Chih-Ying Lin wrote:
Hi
I am going to simulate the lysozyme with some ligand in the low ionic
strength phosphate buffer .
The buffer condition will be
(pH 7.2, 8.3 mM) and (pH 5.0 , 8.3 mM)
For the buffer condition (pH 7.2, 8.3 mM), I will use TIP3P water
model and use CL- ions to nutralize
Hi gmx-users,
I am trying to calculate atomic stress distribution on CNT,s but Gromacs gives
me just
the global stress(virial,Pressure) of the whole system and not the cnt atoms.
Could any one suggest me how to calculate atomic site stress for a certain
structure in Gromacs?
Thanks
Farzaneh
Hi
I am going to simulate the lysozyme with some ligand in the low ionic
strength phosphate buffer .
The buffer condition will be
(pH 7.2, 8.3 mM) and (pH 5.0 , 8.3 mM)
For the buffer condition (pH 7.2, 8.3 mM), I will use TIP3P water
model and use CL- ions to nutralize the lysozyme (+8)
and c
Jacob Durrant wrote:
I recently started using g_cluster and have a question. When I run
g_cluster, the program asks me to select two groups. The output looks
something like this:
Select group for least squares fit and RMSD calculation:
Group 0 ( C-alpha) has 383 elements
Group 1
Itamar Kass wrote:
HI all,
I am trying to compile GROMACS 4.0.5 on my mac (10.5) using
'./configure --enable-mpi --disable-float --with-fft=no && make -j2 &&
make install'. I installed on the system lam 7.0.6 './configure &&
make && make install'.
The error message I get is:
mpicc -O3 -fomit-f
I recently started using g_cluster and have a question. When I run
g_cluster, the program asks me to select two groups. The output looks
something like this:
Select group for least squares fit and RMSD calculation:
Group 0 ( C-alpha) has 383 elements
Group 1 ( active_site) has 2438
HI all,
I am trying to compile GROMACS 4.0.5 on my mac (10.5) using
'./configure --enable-mpi --disable-float --with-fft=no && make -j2 &&
make install'. I installed on the system lam 7.0.6 './configure &&
make && make install'.
The error message I get is:
mpicc -O3 -fomit-frame-pointer -finline
Stefano Meliga wrote:
My integrator is "steep", which should perform EM.
This is my mdp file:
title = 4AKE_PREMsteep
cpp = /usr/bin/cpp
define = -DFLEXIBLE
constraints = all-bonds
integrator = steep
nsteps = 500
nst
My integrator is "steep", which should perform EM.
This is my mdp file:
title = 4AKE_PREMsteep
cpp = /usr/bin/cpp
define = -DFLEXIBLE
constraints = all-bonds
integrator = steep
nsteps = 500
nstlist = 10
ns
Dear Berk:
Thank you so much for your help!
I read your paper: " Determing the shear viscosity of model liquids from
molecular dynamics simulations" You used NVT? My question is which one is
better? NPT or NVT?
"Strictly speaking it might be incorrect, but since pressure scaling is
usually less
On Wed, May 27, 2009 at 3:05 PM, Jussi Lehtola wrote:
> On Wed, 2009-05-27 at 14:33 +0200, Yan Chai wrote:
>
> > It seems that in the twin range cut-off method, rlist does not only
> > play a role as a cut-off for neighbor searching, but also as a cut-off
> > for short-range interactions. Do I und
Hi,
I don't think it matters much if you put the cut-off at a minimum in the rdf.
The real issue is that the force is not updated beyond the cut-off,
while the atoms there still move. You want as little motion,
of better as little change in force due to the motion of the atoms
as possible. The so
On Wed, 2009-05-27 at 14:33 +0200, Yan Chai wrote:
> It seems that in the twin range cut-off method, rlist does not only
> play a role as a cut-off for neighbor searching, but also as a cut-off
> for short-range interactions. Do I understand correctly?
If you're using Coulombic cutoffs, then yes.
On Wed, May 27, 2009 at 1:36 PM, Jussi Lehtola wrote:
> In the twin range method [1] interactions that are in the range
> rlist..rvdw are only calculated during neighborlist updates. In the mean
> time they are considered to stay constant.
>
> The idea behind this is that when r>rlist the interac
Thamu wrote:
Hi gmx-users,
I am a new user of gromacs. I am trying to simulate a protein with cofactor
Acetyl-CoA.
I have generated gromacs topology for cofactor using prodrg server. I used
OPLS-AA force field.
I got the error message " Fatal error: Atomtype OA not found.
PRODRG generate
Hi gmx-users,
I am a new user of gromacs. I am trying to simulate a protein with
cofactor Acetyl-CoA.
I have generated gromacs topology for cofactor using prodrg server. I
used OPLS-AA force field.
I got the error message " Fatal error: Atomtype OA not found.
