Is there really no way to continue this simulation? Thanks in advance!
On 17.04.20 11:35, Johannes Hermann wrote:
Dear all,
I am doing free energy hamiltonian replica exchange simulations and
unfortunately my simulation crashed (not because of the MD system
itself but because of a hardware fa
On 4/21/20 2:08 AM, Rolly Ng wrote:
Dear Gromacs user and Dr. lemkul,
I think my previous email is too large to send on the list. Could you
please kindly look at the link for the plots?
https://www.researchgate.net/post/GROMACS_2020_pull_code_produces_strange_Potential_Mean_Force_PMF_resu
Thank you so much Prof. Lemkul for your reply.
As I don't know what and how to use this pull code, if you have any idea
regarding what you have suggested will be of great help to me.
Meanwhile I will read more about it.
Thank You
On Mon, Apr 20, 2020 at 1:14 AM Justin Lemkul wrote:
> [image: Bo
On 4/21/20 8:07 AM, Shashank Ranjan Srivastava wrote:
Thank you so much Prof. Lemkul for your reply.
As I don't know what and how to use this pull code, if you have any idea
regarding what you have suggested will be of great help to me.
Meanwhile I will read more about it.
General principles
Hi Magnus,
Actually I am confused with the available options for the
"pull-pbc-ref-prev-step-com" and "pull-group1-pbcatom".
For pull-pbc-ref-prev-step-com : YES or NO: where YES should be used when
one of the group is large, even the 2020.1 version of grmacs would give a
warning if one used No in
Dear Justin,
I cut the x-axis to 8nm but I have uploaded the original histogram plot to
RG. Please have a look again, thank you.
I used the following command for wham,
gmx wham -it tpr-files.dat -if pullf-files.dat -o -hist -unit kCal
I used the AMBER99SB-ILDN forcefield and protein protein pair
Dear all,
I am a bit confused about [ dihedral constraints ].
I was planning to contraint a dihedral in a "flat-bottom" way, so that
e.g. angles between 120 and 240 deg are sampled, but above 240 and below
140 are basically "not allowed". In other words, I just want a harmonic
potential, where th
On 4/21/20 10:40 AM, Rolly Ng wrote:
Dear Justin,
I cut the x-axis to 8nm but I have uploaded the original histogram plot to
RG. Please have a look again, thank you.
It's not a matter of changing the axis. Your histograms indicate
sampling from 2 - 8 nm. Your PMF is computed from 0 - 10 nm.
I think the output from WHAM in the terminal may give some information to
detect the problem.
WHAM will tell you the boundary he used to fit your PMF because your
histogram and COM position both tell us your reaction coordinate is range
from about 2-7nm but WHAM fit from 0-10nm is so strange
Best r
Dear Justin and Vu,
Thank you and I am checking the tpr and vxg files by reducing the number of
files in the 2 dat files. The first 10 data points seems giving the correct PMF
reading although the list is incomplete, so I suspect that some of my tpr and
xvg files are bad for wham.
I will repor
Configure with -DGMX_EXTERNAL_BLAS=OFF -DGMX_EXTERNAL_LAPACK=OFF
Cheers,
--
Szilárd
On Fri, Apr 17, 2020 at 2:07 PM Mahmood Naderan
wrote:
> Hi
> How can I disable MKL while building gromacs? With this configure command
>
> cmake .. -DGMX_BUILD_OWN_FFTW=ON -DGMX_GPU=on -DGMX_FFT_LIBRARY=fftw3
Hi,
Note that the new generation Ryzen2-based CPUs perform even better than
those we benchmarked for that paper. The 3900-series Threarippers are great
for workstations, unless you need the workstation form-factor, you are
better off with servers like the TYAN GA88B8021. If so, i EPYC 1P is what
Hi Szilárd,
We haven't decided yet on what price point& performance level we would be
settling on, but this is overall great advice, thanks a lot.
Alex
On 4/21/2020 4:32 PM, Szilárd Páll wrote:
Hi,
Note that the new generation Ryzen2-based CPUs perform even better than
those we benchmarked f
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