Hi,
about the tests:
- ntmpi 1 -ntomp 22 -pin on; doesn't work*
- ntmpi 1 -ntomp 22 -pin off; runs
- ntmpi 1 -ntomp 23 -pin off; runs
- ntmpi 1 -ntomp 23 -pinstride 1 -pin on; doesn't work*
- ntmpi 1 -ntomp 23 -pinstride 2 -pin on; runs
- ntmpi 23 -ntomp 1 -pinstride 1 -pin
Hi,
That's just arbitrary. The alpha, beta, etc nomenclature does not apply to
such a capping group, so they named the carbon using H rather than A, B,
etc. Then the names of the H atoms follows that. That probably simplifies
the job of some bits of code.
Mark
On Fri., 15 Mar. 2019, 16:28 Neena
Hi Users.
I have Performed dssp for 1000ns simulation. On converting the xpm to eps,
the axis are not visible to any extent. I have tried with different values
and I couldn't obtain a good image. Can anyone pass possible suitable
commands for long simulations to obtain a satisfactory image?
--
Hi Szilárd,
thanks for the quick reply.
About the first suggestion, I'll try and give feedback soon.
Regarding the second, I attached the log-file for the case of
mdrun -v -nt 25
Which ends in the known error message.
Again, thanks a lot for your information and help.
Best wishes,
Steffi
On Fri, Mar 15, 2019 at 5:02 PM Tafelmeier, Stefanie <
stefanie.tafelme...@zae-bayern.de> wrote:
> Hi,
>
> about the tests:
> - ntmpi 1 -ntomp 22 -pin on; doesn't work*
>
OK, so this suggests that your previously successful 22-thread runs did not
turn on pinning, I assume?
Can you please try:
Hi,
Please share log files with an external service attachments are not
accepted on the list.
Also, when checking the error with the patch supplied, please run the
following cases -- no long runs are needed just want to know which of these
runs and which of these doesn't:
- ntmpi 1 -ntomp 22
Hello gromacs users,
A small question, why is that atoms of a methyl group named/ labelled
differently in an Acetyl terminal group vs Alanine (below parameters from .rtp
file from OPLS-AA ff)? I do understand naming convention in the methyl group of
Alanine, but not in acetyl group.
[ ACE ]
Did you use a binary compiled generated from patched sources? If so can you
please also share the exact error message on the standard output?
--
Szilárd
On Fri, Mar 15, 2019 at 5:57 PM Szilárd Páll wrote:
> On Fri, Mar 15, 2019 at 5:02 PM Tafelmeier, Stefanie <
>
Hi Gromacs folks,
I ran a test run with an apo protein without any modifications and
simulated for 10 ns. However, the coulombic map of the pdb output from
gromacs is all positive (red colored by using the coloring method in
chimera). At first I thought it is chimera's error because there were
Hi!
I need to add non-bonded CU2+ ion to CHRAMM36. How can I find these
parameters (sigma and epsilon)? Does it enough to define CU2+ by its
charge, mass, sigma and epsilon?
In addition, I want to know that what are the units of sigma and epsilon in
the CHARMM36 force field?
Regards,
Mohsen
Could anyone be more specific?
On Fri, 15 Mar 2019, 2:25 pm RAHUL SURESH, wrote:
> Hi.
>
> for aminoacids.rtp? the already exist for which you dont need any
> additional files. In case of the small molecule, depending of the ff, there
> are few scripts or servers available to generate itp file,
As Justin has pointed out , this process is well documented and UNL is not
often found in molecules. No matter what - you will have to do some leg work.
Because I run into this almost daily, this may at least get you started. First
try using x2top with a selected force field. If your
Hi,
How large is your perturbed region and your normal region? The FEP
short-ranged kernels run on the CPU, and are not written very well for
performance. So the larger the perturbed region, the worse things get.
Because there's a lot of extra CPU work when running FEP, you may see
improvements
Hi all
How can I find the chains interacting, forming H-bonds and hydrophobic
interactions after a protein-ligand simulation? I tried VMD but there seems not
to be good options to characterize them all. Is it possible to do such analysis
in VMD or Gromacs and how?
Thanks.
--
Gromacs Users
Dear all,
I have a small molecule pdb file. I need the itp and rtp entry for the
molecule in OPLS ff. TPPMKTOP is not working properly. Can any one please
suggest me with a server that can automatically produce the itp entry and
rtp entry for aminoacids.rtp.
Thanks in advance-
Soham
--
Hi users
I find few methods of plotting free energy landscape. Of them one is
plotting rg vs rmsd and another one is using Principe components. What is
the difference in these two methods? Is the plot obtained by both the
method are one and the same?
Thank you
--
Gromacs Users mailing list
*
Hi.
for aminoacids.rtp? the already exist for which you dont need any
additional files. In case of the small molecule, depending of the ff, there
are few scripts or servers available to generate itp file, which you can
find from documentation.
All the server generated datas need not be accurate
Hi,
In that case you have 122*87=10614 perturbed atoms in a 91K atom system.
The FEP code in GROMACS is not engineered to run fast anywhere near that
regime. If possible, I'd suggest you explore what you can learn with e.g.
just one drug molecule in a similar system.
Mark
On Fri, 15 Mar 2019 at
Dear Mark
I have a system containing formed lipid-bilayer (Phospholipid + drug
molecules) (~91 K atoms): There are 120 Phospholipids and 87 drug molecules
in the system box of (8 X 8 X 12). I am trying to grow the all the drug
molecules (87) (each drug consist of 122 atoms) from decoupled state
Hi Stefanie,
Unless and until the error and performance-related concerns prove to be
related, let's keep those separate.
I'd first focus on the former. To be honest, I've never encountered such an
issue where if you use more than a certain number of threads, the run
aborts with that error. To
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