[gmx-users] Dividing an MD run

Fri Mar 4 16:58:11 CET 2016

Dear Justin and Jo,

Thanks a lot for your help. I have just noticed that I was typing the name of the .cpt file wrong. Now I corrected it and it works fine :)

Best regards,

Guillem

Sorry, I haven't moved on to 5.X yet. I'm old school :)

/J

On Fri, Mar 4, 2016 at 2:34 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 3/4/16 8:32 AM, Jo?o Henriques wrote:
>
>> tpbconv is the answer for an extension. Choose between -extend or -until,
>> it's up to you. I like -until, because I'm too lazy to do subtractions :)
>>
>> http://www.gromacs.org/Documentation/How-tos/Extending_Simulations
>>
>>
> Correct, though that page is a bit out of date, as tpbconv has been
> renamed convert-tpr.
>
> -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
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------------------------------

Message: 3
Date: Fri, 4 Mar 2016 16:11:01 +0100
From: leila salimi <leilasalimi at gmail.com>
To: gmx-users at gromacs.org
Subject: [gmx-users] save the trajectory
Message-ID:
        <CAFesFksDCi5=LJFoqNDVUMCd0QBOxtqdN_DEYcysG+kkrYmanA at mail.gmail.com>
Content-Type: text/plain; charset=UTF-8

Dear gmx useres,

I have a question. I am interested to have some part of trajectories that
is important for me!
For example only I like to have the trajectory when the polymer close to
the surface, not when it is in the solution!

Is there any solution to do with gromacs?

Thanks very much.
Leila

------------------------------

Message: 4
Date: Fri, 4 Mar 2016 16:28:54 +0100
From: Dries Van Rompaey <dries.vanrompaey at gmail.com>
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] save the trajectory
Message-ID:
        <CAJefogfkV=52BUGzg40T5rtrbq6bDq2QtZ9J45dnEbOWKRm+0A at mail.gmail.com>
Content-Type: text/plain; charset=UTF-8

Hi,

You could use gmx mindist with suitable index groups to find out the
distance between the surface and the polymer as a function of the time.
Then you can use trjconv with the b and e flags to get that part of the
trajectory.

Kind regards

Dries
On 4 Mar 2016 4:11 p.m., "leila salimi" <leilasalimi at gmail.com> wrote:

> Dear gmx useres,
>
> I have a question. I am interested to have some part of trajectories that
> is important for me!
> For example only I like to have the trajectory when the polymer close to
> the surface, not when it is in the solution!
>
> Is there any solution to do with gromacs?
>
> Thanks very much.
> Leila
> --
> 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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> send a mail to gmx-users-request at gromacs.org.
>

------------------------------

Message: 5
Date: Fri, 4 Mar 2016 16:32:18 +0100
From: leila salimi <leilasalimi at gmail.com>
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] save the trajectory
Message-ID:
        <CAFesFksoTxq62RJzpE33asdFzsNyOniEHGCr2H0TNoaGUdOx+w at mail.gmail.com>
Content-Type: text/plain; charset=UTF-8

Hi Dries,

Thanks. Actually I am doing like this. but it is too much.
I am thinking to find a better way!

Regards,

On Fri, Mar 4, 2016 at 4:28 PM, Dries Van Rompaey <
dries.vanrompaey at gmail.com> wrote:

> Hi,
>
> You could use gmx mindist with suitable index groups to find out the
> distance between the surface and the polymer as a function of the time.
> Then you can use trjconv with the b and e flags to get that part of the
> trajectory.
>
> Kind regards
>
> Dries
> On 4 Mar 2016 4:11 p.m., "leila salimi" <leilasalimi at gmail.com> wrote:
>
> > Dear gmx useres,
> >
> > I have a question. I am interested to have some part of trajectories that
> > is important for me!
> > For example only I like to have the trajectory when the polymer close to
> > the surface, not when it is in the solution!
> >
> > Is there any solution to do with gromacs?
> >
> > Thanks very much.
> > Leila
> > --
> > 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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------------------------------

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End of gromacs.org_gmx-users Digest, Vol 143, Issue 24
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