[gmx-users] Difference between output_coordinates.gro and trajectory.xtc coordinates
Diez Fernandez, Amanda
amanda.diez10 at imperial.ac.uk
Thu Jun 22 11:04:07 CEST 2017
Hi Mark,
Thank you for your reply.
It is exactly the opposite though: for output_coordinates.gro which is the
output from:
mdrun Š -c output_coordinates.gro
it seems like atoms are diffusing out of the box.
In the trajectory, I allow atoms to be seen to diffuse out of the box,
using -pbc nojump, and I don¹t 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).
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.
Sorry if I didn¹t explain it very clearly last time.
Thanks!
On 22/06/2017, 06:18, "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: Difference between output_coordinates.gro and
> trajectory.xtc coordinates (Mark Abraham)
> 2. Re: (no subject) (Mark Abraham)
> 3. Re: puzzled by unexpected [ bonds ] section resulting from
> running gmx x2top (Jose Borreguero)
> 4. Re: GROMACS and SIMtoEXP (Sanim Rahman)
> 5. Re: Regarding the charge of the atom in the .rtp file (Dilip H N)
>
>
>----------------------------------------------------------------------
>
>Message: 1
>Date: Wed, 21 Jun 2017 17:29:53 +0000
>From: Mark Abraham <mark.j.abraham at gmail.com>
>To: gmx-users at gromacs.org
>Subject: Re: [gmx-users] Difference between output_coordinates.gro and
> trajectory.xtc coordinates
>Message-ID:
> <CAMNuMARKS3OGwR-gbHt9GotMwbUrCobrbkJc1ES+OY-c2EPSzQ at mail.gmail.com>
>Content-Type: text/plain; charset="UTF-8"
>
>Hi,
>
>On Wed, Jun 21, 2017 at 6:49 PM Diez Fernandez, Amanda <
>amanda.diez10 at imperial.ac.uk> wrote:
>
>> Hi Justin,
>> Thank you for your reply.
>>
>> Here are the links to the images of:
>> -the output coordinates
>> -and last frame of trajectory.
>>
>> Output coordinates which look wrong:
>>
>>http://i1036.photobucket.com/albums/a443/amanda222lld/output_coordinates_
>>zp
>> stuqkgjd2.png
>>
>><http://i1036.photobucket.com/albums/a443/amanda222lld/output_coordinates
>>_zpstuqkgjd2.png>
>>
>> Last frame from trajectory which looks OK:
>>
>>http://i1036.photobucket.com/albums/a443/amanda222lld/last_frame_traj_zps
>>n2
>> 7nzusn.png
>>
>><http://i1036.photobucket.com/albums/a443/amanda222lld/last_frame_traj_zp
>>sn27nzusn.png>
>>
>> For the last frame of the trajectory I used trjconv -pbc nojump to make
>> sure the atoms were not being wrapped around the box.
>
>
>That's what you're getting. See "gmx help trjconv" where it specifically
>says that "-pbc nojump" will lead to atoms appearing to diffuse out of the
>box.
>
>It seems like you want trjconv -pbc atom, so all the atoms are in the same
>box. That won't necessarily match what mdrun -c writes, either, because
>that is not something for which we have designed. There's an infinite
>number of equivalent representations of any system, and a large number of
>plausible representations that someone might want to use for different
>purposes, so we've left the choice to you, with the tools and
>documentation
>to get something that makes you happy :-)
>
>Mark
>
>
>------------------------------
>
>Message: 2
>Date: Wed, 21 Jun 2017 17:35:04 +0000
>From: Mark Abraham <mark.j.abraham at gmail.com>
>To: gmx-users at gromacs.org
>Subject: Re: [gmx-users] (no subject)
>Message-ID:
> <CAMNuMAQMHqcKtT0U_nBka6LKS+jSA53UDgPVmTpvc_QcvuC5Ng at mail.gmail.com>
>Content-Type: text/plain; charset="UTF-8"
>
>Hi,
>
>On Wed, Jun 21, 2017 at 4:32 PM Shivangi Agarwal <
>shivangi.agarwal800 at gmail.com> wrote:
>
>> Hi
>> But it is broken. ..
>>
>
>Nope, it's just in one of the infinite number of equivalent
>representations
>of the same thing ;-) mdrun doesn't know that you want it to write a file
>where your protein and ligand and whatever strand are a cluster of things
>that you'd like it to render centered in the same periodic cell. That's
>what e.g. gmx trjconv -pbc cluster is useful for.
>
>strand with proline with three odr residues has been broken and visible...
>> i have Checked in vmd and pymol
>>
>
>Doesn't matter until you've said to a program "keep these things together"
>:-)
>
>Mark
>
>
>> On 21 Jun 2017 17:16, "Mark Abraham" <mark.j.abraham at gmail.com> wrote:
>>
>> > Hi,
>> >
>> > On Wed, Jun 21, 2017 at 1:21 PM Shivangi Agarwal <
>> > shivangi.agarwal800 at gmail.com> wrote:
>> >
>> > > Hello to all gmx users
>> > >
>> > > I am performing protein ligand complex MD simulation but my protein
>> > > structure has been broken during energy minimization process.
