm of force = 3.1155257e+00 >> >>> >> >>> But, how can I further minimize my protein? >> >>> >> >> >> >> Minimization is not your problem. Post a full .mdp file of the run >> that is failing. >> >> >> >> -Justin >> >> >> >> -- >> >> ================================================== >> >> >> >> Justin A. Lemkul, Ph.D. >> >> Ruth L. Kirschstein NRSA Postdoctoral Fellow >> >> >> >> Department of Pharmaceutical Sciences >> >> School of Pharmacy >> >> Health Sciences Facility II, Room 629 >> >> University of Maryland, Baltimore >> >> 20 Penn St. >> >> Baltimore, MD 21201 >> >> >> >> jalem...@outerbanks.umaryland.edu | (410) 706-7441 >> http://mackerell.umaryland.edu/~jalemkul >> >> >> >> ================================================== >> >> -- >> >> Gromacs Users mailing list >> >> >> >> * Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >> posting! >> >> >> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> >> >> * For (un)subscribe requests visit >> >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >> send a mail to gmx-users-requ...@gromacs.org. >> >> >> > >> > -- >> > ================================================== >> > >> > Justin A. Lemkul, Ph.D. >> > Ruth L. Kirschstein NRSA Postdoctoral Fellow >> > >> > Department of Pharmaceutical Sciences >> > School of Pharmacy >> > Health Sciences Facility II, Room 629 >> > University of Maryland, Baltimore >> > 20 Penn St. >> > Baltimore, MD 21201 >> > >> > jalem...@outerbanks.umaryland.edu | (410) 706-7441 >> > http://mackerell.umaryland.edu/~jalemkul >> > >> > ================================================== >> > -- >> > Gromacs Users mailing list >> > >> > * Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >> posting! >> > >> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> > >> > * For (un)subscribe requests visit >> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >> send a mail to gmx-users-requ...@gromacs.org. >> > >> >> -- >> ================================================== >> >> Justin A. Lemkul, Ph.D. >> Ruth L. Kirschstein NRSA Postdoctoral Fellow >> >> Department of Pharmaceutical Sciences >> School of Pharmacy >> Health Sciences Facility II, Room 629 >> University of Maryland, Baltimore >> 20 Penn St. >> Baltimore, MD 21201 >> >> jalem...@outerbanks.umaryland.edu | (410) 706-7441 >> http://mackerell.umaryland.edu/~jalemkul >> >> ================================================== >> >> >> ------------------------------ >> >> Message: 3 >> Date: Fri, 15 May 2015 18:46:55 +0430 >> From: Golnaz Roudsari <golnaz.c...@gmail.com> >> To: gromacs.org_gmx-users@maillist.sys.kth.se >> Subject: [gmx-users] question >> Message-ID: >> <CAGFO7SEwhXuLkkt= >> 3nwknh2s8vnuzyvq8jhatz_r3vqgcyr...@mail.gmail.com> >> Content-Type: text/plain; charset=UTF-8 >> >> Dear gmx-user >> I want to simulate graphene and surfactants in water. In most of the paper >> they put surfactants perpendicular on the graphene sheet. I have problem in >> initial configuration. I do not know how They put them perpendicular on the >> graphene sheet. I can not put them random in my box because I do not have a >> perfect system for more than 50 ns MD run. >> Thank you in advance >> Golnaz Vahabpour >> >> >> ------------------------------ >> >> Message: 4 >> Date: Fri, 15 May 2015 08:26:44 -0600 >> From: Alex <nedoma...@gmail.com> >> To: Discussion list for GROMACS users <gmx-us...@gromacs.org> >> Subject: Re: [gmx-users] question >> Message-ID: >> <CAMJZ6qHMQ2twVjbYXr5P2SL7GyKeTYXfm_HW7DXristSibSL= >> w...@mail.gmail.com> >> Content-Type: text/plain; charset=UTF-8 >> >> Hi, >> >> I am not sure anyone will be able to help, because this isn't really about >> Gromacs. Can you please clarify who "they" are and what exactly you mean by >> "perpendicular" when talking about surfactants? Also, what are those >> surfactants? Anyway, a reference to a representative paper and some >> instructions on where to quickly see what you're talking about would be >> nice. Once again, this isn't something Gromacs-specific. >> >> Alex >> On May 15, 2015 9:17 AM, "Golnaz Roudsari" <golnaz.c...