Dear Michael,
Thank you for your reply.
Yes, it is relatively clear now. Will try to play around with this later today.
Best,
Joakim
> Date: Thu, 7 Mar 2013 08:55:31 -0500
> From: Michael Shirts
> Subject: Re: [gmx-users] Hamiltonian replica exchange umbrella
> sampling with gmx 4.6
>
Hi Reid,
thanks a lot for sharing your experiences with g_mindist -pi and
non-cubic boxes! Yesterday, this exact problem caused me a lot of trouble!
: )
Best,
Jens
On 2013-03-07 19:02, Reid Van Lehn wrote:
> Hi users,
>
> I was experimenting with using a hexagonal unit cell for a lipid membrane
Dear Users,
I have a system that has been running under gromacs 4.5.5. I can restart it
fine from
a checkpoint file with gromacs 4.5.5 but not with gromacs 4.6.1.
The long description follows, but the short answer seems to be that 4.5.5
recorded My-X/Y/Z values (the internet tells me these rel
> Hello
>
> In the g_density manual it is mentioned that
>
> "When calculating electron densities, atomnames are used instead of types,
> this is bad"
>
> So what should be included in the electrons.dat file. The unique atomtypes
> of the group or all the atomnames of this group?
>
> Thanks in adva
On 3/7/13 1:17 PM, Miguel Ángel Mompeán García wrote:
2013/3/4 Justin Lemkul
Dear Justin,
With 4.5.5 the jobs have completed. I am going to repeat them with 4.6.1
If you find something weird in the mdp file or require further explanations
on the points do mention I will do my best to prov
Hello Steven,
I would suggest you to look if this angle is not defined somewhere else in
your file. Indeed, it seems that the program has another value for this.
The 2 and 6 at the end of the line are the multiplicity, so they don't need
to be changed. The relevant value is the one indicated in th
On 3/7/13 11:14 AM, George Patargias wrote:
Hello
In the g_density manual it is mentioned that
"When calculating electron densities, atomnames are used instead of types,
this is bad"
So what should be included in the electrons.dat file. The unique atomtypes
of the group or all the atomnames
On 3/7/13 10:46 AM, Steven Neumann wrote:
Dear Gmx Users,
I used charmm server to get the parameters for my new molecule -
alkane. i converted it into the gromacs topology.
When I try grompp:
WARNING 1 [file ffbonded.itp, line 7948]:
Overriding Proper Dih. parameters.
Use dihedraltype 4
On 3/7/13 8:31 AM, l@utwente.nl wrote:
Dear all,
When calculation the RDF, it asks:
Select a reference group and 1 group
Group 0 ( System) has 1600 elements
Group 1 ( Other) has 1600 elements
Group 2 ( PE) has 1600 elements
Group 3 ( a
On 3/7/13 5:44 AM, Baptiste Demoulin wrote:
Hello Gromacs users,
I try to link a metallic core to its surrounding amino-acids. Everything
works find for bonding side chains and metal atoms, but I have troubles
when it comes to bonding COO- group from a terminus ALA. The error printed
by pdb2gm
On 3/7/13 3:54 AM, Keerthana S.P Periasamy wrote:
Dear all I have two discrete residues which are being connected together by
sulfur atom in each residue. I need to find how the density varies around the
residues or atoms attached with the sulfur atom and the water molecules
surrounding it. fo
On 3/7/13 3:36 AM, zhhxu wrote:
Hi users:
I want to run a simulation of adsorption of protein on graphite oxide(GO) which
is oxidized at random and
is near 80% coverage by hydroxyl and epoxyl group.
My first question is how to generate a topology filefor GO. Previous to search
solution to t
2013/3/4 Justin Lemkul
> Dear Justin,
>
With 4.5.5 the jobs have completed. I am going to repeat them with 4.6.1
If you find something weird in the mdp file or require further explanations
on the points do mention I will do my best to provide the necessary info.
