1 pN/A = 10^-23 kJ/nm2
So 1pN/A = 6,02214129 kJ/mol nm2
Thank you All,
Steven
On Tue, Jul 3, 2012 at 6:20 PM, Thomas Schlesier wrote:
> You have 1mol of your system.
>
> conversition factor for
> kJ/(mol*nm) -> pN is approx 1.661
>
>
> Am 29.06.2012 10:33, schrieb gmx-users-requ...@gromac
Hi everybody,
is there a possibility to define an energy value and when the change of
the energy between two steps during the minimization is lower than this
value the minimization is finished?
Thank you,
Eva
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Hello,
I am running a simulation of a protein-protein complex using explicit
solvent. (mdrun -v -deffnm run)
I created a box for the simulation (d=5) using editconf:
editconf -princ -f conf.gro -bt dodecahedron -d 5.0 -c -o box.gro
I am using the option pbc=no in the run.mdp file.
Can anyone explai
Hi David,
i saw your recent post in the gmx mailing list about "BAR gives different
result than TI"
i wonder did you get any good answers to this queston so far!?
i was also trying to do some free energy calculations, with BAR i seem to get
the correct
answer (compared to expt and literature
Dear GMX users,
This is Hyungjun Kim.
I try to modify the len= nard jones parameter explicitly.
I knew that gromacs provide the com= bination rule such as
sigma_12=(sigma_1 + sigma_2 ) /2 like.
I fin= d that some specific interaction is quite important, so I want to
give ex
Hello every one,
Im interesting in performing a MD for Protein - RNA complex , Can any
one suggest a good tutorial.
Thanks in advance.
--
Ravi Raja Tejasvi . Merugu
http://www.rsquarelabs.org
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Thanks Mr.Justin,,
I will try them ..
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On 7/4/12 2:31 AM, neeru sharma wrote:
Dear Gromacs Users,
I have some queries about the parameters in the .mdp file for the pull code.
If I want to pull my ligand, towards specific atom/group of atoms from
the protein, how am I supposed to mentioned these in the mdp file?
*
On 7/4/12 6:45 AM, Ravi Raja Merugu wrote:
Hello every one,
Im interesting in performing a MD for Protein - RNA complex , Can any
one suggest a good tutorial.
Such systems do not differ significantly from simulations of simple proteins in
water, since pdb2gmx can produce topologies for bo
Well,
Ill give that a shot from memory of a discussion some time ago, which you could
probably track down on the e-mails of past search engine. I think it has to do
with force field types, either they list the sigma values, or direct 6, 12 or
derived LJ parameters, so it would be related to w
hi,
i'd like to do a simulation of a solute in water - trying to reproduce some
literature data
i try to be consistent and use an atom-based cut-off. for this each atom needs
to be
its own charge-group ...
so when i change spc.itp
from:
1 opls_116 1 SOL OW 1 -0.82
Thanks Mark for your response. These are steps I followed to construct
DNA+Water molecules.
> editconf -f A.pdb -o A.
Mark's suggestions were complete. However, you did not follow them. Please
follow all of his suggestions
and then post back with exactly what you did and exactly what problem you ran
into. If you are having
trouble with g_select, then show us what you did and why it didn't work. The
mailing list
Heard that RNA/DNA system could be a little trickier than proteins due
to the many negative charges.
I found somewhen a nice article about RNA simulations in general.
Probably some questions you have / will have are answered there:
A short guide for molecular dynamics simulations of RNA syste
Thanks Justin for your early response. I was confused about it, but
now it's clear. Thanks
--Neeru
> Dear Gromacs Users,
>
>
> I have some queries about the parameters in the .mdp file for the pull code.
>
> If I want to pull my ligand, towards specific atom/group of atoms from
> the protein, how
On 7/4/12 1:07 PM, Dr. Vitaly V. G. Chaban wrote:
Dear GROMACS people -
I am calculating radial distribution function between the centers of
mass of two large particles in a periodic box.
