Spitaleri Andrea wrote:
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<http://www.sanraffaele.org/grazieate>
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Hi there,
this is a very old issue for me at lest and I still get error running a remd
simulation using restraints for ion. I am using gmx4.0.7
This is my input:
; Distance restraints
disre = simple
disre_weighting = equal
disre_fc = 1000
and in topol.top
[ distance_restraints ]
; ai aj type index type' low up1 up2 fac
957 309 1 0 1 0.18 0.20 0.25 1
957 338 1 1 1 0.18 0.20 0.25 1
957 701 1 2 1 0.18 0.20 0.25 1
957 733 1 3 1 0.18 0.20 0.25 1
956 149 1 4 1 0.18 0.20 0.25 1
956 185 1 5 1 0.18 0.20 0.25 1
956 417 1 6 1 0.18 0.20 0.25 1
956 462 1 7 1 0.18 0.20 0.25 1
So all different restraints. My input run is:
#PBS -l nodes=120
mpirun mdrun_d -s remd -v -deffnm remd -multi 5 -replex 5000 -npme 8 -dd 4 4 1
and immediately I get:
Program mdrun_d, VERSION 4.0.7
Source code file: disre.c, line: 143
Fatal error:
Time or ensemble averaged or multiple pair distance restraints do not work (yet) with domain decomposition, use particle decomposition (mdrun option
-pd)
That's strange since I am not neither using time nor ensemble averages nor multiple dist restraints.
You are using ensemble averaging, which is invoked when combining "disre =
simple" and mdrun -multi, per the manual. You should be able to use mdrun -pd,
as the error message suggests.
-Justin
thansk in advance for any help
and
------------------------------------------------------------
Andrea Spitaleri PhD
Dulbecco Telethon Institute
Center of Genomics, BioInformatics and BioStatistics
c/o DIBIT Scientific Institute
Biomolecular NMR, 1B4
Via Olgettina 58
20132 Milano (Italy)
http://sites.google.com/site/andreaspitaleri/
Tel: 0039-0226434348/5622/3497/4922
Fax: 0039-0226434153
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________________________________________
Da: [email protected] [[email protected]] per conto di
XAvier Periole [[email protected]]
Inviato: giovedì 14 ottobre 2010 1.30
A: Discussion list for GROMACS users
Oggetto: Re: [gmx-users] Martini parameters for monoolein
I do not know what is the structure of monoolein :((
Then it is strongly possible that OH-C-C-OH is best represented
by the P4 particle type. But it might not be that simple :))
you should once your (first) topology made try it out and compare
to as much data you can find ... experimental and from atomistic
simulations ... that should include dynamics, structure et
thermodynamics ...
have fun,
XAvier.
On Oct 13, 2010, at 2:06 PM, George Khelashvili wrote:
Dear Xavier,
I think I have figured out how to deal with the missing part. My
problem was OH-C-C-OH construct which is the headgroup of monoolein.
After some research, it looks like that it is parameterized based on
ethanediol and has P4 type. The rest of the molecule I guess should
be straightforward CG backbone plus CG tail beads. Can you comment
on this?
Thank you,
George
On 10/13/2010 3:56 PM, XAvier Periole wrote:
Have you considered reading the few papers describing the
principle of parameterization with the Martini FF? There are basic
recipes described and specific applications detailed.
Looking at cgmartini.nl might also help you getting more
information and
reach people involved in Martini parameterization :))
XAvier.
On Oct 13, 2010, at 11:42 AM, George Khelashvili wrote:
Dear users,
I am trying to build Martini topology for monoolein molecule (I
assume that no such topology exists at this moment). It is obvious
that the tail part of the molecule is similar to DOPC lipid tail,
however I am not sure how to parametrize the head-group of
monoolein. I would appreciate if somebody could provide a guidance
on this matter.
Thank you,
George
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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