Hi Mark, Thanks.
>mdrun will generally "make molecules whole" for -c, but otherwise doesn't >care. Implementing general triclininc 3D periodicity with domain >decomposition is a messy business. I am not using a triclinic unit cell (all angles are 90 in the input .pdb file). Wouldn¹t the output also be represented in a cuboid unit cell? For this case ³making the molecule whole² is an arbitrary decision as it is an infinite substrate. Is this discrepancy something I should worry about, or is it just a question of visualisation? I am getting a warning ³xx inconsistent shifts check your topology². I can¹t spot anything obvious and I do have periodic-molecules=yes in file.mdp. Thanks! Amanda On 22/06/2017, 12:27, "gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of gromacs.org_gmx-users-requ...@maillist.sys.kth.se" <gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of 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: Simulation of Carbon nanotube (Nikhil Maroli) > 2. Re: Regarding the charge of the atom in the .rtp file > (Mark Abraham) > 3. Re: Difference between output_coordinates.gro and > trajectory.xtc coordinates (Mark Abraham) > 4. Re: Difference between output_coordinates.gro and > trajectory.xtc coordinates (Mark Abraham) > 5. Re: positive potential energy (Mark Abraham) > 6. Re: positive potential energy (Mark Abraham) > > >---------------------------------------------------------------------- > >Message: 1 >Date: Thu, 22 Jun 2017 16:29:49 +0530 >From: Nikhil Maroli <scinik...@gmail.com> >To: gromacs.org_gmx-users@maillist.sys.kth.se >Subject: Re: [gmx-users] Simulation of Carbon nanotube >Message-ID: > <camezy6syjjt2afora13b0oyp4316fwbxysx-j7nx36_6oup...@mail.gmail.com> >Content-Type: text/plain; charset="UTF-8" > >Dear Justin, >I have generated topology for CNT using gmx x2top. There is cyclic peptide >nanotube wrapped over the CNT (eight CP rings in equal intervals) >otherwise >let's say, CNT is inserted into the Cyclic peptide nanotube. I wanted to >put the whole system into the lipid bilayer. I was using charmm-gui for >the >input generator since it provides easy hand on CPN, So is it possible to >convert the CNT topology which generated with gmx x2top to 'Topology and >Parameters' for charmm-gui (*.rtf and *.prm)? >Thanks in advance. > > >------------------------------ > >Message: 2 >Date: Thu, 22 Jun 2017 11:08:45 +0000 >From: Mark Abraham <mark.j.abra...@gmail.com> >To: gmx-us...@gromacs.org >Subject: Re: [gmx-users] Regarding the charge of the atom in the .rtp > file >Message-ID: > <CAMNuMASE4vJWxXvGbXK8rS-pZaP7divm8UXjvNZQ=oxrfh_...@mail.gmail.com> >Content-Type: text/plain; charset="UTF-8" > >Hi, > >I don't understand what you are asking. How does it relate to >parameterization methodology? > >Mark > >On Thu, Jun 22, 2017 at 7:20 AM Dilip H N <cy16f01.di...@nitk.edu.in> >wrote: > >> Thank you for reply.. >> >> But how can i identify the molecule as methylamine (for example) since >>in >> the .rtp the molecule type is written as [MAM1] >> [ MAM1 ] >> [ atoms ] >> N1 NG321 -0.990 0 >> C1 CG3AM2 -0.060 1 >> HN1 HGPAM2 0.390 2 >> HN2 HGPAM2 0.390 3 >> HC1 HGAAM2 0.090 4 >> HC2 HGAAM2 0.090 5 >> HC3 HGAAM2 0.090 6 >> [ bonds ] >> N1 C1 >> N1 HN1 >> N1 HN2 >> C1 HC1 >> C1 HC2 >> C1 HC3 >> Is thr any hint such tht i can identify the molecule type written in >>.rtp >> file.?? >> Or should i manually find it out..??... but in case of Glycine the >>molecule >> type is [GLY] which is easy to find.... >> How can i solve this issue..?? >> >> Thank you... >> >> >> >> <https://mailtrack.io/> Sent with Mailtrack >> < >> >>https://mailtrack.io/install?source=signature&lang=en&referral=cy16f01.di >>l...@nitk.edu.in&idSignature=22 >> > >> >> On Wed, Jun 21, 2017 at 4:23 PM, Mark Abraham <mark.j.abra...@gmail.com> >> wrote: >> >> > Hi, >> > >> > On Wed, Jun 21, 2017 at 11:59 AM Dilip H N <cy16f01.di...