@gmail.com> wrote: >> >> > Dear gmx-user >> > I want to simulate graphene and surfactants in water. In most of the >> paper >> > they put surfactants perpendicular on the graphene sheet. I have problem >> in >> > initial configuration. I do not know how They put them perpendicular on >> the >> > graphene sheet. I can not put them random in my box because I do not >> have a >> > perfect system for more than 50 ns MD run. >> > Thank you in advance >> > Golnaz Vahabpour >> > -- >> > Gromacs Users mailing list >> > >> > * Please search the archive at >> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >> > posting! >> > >> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> > >> > * For (un)subscribe requests visit >> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >> > send a mail to gmx-users-requ...@gromacs.org. >> > >> >> >> ------------------------------ >> >> Message: 5 >> Date: Fri, 15 May 2015 20:14:18 +0530 >> From: abhijit Kayal <abhijitchemi...@gmail.com> >> To: gmx-us...@gromacs.org >> Subject: Re: [gmx-users] question >> Message-ID: >> <CANu9SWi3z= >> uoy12pqsmwpbscmyt7-txb8ox1cwdkcvvkbh8...@mail.gmail.com> >> Content-Type: text/plain; charset=UTF-8 >> >> Hi, >> >> You can use packmol to generate your initial configuration. >> >> >> On Fri, May 15, 2015 at 7:56 PM, Alex <nedoma...@gmail.com> wrote: >> >> > Hi, >> > >> > I am not sure anyone will be able to help, because this isn't really >> about >> > Gromacs. Can you please clarify who "they" are and what exactly you mean >> by >> > "perpendicular" when talking about surfactants? Also, what are those >> > surfactants? Anyway, a reference to a representative paper and some >> > instructions on where to quickly see what you're talking about would be >> > nice. Once again, this isn't something Gromacs-specific. >> > >> > Alex >> > On May 15, 2015 9:17 AM, "Golnaz Roudsari" <golnaz.c...@gmail.com> >> wrote: >> > >> > > Dear gmx-user >> > > I want to simulate graphene and surfactants in water. In most of the >> > paper >> > > they put surfactants perpendicular on the graphene sheet. I have >> problem >> > in >> > > initial configuration. I do not know how They put them perpendicular on >> > the >> > > graphene sheet. I can not put them random in my box because I do not >> > have a >> > > perfect system for more than 50 ns MD run. >> > > Thank you in advance >> > > Golnaz Vahabpour >> > > -- >> > > Gromacs Users mailing list >> > > >> > > * Please search the archive at >> > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >> > > posting! >> > > >> > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> > > >> > > * For (un)subscribe requests visit >> > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >> > > send a mail to gmx-users-requ...@gromacs.org. >> > > >> > -- >> > Gromacs Users mailing list >> > >> > * Please search the archive at >> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >> > posting! >> > >> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> > >> > * For (un)subscribe requests visit >> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >> > send a mail to gmx-users-requ...@gromacs.org. >> > >> >> >> >> -- >> Abhijit kayal >> Research Scholar >> Theoretical Chemistry >> IIT Kanpur >> >> >> ------------------------------ >> >> -- >> Gromacs Users mailing list >> >> * Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >> posting! >> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> * For (un)subscribe requests visit >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >> send a mail to gmx-users-requ...@gromacs.org. >> >> End of gromacs.org_gmx-users Digest, Vol 133, Issue 87 >> ****************************************************** >> -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.