[gmx-users] Difference between output_coordinates.gro and trajectory.xtc coordinates
Diez Fernandez, Amanda
amanda.diez10 at imperial.ac.uk
Wed Jun 21 18:48:43 CEST 2017
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
Last frame from trajectory which looks OK:
http://i1036.photobucket.com/albums/a443/amanda222lld/last_frame_traj_zpsn2
7nzusn.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.
I am simulating an infinite silica slab, using a 4nm by 4nm unit cell.
Thanks!
Amanda
On 21/06/2017, 15:46, "gromacs.org_gmx-users-bounces at maillist.sys.kth.se
on behalf of gromacs.org_gmx-users-request at maillist.sys.kth.se"
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>Today's Topics:
>
> 1. Re: (no subject) (Shivangi Agarwal)
> 2. Genion (Sergio Manzetti)
> 3. Re: non-bonded sigma for amino nitrogen?carboxylate oxygen
> interactions in OPLSAA in GROMACS (gozde ergin)
> 4. Re: Difference between output_coordinates.gro and
> trajectory.xtc coordinates (Justin Lemkul)
> 5. Re: Genion (Justin Lemkul)
> 6. Re: non-bonded sigma for amino nitrogen?carboxylate oxygen
> interactions in OPLSAA in GROMACS (Justin Lemkul)
>
>
>----------------------------------------------------------------------
>
>Message: 1
>Date: Wed, 21 Jun 2017 20:02:01 +0530
>From: Shivangi Agarwal <shivangi.agarwal800 at gmail.com>
>To: gmx-users at gromacs.org
>Subject: Re: [gmx-users] (no subject)
>Message-ID:
> <CA+FragisNxhLM2X2JBzu-+GOVky=mbSsqgChPLQ99h8JoDgFwA at mail.gmail.com>
>Content-Type: text/plain; charset="UTF-8"
>
>Hi
>But it is broken. ..
>strand with proline with three odr residues has been broken and visible...
>i have Checked in vmd and pymol
>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!
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>
>
>------------------------------
>
>Message: 2
>Date: Wed, 21 Jun 2017 16:30:01 +0200 (CEST)
>From: Sergio Manzetti <sergio.manzetti at fjordforsk.no>
>To: gmx-users <gmx-users at gromacs.org>
>Subject: [gmx-users] Genion
>Message-ID:
> <1713198892.5603815.1498055401007.JavaMail.zimbra at fjordforsk.no>
>Content-Type: text/plain; charset=utf-8
>
>Hello, genion worked, and grompp was used to run the output conf from
>genion. Mdrun minimized all OK, however, mdrun produced a counfout.gro
>file that no longer contains the Na Cl ions added to the system. When
>setting up the simulation, the input confout.gro has no Na Cl ions, and
>the procedure is therefore not working.
>
>Why is this so? Does one have to do the genion procedure each time one
>wants to use gromp with a new mdp file?
>
>Sergio Manzetti
>
>[ http://www.fjordforsk.no/logo_hr2.jpg ]
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>
>------------------------------
>
>Message: 3
>Date: Wed, 21 Jun 2017 16:39:40 +0200
>From: gozde ergin <gozdeeergin at gmail.com>
>To: gmx-users at gromacs.org
>Subject: Re: [gmx-users] non-bonded sigma for amino
> nitrogen?carboxylate oxygen interactions in OPLSAA in GROMACS
>Message-ID: <03F1D960-7F47-4921-90DE-CBFEEFB322DD at gmail.com>
>Content-Type: text/plain; charset=utf-8
>
>Hi MArk,
>
>Thanks for the respond. I understood that point however I still do not
>get which sigma to change.
>I the paper JCTC 2017, Miller et. al. they have mentioned that they
>increase the for nitrogen?carboxylate oxygen interactions in OPLSAA.
>However there are two sigma in oplsaa.ff/ffnonbonded.itp one for amino
>notrogen and one for carboxylate oxygen.
>
>
> sigma epsilon
> opls_287 N3 7 14.00670 -0.300 A 3.25000e-01 7.11280e-01
> opls_272 O2 8 15.99940 -0.800 A 2.96000e-01 8.78640e-01
>
>Which one defines the amino nitrogen?carboxylate oxygen interactions?
>Which sigma should I change?
>
>Thanks
>> On 21 Jun 2017, at 16:21, Mark Abraham <mark.j.abraham at gmail.com> wrote:
>>
>> Hi,
>>
>> Different force fields work differently and thus are implemented
>> differently. Look at oplsaa.ff/ffnonbonded.itp and you will see that
>>sigma
>> is a property of the atomtype
>>
>> Mark
>>
>> On Wed, Jun 21, 2017 at 4:16 PM gozde ergin <gozdeeergin at gmail.com>
>>wrote:
>>
>>> Dear users,
>>>
>>> I am trying to change the sigma value of amino nitrogen?carboxylate
>>>oxygen
>>> interactions in OPLSAA in GROMACS.
>>> However I have difficulties to understand which parameter i should
>>>change
>>> in ffnonbonded.itp file?
>>> I am looking something like [ nonbond_params ] section however it is
>>>not
>>> exist in ffnonbonded.itp?
>>> Any help would be appreciated.
>>>
>>> Thanks in advance.
>>> --
>>> 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.
>> --
>> 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.
