[gmx-users] Difference between output_coordinates.gro and trajectory.xtc coordinates
Mark Abraham
mark.j.abraham at gmail.com
Thu Jun 22 16:03:22 CEST 2017
Hi,
On Thu, Jun 22, 2017 at 3:57 PM Diez Fernandez, Amanda <
amanda.diez10 at 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-bounces at maillist.sys.kth.se
> on behalf of gromacs.org_gmx-users-request at maillist.sys.kth.se"
> <gromacs.org_gmx-users-bounces at maillist.sys.kth.se on behalf of
> gromacs.org_gmx-users-request at maillist.sys.kth.se> wrote:
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> >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 <scinikhil at gmail.com>
> >To: gromacs.org_gmx-users at maillist.sys.kth.se
> >Subject: Re: [gmx-users] Simulation of Carbon nanotube
> >Message-ID:
> > <
> CAMEzy6SYjJt2AfOrA13b0oyP4316fWbxySx-J7NX36_6ouPuew at 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.abraham at gmail.com>
> >To: gmx-users at gromacs.org
> >Subject: Re: [gmx-users] Regarding the charge of the atom in the .rtp
> > file
> >Message-ID:
> > <CAMNuMASE4vJWxXvGbXK8rS-pZaP7divm8UXjvNZQ=
> OXRfH_TSA at 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.dilip at 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
> >>lip at nitk.edu.in&idSignature=22
> >> >
> >>
> >> On Wed, Jun 21, 2017 at 4:23 PM, Mark Abraham <mark.j.abraham at gmail.com
> >
> >> wrote:
> >>
> >> > Hi,
> >> >
> >> > On Wed, Jun 21, 2017 at 11:59 AM Dilip H N <cy16f01.dilip at 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.dilip at 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-request at gromacs.org.
> >> > >
> >> > --
> >> > Gromacs Users mailing list
> >> >
> >> > * Please search the archive at http://www.gromacs.org/
> >> > Support/Mailing_Lists/GMX-Users_List before posting!
> >> >
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> >> > send a mail to gmx-users-request at 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
> >>
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> >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> >> send a mail to gmx-users-request at gromacs.org.
> >>
> >
> >
> >------------------------------
> >
> >Message: 3
> >Date: Thu, 22 Jun 2017 11:25:56 +0000
> >From: Mark Abraham <mark.j.abraham at gmail.com>
> >To: gmx-users at gromacs.org, "gromacs.org_gmx-users at maillist.sys.kth.se"
> > <gromacs.org_gmx-users at maillist.sys.kth.se>
> >Subject: Re: [gmx-users] Difference between output_coordinates.gro and
> > trajectory.xtc coordinates
> >Message-ID:
> > <CAMNuMAS=XsFO4UjYREDBV=
> OcGYHq5N+EbKm1xJ1+aPoQE1zQpg at mail.gmail.com>
> >Content-Type: text/plain; charset="UTF-8"
> >
> >Hi,
> >
> >On Thu, Jun 22, 2017 at 11:05 AM Diez Fernandez, Amanda <
> >amanda.diez10 at 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.abraham at gmail.com>
> >To: gmx-users at gromacs.org, "gromacs.org_gmx-users at maillist.sys.kth.se"
> > <gromacs.org_gmx-users at maillist.sys.kth.se>
> >Subject: Re: [gmx-users] Difference between output_coordinates.gro and
> > trajectory.xtc coordinates
> >Message-ID:
> > <CAMNuMAS=XsFO4UjYREDBV=
> OcGYHq5N+EbKm1xJ1+aPoQE1zQpg at mail.gmail.com>
> >Content-Type: text/plain; charset="UTF-8"
> >
> >Hi,
> >
> >On Thu, Jun 22, 2017 at 11:05 AM Diez Fernandez, Amanda <
> >amanda.diez10 at 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.abraham at gmail.com>
> >To: gmx-users at gromacs.org, gromacs.org_gmx-users at maillist.sys.kth.se
> >Subject: Re: [gmx-users] positive potential energy
> >Message-ID:
> > <CAMNuMASeubYXo2cq8h5BeAmdupO4HUgUNwiDrJ0=
> QrEf_Bstmg at mail.gmail.com>
> >Content-Type: text/plain; charset="UTF-8"
> >
> >Hi,
> >
> >On Thu, Jun 22, 2017 at 11:30 AM Emran Heshmati <compbioph at 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-request at gromacs.org.
> >>
> >
> >
> >------------------------------
> >
> >Message: 6
> >Date: Thu, 22 Jun 2017 11:27:27 +0000
> >From: Mark Abraham <mark.j.abraham at gmail.com>
> >To: gmx-users at gromacs.org, gromacs.org_gmx-users at maillist.sys.kth.se
> >Subject: Re: [gmx-users] positive potential energy
> >Message-ID:
> > <CAMNuMASeubYXo2cq8h5BeAmdupO4HUgUNwiDrJ0=
> QrEf_Bstmg at mail.gmail.com>
> >Content-Type: text/plain; charset="UTF-8"
> >
> >Hi,
> >
> >On Thu, Jun 22, 2017 at 11:30 AM Emran Heshmati <compbioph at 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-request at gromacs.org.
> >>
> >
> >
> >------------------------------
> >
> >--
> >Gromacs Users mailing list
> >
> >* Please search the archive at
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> >posting!
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> >End of gromacs.org_gmx-users Digest, Vol 158, Issue 141
> >*******************************************************
>
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