Right below are the comments:
On 2013-03-07 19:02, Reid Van Lehn wrote:
Hi users,
I was experimenting with using a hexagonal unit cell for a lipid membrane
system by building a box with vectors A A C (i.e. two equivalent vectors in
the xy plane and distinct z vector) and angles 90 90 60, which is correctly
represented as hex
Hello
In the g_density manual it is mentioned that
"When calculating electron densities, atomnames are used instead of types,
this is bad"
So what should be included in the electrons.dat file. The unique atomtypes
of the group or all the atomnames of this group?
Thanks in advance.
Dr. George
On Thu, 7 Mar 2013, Szilárd Páll wrote:
On Thu, Mar 7, 2013 at 2:02 PM, Berk Hess wrote:
Hi,
This was only a note, not a fix.
I was just trying to say that what linear algebra library you use for
Gromacs is irrelevant in more than 99% of the cases.
But having said that, the choice of librar
On Thu, Mar 7, 2013 at 2:02 PM, Berk Hess wrote:
>
> Hi,
>
> This was only a note, not a fix.
> I was just trying to say that what linear algebra library you use for
> Gromacs is irrelevant in more than 99% of the cases.
> But having said that, the choice of library should not complicate the
> co
Hi, Joakim-
Hamiltonian exchange only should work if there is a lambda coupling
parameter that defines the potential at each state. You need to
define your pulling potential so that the coupling-lambda parameter
can be used to define the different pulling location centers along
your trajectory.
Dear all,
When calculation the RDF, it asks:
Select a reference group and 1 group
Group 0 ( System) has 1600 elements
Group 1 ( Other) has 1600 elements
Group 2 ( PE) has 1600 elements
Group 3 ( a_1-1600) has 1600 elements
My question is wha
Hi,
This was only a note, not a fix.
I was just trying to say that what linear algebra library you use for Gromacs
is irrelevant in more than 99% of the cases.
But having said that, the choice of library should not complicate the configure
stage of Gromacs.
Cheers,
Berk
-
On Thu, 7 Mar 2013, Berk Hess wrote:
Hi,
Note that the linear algebra in Gromacs is limited to eigenvalue solving in two
analysis tools,
the MD engine does not use any (large) linear algebra.
So linear algebra library performance is irrelevant, except for the cases where
users
would want t
Dear gmx-users,
I am currently trying to runt Hamiltonian replica exchange umbrella sampling in
hope to do some better sampling.
I have generated a number of tpr-files along my reaction coordinate and they
all run fine in independent simulations. The issue comes when I would like the
replica e
Hi,
Note that the linear algebra in Gromacs is limited to eigenvalue solving in two
analysis tools,
the MD engine does not use any (large) linear algebra.
So linear algebra library performance is irrelevant, except for the cases where
users
would want to repeated uses one of the two tools with
On Wed, 6 Mar 2013, Christoph Junghans wrote:
I had a another look at the issue and I guess cmake's blas detention
is a bit flaky, when it comes to static libraries.
You are using liblapack.a, which has no link information, with
liblapack.so it should have worked.
Anyhow, thanks for reporting th
On Mar 7, 2013, at 2:59 AM, Justin Lemkul wrote:
On 3/6/13 8:57 PM, Vishwambhar Bhandare wrote:
dear gromacs user,
how i can do binding free energy calculation for RNA duplex in
gromacs?
any tutorial for the same??
Free energy calculations involving interactions between
macromolecules
Dear all
I have two discrete residues which are being connected together by sulfur
atom in each residue. I need to find how the density varies around the residues
or atoms attached with the sulfur atom and the water molecules surrounding it.
for that I created a group by selecting the two su
Hi Nilesh,
So far I have not been able to figure out the problem. I also ran some new
simulations with Gromacs 4.6 for 100ps of EMIMDCA and everything worked
fine. I looked into the code, but was not able to detect the problem that
causes the strange behavior you are observing. Can you update your
Hi users:
I want to run a simulation of adsorption of protein on graphite oxide(GO) which
is oxidized at random and
is near 80% coverage by hydroxyl and epoxyl group.
My first question is how to generate a topology filefor GO. Previous to search
solution to this problem in
this forum, I had tri
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