My command is -- g_rdf_455 -n 2drops.ndx -rdf mol_com -s topol.tpr -f conf.gro
My index file contains t
>> Dear GROMACS people -
>>
>> I am calculating radial distribution function between the centers of
>> mass of two large particles in a periodic box.
>>
>> My command is -- g_rdf_455 -n 2drops.ndx -rdf mol_com -s topol.tpr -f
>> conf.gro
>>
>> My index file contains two groups of atoms standing fo
On 7/4/12 1:31 PM, Dr. Vitaly V. G. Chaban wrote:
Dear GROMACS people -
I am calculating radial distribution function between the centers of
mass of two large particles in a periodic box.
My command is -- g_rdf_455 -n 2drops.ndx -rdf mol_com -s topol.tpr -f
conf.gro
My index file contains t
Hi,
I'm using gromacs 4.5.4 and I've got a detailed question on how the mass
weighting works.
Given a trajectory and a pdb from
http://code.google.com/p/mdanalysis/source/browse/testsuite/MDAnalysisTests/data/adk_oplsaa.pdb
http://code.google.com/p/mdanalysis/source/browse/testsuite/MDAnalysisTes
On 4/07/2012 6:17 PM, ifat shub wrote:
Hello,
I am running a simulation of a protein-protein complex using explicit
solvent. (mdrun -v -deffnm run)
I created a box for the simulation (d=5) using editconf:
editconf -princ -f conf.gro -bt dodecahedron -d 5.0 -c -o box.gro
I am using the option pbc=
On 5/07/2012 10:11 AM, Jan Domanski wrote:
Hi,
I'm using gromacs 4.5.4 and I've got a detailed question on how the mass
weighting works.
Given a trajectory and a pdb from
http://code.google.com/p/mdanalysis/source/browse/testsuite/MDAnalysisTests/data/adk_oplsaa.pdb
http://code.google.com/p/mda
On 5/07/2012 12:28 AM, SatyaK wrote:
Thanks Mark for your response. These are steps I followed to construct
DNA+Water molecules.
> editconf -f A.pdb -o A.gro -d 0.3
> genbox -cp A.gro -cs -nice -20 -o A_water.gro
That's not going to achieve your objective. I gave you a workf
On 4/07/2012 11:43 PM, Michael Brunsteiner wrote:
hi,
i'd like to do a simulation of a solute in water - trying to reproduce some
literature data
i try to be consistent and use an atom-based cut-off. for this each atom needs
to be
its own charge-group ...
so when i change spc.itp
from:
1
On 4/07/2012 6:45 PM, Hyungjun Kim wrote:
>Dear GMX users,
>
>This is Hyungjun Kim.
>
>I try to modify the len=ard jones parameter explicitly.
>
>I knew that gromacs provide the com=ination rule such as
>sigma_12=(sigma_1 + sigma_2 ) /2 like.
>
>I fin= that some specific int
On 4/07/2012 5:46 PM, reising...@rostlab.informatik.tu-muenchen.de wrote:
Hi everybody,
is there a possibility to define an energy value and when the change of
the energy between two steps during the minimization is lower than this
value the minimization is finished?
If it's in manual 7.3.5,
On 07/04/2012 08:34 PM, Mark Abraham wrote:
> On 5/07/2012 10:11 AM, Jan Domanski wrote:
>> (BTW, the g_rms -h mentions something about a '-debug flag' but it
>> seems not to be working.)
>
> See manual D.1 - the -debug flag takes an argument.
>
Ah, I see... yes, sorry.
>
> This is expected. Se
Thanks once again Mark. I am trying to figure out things. Basically, I am
using ReaxFF for my simulations. The basic problem I want to address is, to
place OH radicals as close as possible to the DNA and rest with water
molecules in a box.
Thanks,
Satya.
--
View this message in context:
htt
On 07/05/2012 01:04 PM, SatyaK wrote:
Thanks once again Mark. I am trying to figure out things. Basically, I am
using ReaxFF for my simulations.
Has that been ported to GROMACS? If not, you have that issue to consider
first.
The basic problem I want to address is, to
place OH radicals a
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