I couldn't fix this problem. Could an
On Wed, 2009-05-27 at 11:00 +0200, Yan Chai wrote:
> If my understanding above is correct, it seems that the concept or
> the algorithm of neighborlist for the twin range cut-off's in Gromacs
> is different from the original concept of Verlet neighborlist which is
> discussed in the textbook on
Hi,
I was trying to get the static structure factor using the following
command line:
g_rdf -f -s -sq -b 15000 -e 2 -endq 0.5
The output sq.xvg came as follows:
0.0 0.0
0.0861717775.32914
0.1723317292.77243
0.2585016632.64157
0.3446615728.30566
vivek sharma wrote:
Hi All,
I was doing some MD simulation over the docked complex and following the
drug-enzyme tutorial for the same. The tutorial provided by Kerrigan's
is really helpful. Only problem with the tutorial is generating
topologies, for which PRODRG server is suggested. I wa
Hi All,
I was doing some MD simulation over the docked complex and following the
drug-enzyme tutorial for the same. The tutorial provided by Kerrigan's is
really helpful. Only problem with the tutorial is generating topologies, for
which PRODRG server is suggested. I want to use some stand alone p
This was done with verision 4.0.4, taken straight from the website. I've
already simulated a great deal with this version and I'd hate to swap
versions in the middle of the project.
As for the -debug runs, I did it for the dry analyte and for one with a
6 Å water layer. It seems that the prote
Hi,
This is plain 4.0 code is presume?
This problem should be fixed then.
But I now also made vacuum without cut-off working with domain decomposition in
CVS head.
Compared to a not-unbalanced PD (for instance only a protein, no water) DD is
slightly slower.
But DD will be faster than a badly
Erik Marklund wrote:
David van der Spoel skrev:
Erik Marklund wrote:
I should add that this problem only seem to arise when the analyte is
covered with a thin sheet of water. When simulating a dry analyte I
get good scaling. In the latter case the charges, and therefore the
topology, is sligh
Dear Gromacs users,
I have a question about the twin range cut-off's in Gromacs.
If I choose vdwtype as Cut-off, the manual on run parameters tells me
that I need to choose rvdw>=rlist in this case. I have read the section on
the treatment of cutoffs in the manual and also the mailing lis
David van der Spoel skrev:
Erik Marklund wrote:
I should add that this problem only seem to arise when the analyte is
covered with a thin sheet of water. When simulating a dry analyte I
get good scaling. In the latter case the charges, and therefore the
topology, is slightly different.
How abo
Hi,
I don't know exactly what went wrong when I tried to patch the file. There
was a > on line 18 in the fix file, actually. I checked it. With the file
you sent me, gmxdump works fine.
Thank you very much for your help.
Best regards, Franzi
---
Franziska Hoffgaard
PhD Student
Bioinformatics &
Erik Marklund wrote:
I should add that this problem only seem to arise when the analyte is
covered with a thin sheet of water. When simulating a dry analyte I get
good scaling. In the latter case the charges, and therefore the
topology, is slightly different.
How about vsites? Did you happen to
Hi Mark,
Thanks!
S.
On Wed, May 27, 2009 at 12:03 PM, Mark Abraham wrote:
> Mark Abraham wrote:
>
>> Simba Xiao wrote:
>>
>>> Dear all,
>>>
>>> Does your GMX 4 past the gmxtest package in the gmx wiki ?
>>>
>>> My Gromacs 4.0.4 can not pass all the test. The test tip4p, ti4pflex and
>>> some k
I should add that this problem only seem to arise when the analyte is
covered with a thin sheet of water. When simulating a dry analyte I get
good scaling. In the latter case the charges, and therefore the
topology, is slightly different.
/Erik
Erik Marklund skrev:
Hi,
I'm simulating non-pe
Hi,
I'm simulating non-periodic systems in vacuo, using constrained h-bonds
and particle decomposition. For some of my simulations the cpu-usage
seem far from optimal. The first cpu gets no atoms, while the second one
gets plenty and the remaining cpus get less than I expected. Is this a bug?
On Wed, 2009-05-27 at 15:05 +0900, Makoto Yoneya wrote:
> I found the libtool within gromacs source (both 3.3.3 and 4.0.4) is not as
> new as that of e.g. fftw-3.2.1 (which use the libtool-2.2.6).
> I'm wondering if the libtool version was updated to the newer one,
> then the DLLs could be generate
zhangjianguo2002 wrote:
>zhangjianguo2002 wrote:
>>
>>
>>Firstly, thanks Berk and David van der Spoel for your replies. Maybe
>> I have not explain my problems clearly, there is only one type of
>> particle,namely one full-atom benzene molecule is replaced by one
>> coarse-grain
>zhangjianguo2002 wrote:
>>
>>
>>Firstly, thanks Berk and David van der Spoel for your replies. Maybe
>> I have not explain my problems clearly, there is only one type of
>> particle,namely one full-atom benzene molecule is replaced by one
>> coarse-grained benzene particle,so there in n
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