@nitk.edu.in> >> > wrote: >> > >> > > Hello all. >> > > 1] I want to knw how the charges are designated/assigned for the >>each >> > atoms >> > > in molecule in the .rtp file. ie., as example for methylamine in >> CHARMM >> > > FF:- >> > > >> > > [ MAM1 ] >> > > [ atoms ] >> > > N1 NG321 -0.990 0 >> > > C1 CG3AM2 -0.060 1 >> > > HN1 HGPAM2 0.390 2 >> > > HN2 HGPAM2 0.390 3 >> > > HC1 HGAAM2 0.090 4 >> > > HC2 HGAAM2 0.090 5 >> > > HC3 HGAAM2 0.090 6 >> > > [ bonds ] >> > > N1 C1 >> > > N1 HN1 >> > > N1 HN2 >> > > C1 HC1 >> > > C1 HC2 >> > > C1 HC3 >> > > ie how are the charges -0.990, -0.060, 0.390 etc., are assigned... >> > > >> > >> > The parameterization methodology is unique to each force field, and >> perhaps >> > to each tool that generates compatible topologies. You need to read >>that >> > documentation and literature to understand how they were derived. >> > >> > >> > > 2] and if i get the topology/itp file from the automated topology >> builder >> > > as in SwissParam for CHARMM forcefield, how can i confirm that the >> > charges >> > > assigned are exact..?? >> > > >> > >> > You can see if they are correct in the sense of being a valid model of >> > reality by running a simulation and observing whether you can get >> > reasonable agreement with suitable e.g. experimental data. >> > >> > Mark >> > >> > >> > > Any help/suggestion is most welcome. >> > > Thank you... >> > > -- >> > > With Best Regards, >> > > >> > > DILIP.H.N >> > > Ph.D Student >> > > >> > > >> > > >> > > <https://mailtrack.io/> Sent with Mailtrack >> > > < >> > > https://mailtrack.io/install?source=signature&lang=en& >> > referral=cy16f01.di...@nitk.edu.in&idSignature=22 >> > > > >> > > -- >> > > 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. >> > >> >> >> >> -- >> With Best Regards, >> >> DILIP.H.N >> Ph.D Student >> -- >> 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: 3 >Date: Thu, 22 Jun 2017 11:25:56 +0000 >From: Mark Abraham <mark.j.abra...@gmail.com> >To: gmx-us...@gromacs.org, "gromacs.org_gmx-users@maillist.sys.kth.se" > <gromacs.org_gmx-users@maillist.sys.kth.se> >Subject: Re: [gmx-users] Difference between output_coordinates.gro and > trajectory.xtc coordinates >Message-ID: > <CAMNuMAS=XsFO4UjYREDBV=ocgyhq5n+ebkm1xj1+apoqe1z...@mail.gmail.com> >Content-Type: text/plain; charset="UTF-8" > >Hi, > >On Thu, Jun 22, 2017 at 11:05 AM Diez Fernandez, Amanda < >amanda.die...@imperial.ac.uk> wrote: > >> Hi Mark, >> Thank you for your reply. >> >> It is exactly the opposite though: > > >OK, I understood the images the other way around, without titles. > > >> for output_coordinates.gro which is the >> output from: >> >> mdrun ? -c output_coordinates.gro >> >> it seems like atoms are diffusing out of the box. >> > >They're just in whichever representation was convenient for mdrun, which >as >I said is not intended to be the same as the output of any of the things >you might do with trjconv. > >In the trajectory, I allow atoms to be seen to diffuse out of the box, >> using -pbc nojump, and I don?t see them diffuse out (They stay within >>the >> unit cell, which is what I expect being a silica substrate at room >> temperature over a very short period of time). >> > >Sure. > > >> So what puzzles me is why for the output of (mdrun -c) the atoms seem to >> diffuse out, specially so if I cannot see this in the trajectory. >> > >mdrun will generally "make molecules whole" for -c, but otherwise doesn't >care. Implementing general triclininc 3D periodicity with domain >decomposition is a messy business. If you've written the final frame to >the >trajectory, you can use trjconv to make the two outputs have the same >representation, but they still might be different by a translation. > >Mark > >Sorry if I didn?t explain it very clearly last time. >> >> Thanks! >> >> > > >------------------------------ > >Message: 4 >Date: Thu, 22 Jun 2017 11:25:56 +0000 >From: Mark Abraham <mark.j.abra...@gmail.com> >To: gmx-us...@gromacs.org, "gromacs.org_gmx-users@maillist.sys.kth.se" > <gromacs.org_gmx-users@maillist.sys.kth.se> >Subject: Re: [gmx-users] Difference between output_coordinates.gro and > trajectory.xtc coordinates >Message-ID: > <CAMNuMAS=XsFO4UjYREDBV=ocgyhq5n+ebkm1xj1+apoqe1z...