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_Po
tential_Mean_Force_PMF_result
I tried to applied the umbrella t
Hi Alex,
I don't see why it would need pull-group1-pbcatom = -1. Why not pick a
central atom?
Regards,
Magnus
On 2020-04-20 13:40, Alex wrote:
Hi Magnus,
Thanks.
The problem raises only because of using the pull-pbc-ref-prev-step-com
which needs the pull-group1-pbcatom to be -1 to be meanin
Hi Magnus,
Thanks.
The problem raises only because of using the pull-pbc-ref-prev-step-com
which needs the pull-group1-pbcatom to be -1 to be meaningful.
For an identical system and mdp parameters using 2018 version of gromacs
which is independent to the pull-pbc-ref-prev-step-com, I see no issue.
On 4/20/20 6:39 AM, Mijiddorj B wrote:
Dear Justin,
Thank you very much for your reply. I see. I cut trr file several ns before
the stopped frame, and I would like to cut the corresponding checkpoint
file before the stopped frame.
Checkpoint files are not trajectories; they only contain one
Dear Justin,
Thank you very much for your reply. I see. I cut trr file several ns before
the stopped frame, and I would like to cut the corresponding checkpoint
file before the stopped frame.
Is it possible to get the specific frame checkpoint using gmx?
I would like to re-perform the extended sim
On 4/20/20 3:51 AM, 변진영 wrote:
Hi Prasanth
Firstly Sorry for late reply…
The force field I used is Gromacs 5.x.x 54a7 came from ATB.
I downloaded and used the all-atom topology file(.itp) so I said that it is
all-atom simulation.
By any chance, is it wrong approach??
The GROMOS force
Hi Jinyoung,
I'm glad to hear that you have found the problem. You can always use grompp to
check your topology of the whole system. If you want to understand the GROMACS
topology, check Chapter 5. Topologies in GROMACS Manual.
Words in the end: If you have mastered the basic process of protein
Hi Prasanth
Firstly Sorry for late reply…
The force field I used is Gromacs 5.x.x 54a7 came from ATB.
I downloaded and used the all-atom topology file(.itp) so I said that it is
all-atom simulation.
By any chance, is it wrong approach??
> 2020. 4. 17. 오후 7:58, Prasanth G, Research Scholar
Sorry, about the statement about pbcatom -1. I was thinking about 0. I
don't know if pbcatom -1 is good or not in this case.
Regards,
Magnus
On 2020-04-20 09:24, Magnus Lundborg wrote:
Hi Alex,
I don't think this is related to using pull-pbc-ref-prev-step-com.
Have you tried without it? How
Hi Yu
I simulated the both case (1), (2) for only all-atom ligand system and only
protein system respectively you mentioned.
I run the each case; the NVT and NPT equilibration with 200ps and 1ns
respectively. And there are no problems during NVT and NPT equilibration.
And while I wrote the liga
Hi Alex,
I don't think this is related to using pull-pbc-ref-prev-step-com. Have
you tried without it? However, it is risky using pbcatom -1, since you
don't know what atom you are using as the initial reference. I would
suggest picking an atom you know is located at the centre of the structur
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