Re: [gmx-users] problems about number of frames in the edr file

[Mark Abraham]

 
 
On 23/07/11, Zhuyi Xue  wrote:

> 
> Sorry, maybe I was not clear. Even before I do any eneconv on the edr file I 
> mentioned, I could still only extract data of 4 frames though it seems there 
> are around 2000 frames in it.
> 
> Why is this happening?

 
We don't know, because we don't know how the file was created. 
 
Mark
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[gmx-users] shift functions in gromacs

[Павел Кудрявцев]

Hello everyone,

I'd like to ask for some clarification of actual form of shift
fuctions used in gromacs.
Due to gromacs tutorial 4.5.4 (section 4.1.5) and equations 4.23,
4.26-4.31 shift fuction seems to depend only on 2 user-defined
conctants - r1 and rc which seems to be rvdw_switch and rvdw
respectively. Nevertheless in section 7.3.11 declared that using of
VdW type Shift decrease LJ potential over the whole range regardless
of rvdw_switch and only forces depends on both rvdw_switch and rvdw.
Such behaviour seems to be ok if take into account next words from
section 4.1.5 "When r1 = 0 this is a traditional shift
function,otherwise it acts as a switch function" but it does not fit
given aquations because then  there must third constant besides r1=0
and rc.

One more question: several times I saw in articles people using short
VdW cut-off like 8 A with Amber force fields (for example recent
article "Iterative Optimization of Molecular Mechanics Force Fields
from NMR Data of Full-Length Proteins" DOI: 10.1021/ct200094b), but
they dont say anything about trucation type. Does it mean there is
some kind of standart parameters set for such small cut-off or is it
ok to use it without shifting/switching?

thanks in advance,
Pavel
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[gmx-users] Graphene growth simulation in gromacs

[neclaoz]

Hello gromacs users,

I am trying to do a MD simulation of graphene growth using Gromacs. However
I don't know where to begin? Which potential should I use? So far I was only
involved in CNT simulations in gromacs, and I am confused about this growth.

Any help would be very usefull

Thanks..
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