Hi,
I've been working a time ago with Pull code in Gromacs 3.3.1, calculating the
components of the applied force from pull.pdo file.
Now, using 4.0.5 version and re-starting with COM Pulling, as well as the
great optimization, I've found that the outputs show something like the
modulus
o
Jianhui Tian wrote:
Dear GMX users,
I am running a replica simulation and the job crashed with the following
message:
File input/output error:
Cannot rename checkpoint file; maybe you are out of quota?
From the mailling list, I see this might be a permission problem.
However, I checked t
Dear GMX users,
I am running a replica simulation and the job crashed with the following
message:
File input/output error:
Cannot rename checkpoint file; maybe you are out of quota?
>From the mailling list, I see this might be a permission problem. However, I
checked the file permission and noth
I'd take a look at do_md in src/kernel/md.c and see for myself :-)
I think the question is moot, because I have the off-hand impression that, for
the md integrator, constraints are not implemented through modifying the force
vectors, but rather imposed by the constraint algorithm upon the
post-
Kamalesh Roy wrote:
Hi.. every body
I am trying to install Gromacs 4.5.1 using updated version of fftw-3.3.1
in single precision in Fedora 9...
Giving an error "fftw3f library not found..."
I am mentioning the path before installing but still giving that error
Please copy and paste yo
Could anyone please clarify on my previous question? I am very confused
about the force value issue.
thanks
sikandar
On Thu, Oct 7, 2010 at 2:27 PM, Sikandar Mashayak wrote:
> Hi
>
> In the post-processing ( analysis) code using gromacs trajectory, I access
> force values on atom using fr.x[indx_
Hi.. every body
I am trying to install Gromacs 4.5.1 using updated version of fftw-3.3.1 in
single precision in Fedora 9...
Giving an error "fftw3f library not found..."
I am mentioning the path before installing but still giving that error
Will it be successful in Red Hat enterprize edition.
Hi,
just tried to start my first MD with gmx 4.5, and have
a couple of questions regarding some mdp options:
for the impatient ones, the short versions:
1) what is the parameter "nstcalcenergy" ?
(doesn't seem to be documented)
also, in the mailing list there's a discussion about a bug w
This is the normal behaviour for a MSD vs. time plot. Actually, as set
by default in g_msd, neither the first seconds nor the last ones are
taking into consideration to calculate the difussion constant.
The explanation for the non-liear curves might be the following. On one
hand, at the begini
Hi,
one possible reason could be that the files are not included correctly.
Check the -pp output. Otherwise it is difficult to tell without the files.
Roland
On Fri, Oct 8, 2010 at 5:48 AM, Christian Seifert <
cseif...@bph.ruhr-uni-bochum.de> wrote:
> Hi GMXers,
>
> this is a Mail from one of m
Hi,
see here for a start:
http://www.gromacs.org/Documentation/How-tos/Parameterization
Cheers,
Jochen
On 10/8/10 Oct 8,3:51 PM, lammps lammps wrote:
>
> Hi everybody,
>
> I want to use OPLS-AA force field to do simulation for dendrimer(see
> the attached files for figure and .pdb). If the
Hi everybody,
I want to use OPLS-AA force field to do simulation for dendrimer(see the
attached files for figure and .pdb). If the pH<4.0，the tertiary amines on
the dendrimer will be protonated, i.e. (CH2)3-N will be changed to
(CH2)3-NH+. Now, I have two questions as follows.
1. How can I use p
2010/10/4 Jochen Hub
> On 10/2/10 Oct 2,10:51 PM, Петр Попов wrote:
>
>> Hello, dears gmx-users!
>>
>> I posted a message, but didn't get a response, it was my first one, so may
>> be I did something wrong. Anyway, here it is:
>>
>> I've already run md and got pmf and it's correct. But I want to
Павел Кудрявцев wrote:
Hi,
I wanna perform free energy calculation by changing parameters of
amino acid residue. Since my case is rathe complicated first I tried
to perform a very simplified task - to change only charges of atoms.
So I peeked out one residue, keeped all its atom types and mass
Hi GMXers,
this is a Mail from one of my colleagues (who is not yet member of
this )
Hi GMXers,
a colleague of mine (who is not yet member of our enlightened list, but
maybe I can convince him, if we find a solution.. ^^) has a problem
after he had copied functioning CHARMM parameters to GMX. I
Finally, I compiled and ran simulations with gpu version of gromacs-4.5.1.
There were several issues:
1) Precompiled OpenMM2.0 libraries and headers must be downloaded (which
requires registration on their web page) and installed, otherwise cmake
doesn't find some source files.
2) cmake sh
Hi,
I wanna perform free energy calculation by changing parameters of
amino acid residue. Since my case is rathe complicated first I tried
to perform a very simplified task - to change only charges of atoms.
So I peeked out one residue, keeped all its atom types and masses and
changed charges of N
Hi,
Have you checked that your numbers are converged?
Such differences can easily occur when you don't sample enough.
You will have to try very many orientations before you hit the right one
which satisfies all hydrogen bonds.
I tested PME a long time ago. Then it worked correctly.
But it could
Hello Gromacs users,
Recently I ran some test particle insertion simulations of TIP4P/2005
water to measure the chemical potential at 470 K and 0.861 g/cc. I
found that the chemical potential was 20%-25% higher than literature
values. I believe there may be a problem related to using PME with
te
19 matches
Mail list logo