>
>
>
>------------------------------
>
>Message: 4
>Date: Wed, 21 Jun 2017 10:42:42 -0400
>From: Justin Lemkul <jalemkul at vt.edu>
>To: gmx-users at gromacs.org
>Subject: Re: [gmx-users] Difference between output_coordinates.gro and
> trajectory.xtc coordinates
>Message-ID: <563e25e1-a01a-ad3b-94c6-6d0962acd7c3 at vt.edu>
>Content-Type: text/plain; charset=windows-1252; format=flowed
>
>
>
>On 6/21/17 7:11 AM, Diez Fernandez, Amanda wrote:
>> Hi all,
>> I am running a simulation and I find that the output coordinates of the
>>simulation stored in ?final_coordinates.gro? are distinctively different
>>to any of the frames from ?trajectory.gro? which I obtain from :
>>
>> trjconv ?s file.tpr ?f trajectory.xtc ?o trajectory.gro
>>
>> When I visualise final_coordinates.gro they look wrong, when I
>>visualise trajectory.gro frame by frame it looks correct.
>>
>> How can this be possible? Is it a common problem?
>>
>
>Please define what "wrong" and "correct" mean. The raw trajectory from
>mdrun
>does not have PBC-corrected frames, so things may be broken. If you're
>done
>reimaging with trjconv, you've changed the representation. You can dump
>the
>final coordinates from the .xtc, make molecules whole, and these should
>match
>the final configuration written by mdrun.
>
>-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
>
>==================================================
>
>
>------------------------------
>
>Message: 5
>Date: Wed, 21 Jun 2017 10:44:16 -0400
>From: Justin Lemkul <jalemkul at vt.edu>
>To: gmx-users at gromacs.org
>Subject: Re: [gmx-users] Genion
>Message-ID: <bd985218-fc7e-c85d-4b8a-88c68855a756 at vt.edu>
>Content-Type: text/plain; charset=utf-8; format=flowed
>
>
>
>On 6/21/17 10:30 AM, Sergio Manzetti wrote:
>> Hello, genion worked, and grompp was used to run the output conf from
>>genion. Mdrun minimized all OK, however, mdrun produced a counfout.gro
>>file that no longer contains the Na Cl ions added to the system. When
>>setting up the simulation, the input confout.gro has no Na Cl ions, and
>>the procedure is therefore not working.
>>
>> Why is this so? Does one have to do the genion procedure each time one
>>wants to use gromp with a new mdp file?
>>
>
>You run genion once to add ions to your system. Please provide the exact
>sequence of commands you're using. It's very hard to follow what you're
>describing. mdrun cannot delete anything, so "no longer contains the Na
>Cl
>ions" is impossible. Either the ions are there in the beginning or
>they're not.
> If you're using mdrun to run the .tpr file you're sending to genion,
>don't.
>There's no point. That .tpr file is not for a simulation, it's just for
>genion.
>
>-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
>
>==================================================
>
>
>------------------------------
>
>Message: 6
>Date: Wed, 21 Jun 2017 10:46:05 -0400
>From: Justin Lemkul <jalemkul at vt.edu>
>To: gmx-users at gromacs.org
>Subject: Re: [gmx-users] non-bonded sigma for amino
> nitrogen?carboxylate oxygen interactions in OPLSAA in GROMACS
>Message-ID: <199502bc-3645-c0f8-59dc-0a5839650029 at vt.edu>
>Content-Type: text/plain; charset=utf-8; format=flowed
>
>
>
>On 6/21/17 10:39 AM, gozde ergin wrote:
>> Hi MArk,
>>
>> Thanks for the respond. I understood that point however I still do not
>>get which sigma to change.
>> I the paper JCTC 2017, Miller et. al. they have mentioned that they
>>increase the for nitrogen?carboxylate oxygen interactions in OPLSAA.
>> However there are two sigma in oplsaa.ff/ffnonbonded.itp one for amino
>>notrogen and one for carboxylate oxygen.
>>
>>
>> sigma epsilon
>> opls_287 N3 7 14.00670 -0.300 A 3.25000e-01
>>7.11280e-01
>> opls_272 O2 8 15.99940 -0.800 A 2.96000e-01
>>8.78640e-01
>>
>> Which one defines the amino nitrogen?carboxylate oxygen interactions?
>> Which sigma should I change?
>>
>
>What people are doing more and more is introducing pair-specific
>parameters to
>override the combination rule values. That's likely what is being
>referred to.
>OPLS-AA by default does not use pair-specific LJ interactions, hence why
>you
>find no [nonbond_params] in ffnonbonded.itp. The same is true of AMBER.
>CHARMM
>uses some (also called NBFIX in the literature), while GROMOS uses a ton
>of these.
>
>To override the LJ combination rules, add a [nonbond_params] directive
>with the
>published parameters, which refer to an *interaction*, not an atom type.
>
>-Justin
>
>> Thanks
>>> On 21 Jun 2017, at 16:21, Mark Abraham <mark.j.abraham at gmail.com>
>>>wrote:
>>>
>>> Hi,
>>>
>>> Different force fields work differently and thus are implemented
>>> differently. Look at oplsaa.ff/ffnonbonded.itp and you will see that
>>>sigma
>>> is a property of the atomtype
>>>
>>> Mark
>>>
>>> On Wed, Jun 21, 2017 at 4:16 PM gozde ergin <gozdeeergin at gmail.com>
>>>wrote:
>>>
>>>> Dear users,
>>>>
>>>> I am trying to change the sigma value of amino nitrogen?carboxylate
>>>>oxygen
>>>> interactions in OPLSAA in GROMACS.
>>>> However I have difficulties to understand which parameter i should
>>>>change
>>>> in ffnonbonded.itp file?
>>>> I am looking something like [ nonbond_params ] section however it is
>>>>not
>>>> exist in ffnonbonded.itp?
>>>> Any help would be appreciated.
>>>>
>>>> Thanks in advance.
>>>> --
>>>> 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.
>>
>
>--
>==================================================
>
>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
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