@mail.gmail.com> >Content-Type: text/plain; charset="UTF-8" > >Hi, > >On Thu, Jun 22, 2017 at 11:05 AM Diez Fernandez, Amanda < >amanda.die...@imperial.ac.uk> wrote: > >> Hi Mark, >> Thank you for your reply. >> >> It is exactly the opposite though: > > >OK, I understood the images the other way around, without titles. > > >> for output_coordinates.gro which is the >> output from: >> >> mdrun ? -c output_coordinates.gro >> >> it seems like atoms are diffusing out of the box. >> > >They're just in whichever representation was convenient for mdrun, which >as >I said is not intended to be the same as the output of any of the things >you might do with trjconv. > >In the trajectory, I allow atoms to be seen to diffuse out of the box, >> using -pbc nojump, and I don?t see them diffuse out (They stay within >>the >> unit cell, which is what I expect being a silica substrate at room >> temperature over a very short period of time). >> > >Sure. > > >> So what puzzles me is why for the output of (mdrun -c) the atoms seem to >> diffuse out, specially so if I cannot see this in the trajectory. >> > >mdrun will generally "make molecules whole" for -c, but otherwise doesn't >care. Implementing general triclininc 3D periodicity with domain >decomposition is a messy business. If you've written the final frame to >the >trajectory, you can use trjconv to make the two outputs have the same >representation, but they still might be different by a translation. > >Mark > >Sorry if I didn?t explain it very clearly last time. >> >> Thanks! >> >> > > >------------------------------ > >Message: 5 >Date: Thu, 22 Jun 2017 11:27:27 +0000 >From: Mark Abraham <mark.j.abra...@gmail.com> >To: gmx-us...@gromacs.org, gromacs.org_gmx-users@maillist.sys.kth.se >Subject: Re: [gmx-users] positive potential energy >Message-ID: > <CAMNuMASeubYXo2cq8h5BeAmdupO4HUgUNwiDrJ0=qref_bs...@mail.gmail.com> >Content-Type: text/plain; charset="UTF-8" > >Hi, > >On Thu, Jun 22, 2017 at 11:30 AM Emran Heshmati <compbi...@gmail.com> >wrote: > >> Hi all >> I run two simulations on a 16 aa peptide under the same conditions >> (forcefield, simulation duration, ...) except the solvent in one of >> the simulations was TFE instead of water. The potential energy in the >>TFE >> containing system was positive (about 140000 Kj/mol), while in water >> containing system was negative (about -70000 Kj/mol). Is it normal? or >>some >> kind of error has occurred? >> > >Seems normal. Models are typically not parameterized to have meaningful >total energies (but the differences and gradients are useful). > >Mark > > >> -- >> 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: 6 >Date: Thu, 22 Jun 2017 11:27:27 +0000 >From: Mark Abraham <mark.j.abra...@gmail.com> >To: gmx-us...@gromacs.org, gromacs.org_gmx-users@maillist.sys.kth.se >Subject: Re: [gmx-users] positive potential energy >Message-ID: > <CAMNuMASeubYXo2cq8h5BeAmdupO4HUgUNwiDrJ0=qref_bs...@mail.gmail.com> >Content-Type: text/plain; charset="UTF-8" > >Hi, > >On Thu, Jun 22, 2017 at 11:30 AM Emran Heshmati <compbi...@gmail.com> >wrote: > >> Hi all >> I run two simulations on a 16 aa peptide under the same conditions >> (forcefield, simulation duration, ...) except the solvent in one of >> the simulations was TFE instead of water. The potential energy in the >>TFE >> containing system was positive (about 140000 Kj/mol), while in water >> containing system was negative (about -70000 Kj/mol). Is it normal? or >>some >> kind of error has occurred? >> > >Seems normal. Models are typically not parameterized to have meaningful >total energies (but the differences and gradients are useful). > >Mark > > >> -- >> 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. > >End of gromacs.org_gmx-users Digest, Vol 158, Issue 141 >******************************************************* -- 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.