---
Coul-SR:Lipid-Lipid -132802 27 241.483 170.225 (kJ/mol)
Coul-SR:CHOL-Lipid -1902.18 16 126.736 -19.2265 (kJ/mol)
Any help will be appreciated
Jose A. Teruel
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)
>
> Mark
>
> On Wed, Jul 12, 2017 at 5:39 PM Jose Borreguero <borregu...@gmail.com>
> wrote:
>
> > Dear Gromacs users,
> >
> > I'm a relatively new user of Gromacs and recently realized there is a
> > "2016" branch that is still being updated.
rom source.
Best,
.Jose
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Thanks, Justin. I suspected that was the case but I wanted to be 100% sure
:D
.Jose
On Tue, Jun 27, 2017 at 9:48 PM, Justin Lemkul <jalem...@vt.edu> wrote:
>
>
> On 6/27/17 12:32 PM, Jose Borreguero wrote:
>
>> Dear Gromacs users,
>>
>> I have creat
this residue in file aminoacids.rtp?
Best,
Jose
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yes, the ions I have can be considered as bound. I found out I also had to
declare the type of residue as "Ion" in file residues.dat :)
On Fri, Jun 23, 2017 at 4:44 PM, Justin Lemkul <jalem...@vt.edu> wrote:
>
>
> On 6/23/17 3:50 PM, Jose Borreguero wrote:
>
>
required?
Best,
Jose Borreguero
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Victory! The -noparam did the trick :)
Thanks a million.
On Wed, Jun 21, 2017 at 11:43 AM, Justin Lemkul <jalem...@vt.edu> wrote:
>
>
> On 6/21/17 11:39 AM, Jose Borreguero wrote:
>
>> Hi Justin,
>>
>> Thanks for your quick reply!
>> This m
nformation in the output
.top file is overridden with that gmx later finds under
./oplsaa.ff
?
If so, then the particular value of the force constant in the .top file
would be irrelevant and my problem would be solved! :)
.Jose
.Jose
On Wed, Jun 21, 2017 at 10:51 AM, Justin Lemkul <ja
the
40
number.
Best,
.Jose
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Hi Mark,
I decided to write my own script, which computes distances between silica
and protein atoms as you suggested. Removing the silica is not trivial
because one must remove SiO2 molecules but there is no unique way to
partition a silica block into SiO2 molecules.
.Jose
On Fri, Jun 16, 2017
is inside the volume.
Does anyone know how to parameterize the volume occupied by a protein?
Best,
Jose Borreguero.
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d then the steps to "merge" this residue with the rest of
the OPLS force-field?
Best.
Jose Borreguero
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Protein" or close_solvent_molecules;
It's not exactly what I wanted, butI can select N closest water molecules
by tuning the cutoff distance.
.Jose
On Thu, Jun 8, 2017 at 4:34 AM, Mark Abraham <mark.j.abra...@gmail.com>
wrote:
> Hi,
>
> Or gmx select to make an index group for t
Dear Gromacs users,
I'm a newbie with Gromacs. Is there a Gromacs native tool that will allow
me to create a new *.gro file containing the protein and the N closest
water molecules to the protein
, starting from a system of a solvated protein
?
Best,
Jose Borreguero
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Dear gromacs users and developers,
I would like to decouple independently the dispersion and repulsion
components of the Lennard-Jones term in a FEP/TI run such as it happens
with electrostatics and Lennard-Jones interactions. How can I do this
decouple independently?.
I know the great effort
Hi Mark,
I followed your instructions and had no problem at all with the install.
Thanks a lot!
.Jose
On Tue, Aug 2, 2016 at 7:00 PM, Mark Abraham <mark.j.abra...@gmail.com>
wrote:
> Hi,
>
> That seems a lot more complicated than you should need. First, don't run
> the wh
'-I' '/usr/include/openmpi-x86_64' '-pthread'
'-L/usr/lib64/openmpi/lib' '-mtune=generic' '-march=x86-64']
The last info, the ignore line seems suspicious but I don't know what it
means.
I'm stuck here, please any help will be much appreciated.
Best,
.Jose
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* Please
this case?. Also, Is
it necessary to add this (small) dispersion correction for this second case?
Thank you in advances,
Joel
2016-07-20 19:21 GMT+02:00 David van der Spoel <sp...@xray.bmc.uu.se>:
> On 20/07/16 17:01, Joel Jose Montalvo Acosta wrote:
>
>> Dear Gromacs users
Dear Gromacs users and developers,
I want to understand how the long-range dispersion correction is
implemented in gromacs when van der waals (vdw) interactions are computed
with cut-off or PME, so I started reading the section 4.9.1 in the gromacs
(version 5.1.2) manual to check the involved
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