Hi, On Thu, Jun 22, 2017 at 3:57 PM Diez Fernandez, Amanda < amanda.die...@imperial.ac.uk> wrote:
> 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? > In this case, sure. I was merely illustrating why the code is complex and doesn't necessarily work the way people assume. > For this case ³making the molecule whole² is an arbitrary decision as it > is an infinite substrate. > Sure, hence "generally" Is this discrepancy something I should worry about, or is it just a > question of visualisation? > There's no discrepancy. Which equivalent representation to use is arbitrary. 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. > I don't know what that means or how it should work. Very little testing of that code takes place. Mark > 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. > -- 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.