On 28/03/11, Parul tew wrote:
> Dear GMX users,
>
> I am facing problem while doing energy minimization of the inflated system
> of a protein with membrane. I inflated the system and updated the removed
> lipids in the topology file. Now I am stuck during the energy minimization
> state. B
Dear GMX users,
I am facing problem while doing energy minimization of the inflated system
of a protein with membrane. I inflated the system and updated the removed
lipids in the topology file. Now I am stuck during the energy minimization
state. Below is the .mdp file for minimization.
-
On 27/03/11 20:55, David van der Spoel wrote:
On 2011-03-27 21.27, devicerandom wrote:
On 27/03/11 16:29, David van der Spoel wrote:
On 2011-03-27 16.42, devicerandom wrote:
Hi,
I am trying to use g_clustsize to follow aggregation of peptides. I am
currently using the following line:
g_clust
Sai Pooja wrote:
Hi,
I am running a simulation for capped alanine dipeptide and I now need to
extract the dihedral angles. However, one of the nitrogen is named NT
instead of NH due to which g_rama is not able to give the dihedral
angles. Is there any other program I can use to get dihedra
Hi,
I am running a simulation for capped alanine dipeptide and I now need to
extract the dihedral angles. However, one of the nitrogen is named NT
instead of NH due to which g_rama is not able to give the dihedral angles.
Is there any other program I can use to get dihedral angles? I tried g_dih
a
Hi all,
I have seen a few posts on gmx-users indicating a desire to treat certain
atom groups as rigid bodies in MD simulations. I just started implementing
this, and so far I have it working for translational forces (not rotation,
though this should be simple to add), even when the group is split
sa wrote:
Dear All,
I would like to compute the C6 and C12 LJ terms for the GROMOS 53A6 ff
for a new atom type and incorporate them in my ffnonbonded.itp. Does
anybody know the mathematical expressions used to obtain these terms
from a sigma (nm) and an epsilon (kj/mol) values manually.
On 2011-03-27 21.27, devicerandom wrote:
On 27/03/11 16:29, David van der Spoel wrote:
On 2011-03-27 16.42, devicerandom wrote:
Hi,
I am trying to use g_clustsize to follow aggregation of peptides. I am
currently using the following line:
g_clustsize -f my.trr -s ../my.tpr -nc nclusters.xvg -
On 27/03/11 16:29, David van der Spoel wrote:
On 2011-03-27 16.42, devicerandom wrote:
Hi,
I am trying to use g_clustsize to follow aggregation of peptides. I am
currently using the following line:
g_clustsize -f my.trr -s ../my.tpr -nc nclusters.xvg -mol
Problem is, it actually counts monome
On 2011-03-27 19.23, Elisabeth wrote:
Thanks David for replying me. I appreciate your attention to
comment on the following short inquiries.
1- g_energy says:
you will need to give the number of constraints per molecule
–nconstr and
for water this is 3
Dear GROMACS users,
I am starting to setup a molecular dynamics simulation and I want to use the
MARTINI force field. I was reading the tutorial in website:
http://md.chem.rug.nl/cgmartini/index.php/tutorial/reverse-transformationand
I have a beginner question for you: How can I use the MARTINI in
LinkedIn
ram prasad requested to add you as a connection on LinkedIn:
--
Chinmay,
I'd like to add you to my professional network on LinkedIn.
- ram
Accept invitation from ram prasad
http://www.linkedin.com/e/-85v1n9-gls95twz-50/Xl9gjr6GAOlB4vI
Dear All,
I would like to compute the C6 and C12 LJ terms for the GROMOS 53A6 ff for a
new atom type and incorporate them in my ffnonbonded.itp. Does anybody know
the mathematical expressions used to obtain these terms from a sigma (nm)
and an epsilon (kj/mol) values manually.
Thank you for your
>
> Thanks David for replying me. I appreciate your attention to comment on
>> the following short inquiries.
>>
>> 1- g_energy says:
>>
>> you will need to give the number of constraints per molecule –nconstr and
>
> for water this is 3. Can you elaborate on how to set this option. When
constrai
On 2011-03-27 16.42, devicerandom wrote:
Hi,
I am trying to use g_clustsize to follow aggregation of peptides. I am
currently using the following line:
g_clustsize -f my.trr -s ../my.tpr -nc nclusters.xvg -mol
Problem is, it actually counts monomers as clusters. I have a system
with 125 separa
Hi,
I am trying to use g_clustsize to follow aggregation of peptides. I am
currently using the following line:
g_clustsize -f my.trr -s ../my.tpr -nc nclusters.xvg -mol
Problem is, it actually counts monomers as clusters. I have a system
with 125 separate molecules, and the number of cluster
Hey :)
You probably want to fit on the protein and calculate the RMSD on the
ligand. You may need to specify these groups in an index file.
Hope it helps,
Tsjerk
On Mar 27, 2011 3:28 AM, "Justin A. Lemkul" wrote:
Nancy wrote: > > Hi All, > > I need to determine the RMSD of a small
molecule co
On 27/03/11, Kishore wrote:
> Dear Mark/Justin,
>
You were asked yesterday to do things when you reply to digest emails. Do
change the subject to something useful, and do not include the entire digest in
your email. Not taking actions to play nicely with the other children will lead
to the o
On 27/03/11, XUEMING TANG wrote:
> Hi
>
>
>
> May I ask if anyone know a good reference for partial charges of
> "-CH2-NH-CO-CH2-CH2"(amide)? I plan to use gromos 53A6 force field.
> I searched the internet quite a while but not sure what is the best. I will
> be appreciated if you coul
On 2011-03-27 07.36, Elisabeth wrote:
Dear all,
I am trying to calculate Cv of a pure alkane 125 molecules with actual
density, and here is what I have done:
As indicated in an earlier post this is a non-solved problem, but we are
working on it.
The computation of heat capacity in g_energy w
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