[gmx-users] Difference between output_coordinates.gro and trajectory.xtc coordinates

Diez Fernandez, Amanda amanda.diez10 at imperial.ac.uk
Thu Jun 22 15:56:50 CEST 2017


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-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:

>Send gromacs.org_gmx-users mailing list submissions to
>	gromacs.org_gmx-users at 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-request at maillist.sys.kth.se
>
>You can reach the person managing the list at
>	gromacs.org_gmx-users-owner at 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 <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!
>> >
>> > * 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.
>> >
>>
>>
>>
>> --
>> 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-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
>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.
>
>End of gromacs.org_gmx-users Digest, Vol 158, Issue 141
>*******************************************************



More information about the gromacs.org_gmx-users mailing list