Dear Alexander,
in gromacs you have lots of implemented tools for analysis like to compute
energy between surfacant and surface by energy groups, tilt angle, order
parameter, angle distribution,... But I would suggest you first to look in
previous publication connected with your studies, that coul
Potential energy for one atom is not well defined physical quantity as far
as I know, you can only calculate potential energy for at least two body
(atoms). You need to give more details about what you want and I do not
know what LAMMPS do.
Josip
2016-03-18 11:03 GMT+01:00 张正财 :
> > Subject: Re:
>From my experience, yes it can.
Josip
2015-03-05 11:56 GMT+01:00 xy21hb :
> Dear GMXers,
>
>
> I used g_select to select some distance e.g. 5A of the solvent e.g. water
> w.r.t. a protein,
> The results gives atoms within that range. However, what if I need to have
> those solvent molecules tha
Hello,
I am also interested in tabulated potentials and I am working to implement
it in my program.
I am interested do you think is it possible to put parameters (A, B, C) in
to the functions h(r) and and g(r)
and give value with parameters in the table and in the topology just set
parameters 1. I
Sorry you are looking for dihedrals I have just sow that, I think gmx
gangle can not do that.
2014-04-14 23:34 GMT+02:00 Josip Lovrić :
> If I understood you correctly, I think you are looking for gmx gangle. It
> is part of 5.0 version. You need to install new version.
> Check he
If I understood you correctly, I think you are looking for gmx gangle. It
is part of 5.0 version. You need to install new version.
Check hear http://www.gromacs.org/Documentation/How-tos/Tool_Changes_for_5.0
2014-04-14 23:09 GMT+02:00 sbowerma :
> Hi Justin,
>
> Thanks for your response. I did
That I do not know.
2014-04-04 11:25 GMT+02:00 michael.b :
>
> thanks for the reply! ...
>
> to be precise i should add that when i say analyze i actually
> mean rerun 4.5.6 trajectories with mdrun-5.0-breta ...
>
> cheers
> michael
>
>
>
> --
> View this message in context:
> http://gromacs.508
Hello,
I can maybe give you answer on second question. I have used analyzes tool
gmx gangle from 5.0-beta to analyzes trajectories from 4.6.5 and it was OK
for me.
Cheers,
Josip
2014-04-04 9:35 GMT+02:00 michael.b :
>
> two questions:
>
> 1) searching this list if found this comment:
> "NOTE:
flag but it is not
possible so I need to put it both in one .ndx file.
Thank you very much, you deserve chocolate :-).
2014-03-26 18:38 GMT+01:00 Justin Lemkul :
>
>
> On 3/26/14, 11:57 AM, Josip Lovrić wrote:
>
>> Thank you for the tips!
>>
>> This is my .mdp fil
#Entries FirstLast
0 notattached_0.000 30505901 16800
2014-03-26 16:36 GMT+01:00 Justin Lemkul :
>
>
> On 3/26/14, 11:30 AM, Josip Lovrić wrote:
>
>> Hello,
>>
>> I managed to create notattached group but now it is not recognizing system
>>
el free to ask me more information, I am quite new in gromacs and I am
not sure if I am giving you all the information.
2014-03-25 17:31 GMT+01:00 Justin Lemkul :
>
>
> On 3/25/14, 12:10 PM, Josip Lovrić wrote:
>
>> Dear GROMACS community,
>>
>> I am trying to in
Dear GROMACS community,
I am trying to index some molecules with g_select. I have system of
carboxylic molecules(group named MOL) forming monolayer on NaCl surface.
Some of the molecule are attached to surface and some not. With g_select I
want to select molecule which are not attached to
surface.
tein. Moreover, you'd have no reason to suppose the
> combination would work. See
> http://www.gromacs.org/Documentation/Terminology/Force_Fields
>
> Mark
>
>
> On Fri, Mar 21, 2014 at 2:44 PM, Josip Lovrić >wrote:
>
> > Hello dear gromacs users,
> >
&g
Hello dear gromacs users,
lets say that we have 3 kinds of molecules in our system, for example
water, protein and some ions. Is it possible to have one set Force field
parameters of protein for protein-water and other for protein-ions
interaction.
Best Regards,
Josip Lovrić
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