>> > >
>> >
>> > It's not broken, but rather in an unexpected representation. See
>> > http://www.gromacs.org/Documentation/Terminology/
>> > Periodic_Boundary_Conditions
>> > for
>> > background and suggestions.
>> >
>> > Mark
>> >
>> >
>> > > What may be the suitable reason? How I can solve this?
>> > > Your support is highly appreciated
>> > > --
>> > > 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.
>> >
>> --
>> 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: Wed, 21 Jun 2017 15:04:56 -0400
>From: Jose Borreguero <borreguero at gmail.com>
>To: gmx-users at gromacs.org
>Subject: Re: [gmx-users] puzzled by unexpected [ bonds ] section
> resulting from running gmx x2top
>Message-ID:
> <CAEee4gXKarkgv+XeQBmxx+axvPNTStZUKC4GbPnMrE4qpFLgTw at mail.gmail.com>
>Content-Type: text/plain; charset="UTF-8"
>
>Victory! The -noparam did the trick :)
>Thanks a million.
>
>On Wed, Jun 21, 2017 at 11:43 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>>
>> On 6/21/17 11:39 AM, Jose Borreguero wrote:
>>
>>> Hi Justin,
>>>
>>> ?Thanks for your quick reply! ?
>>> This means x2top is not finding
>>> ?
>>> or using
>>> the right force constant value, right?
>>> ? I
>>>
>>> ?
>>> did
>>> add the bond info into file ffbonded.itp
>>> ?of
>>> the oplsa.ff/ directory
>>> ?
>>> (https://goo.gl/z5UMot)
>>> .
>>> I also included the types in file
>>> atomtypes.atp
>>> ?
>>> and the non bonded info in
>>> ffnonbonded.itp file. Maybe related to this issue is this line also
>>>found
>>> in the output .top file:
>>> ? ?
>>> #include "
>>> ??
>>> ./oplsaa.ff/forcefield.itp"
>>> This line should not be necessary because the .top? file contains all
>>> information. Does the line mean that the bond information in the output
>>> .top file is overridden with that gmx later finds under
>>> ?
>>> ./oplsaa.ff
>>> ??
>>> ? If so, then the particular value of the force constant in the .top
>>>file
>>> would be irrelevant and my problem would be solved! :)
>>>
>>>
>> Any value found in the .top overrides the force field. Any blank in the
>> topology is referenced from ffbonded.itp. Anything missing after that
>> generates a fatal error in grompp. Use -noparam when running x2top if
>> everything is accounted for in the force field parameter files.
>>
>>
>> -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
>>
>> jalemkul at 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-request at gromacs.org.
>>
>
>
>------------------------------
>
>Message: 4
>Date: Wed, 21 Jun 2017 22:18:17 -0400
>From: Sanim Rahman <sanimr at mail.usf.edu>
>To: gmx-users at gromacs.org
>Subject: Re: [gmx-users] GROMACS and SIMtoEXP
>Message-ID:
> <CAJ4iXqZep_TWhLOm8SuE5SvFBcco6AnsF1p2R+R7EHdVEJPjSQ at mail.gmail.com>
>Content-Type: text/plain; charset="UTF-8"
>
>Thank you David,
>
>I realized my mistake and I need to be using number density when working
>with SIMtoEXP however, I was wondering if there is some script out there
>to
>easily convert my number density from gromacs to the compatible file
>format
>for SIMtoEXP.
>
>Regards,
>Sanim Rahman
>
>On Wed, Jun 21, 2017 at 2:02 AM, David van der Spoel
><spoel at xray.bmc.uu.se>
>wrote:
>
>> On 20/06/17 23:16, Sanim Rahman wrote:
>>
>>> Hello Everyone,
>>>
>>> I am interested in using the SIMtoEXP program to directly compare my
>>> simulation results to experimental values. The program only can process
>>> electron density profiles written as .dat and .sim files.
>>>
>>> Is anyone aware of scripts or GROMACS options that will allow me to
>>>output
>>> my electron density profile into a .dat or .sim file that can be
>>>processed
>>> by SIMtoEXP?
>>>
>>> Regards,
>>> Sanim Rahman
>>>
>>> You have the wrong program if you need electron densities.
>>
>> --
>> David van der Spoel, Ph.D., Professor of Biology
>> Head of Department, Cell & Molecular Biology, Uppsala University.
>> Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
>> http://www.icm.uu.se
>> --
>> 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: 5
>Date: Thu, 22 Jun 2017 10:48:25 +0530
>From: Dilip H N <cy16f01.dilip at nitk.edu.in>
>To: gmx-users at gromacs.org
>Subject: Re: [gmx-users] Regarding the charge of the atom in the .rtp
> file
>Message-ID:
> <CAD6GXy2vTkrSMcnU5PLWgFSYVpbdfOygKdUf8AWWGeWqa86nmA at mail.gmail.com>
>Content-Type: text/plain; charset="UTF-8"
>
>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.
>
>End of gromacs.org_gmx-users Digest, Vol 158, Issue 138
>*******************************************************
More information about the gromacs.org_gmx-users
mailing list