On 9/2/15 9:04 AM, Reisser, Sabine (IPC) wrote:
Thanks, I made them whole and tried to cluster the lipids with -pbc cluster.
However, I keep getting a Fatal error:
Molecule 1 marked for clustering but not atom 1 in it - check your index!
This happens no matter which index group I use.
Do you have any ideas what's the reason?
Does it even make sense to try to cluster these molecules? Note that not every
step on that list is needed.
-Justin
Cheers
Sabine
--
Dr. Sabine Reißer
Theoretical Chemical Biology
Institute of Physical Chemistry
Karlsruhe Institute of Technology
________________________________________
Von: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
<gromacs.org_gmx-users-boun...@maillist.sys.kth.se> im Auftrag von Justin Lemkul
<jalem...@vt.edu>
Gesendet: Mittwoch, 2. September 2015 14:13
An: gmx-us...@gromacs.org
Betreff: Re: [gmx-users] trjconv -pbc nojump
On 9/2/15 7:17 AM, Reisser, Sabine (IPC) wrote:
Thanks for the reply, but I don't want the lipids to jump from one edge of the
box to the other, which they do with this option, even though they remain
complete.
Making molecules whole should be the first step, followed by removing jumps.
http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions#Suggested_trjconv_workflow
-Justin
Cheers
Sabine
--
Dr. Sabine Reißer
Theoretical Chemical Biology
Institute of Physical Chemistry
Karlsruhe Institute of Technology
________________________________________
Von: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
<gromacs.org_gmx-users-boun...@maillist.sys.kth.se> im Auftrag von Ganesh Shahane
<ganesh7shah...@gmail.com>
Gesendet: Mittwoch, 2. September 2015 12:19
An: gmx-us...@gromacs.org
Betreff: Re: [gmx-users] trjconv -pbc nojump
Hi Reisser,
Instead of using -pbc nojump, use -pbc whole.
On Wed, Sep 2, 2015 at 2:47 PM, Reisser, Sabine (IPC) <
sabine.reis...@kit.edu> wrote:
Hi,
I want to use trjconv -pbc nojump to create a trajectory without box
jumping of molecules. The molecules (lipids) also start to diffuse out of
the box like they should, but in some a part of the molecule still jumps
(as I could observe in xy direction), while the rest doesn't, leading to
artificially long bonds in VMD. I tried trjconv -pbc nojump both with a tpr
file in the -s option, or a gro file (with only complete molecules), same
result.
I'd be glad if somebody could give me a hint.
Cheers
Sabine
--
Dr. Sabine Reißer
Theoretical Chemical Biology
Institute of Physical Chemistry
Karlsruhe Institute of Technology
--
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-requ...@gromacs.org.
--
Best Regards,
Ganesh Shahane
--
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-requ...@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
jalem...@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-requ...@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
jalem...@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-requ...@gromacs.org.
