[gmx-users] remd with disre in gmx4.0.7

Justin A. Lemkul jalemkul at vt.edu
Thu Oct 14 03:09:42 CEST 2010 


Spitaleri Andrea wrote:
> 
> ------------------------------------------------------------------------
> <http://www.sanraffaele.org/grazieate>
> ------------------------------------------------------------------------
> 
> ------------------------------------------------------------------------
> 
> 
> 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
> ------------------------------------------------------------
> ________________________________________
> Da: gmx-users-bounces at gromacs.org [gmx-users-bounces at gromacs.org] per conto di XAvier Periole [x.periole at rug.nl]
> 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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>> --
>> George Khelashvili, Ph.D.
>> Department of Physiology and Biophysics
>> Weill Medical College of Cornell University
>> 1300 York Avenue, Room LC501
>> New York, NY, 10065, USA
>> gek2009 at med.cornell.edu
>> Phone: 1-212-746-6539
>> Fax:   1-212-746-6226
>>
>>
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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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