Hi Zhang,
I'm fairly sure GLU0 does what you want, but I'm not 100% sure on the
terminus. It'll probably do what you want, but I've forwarded your
question to the group to be sure.
Peter
On 29-01-19 01:38, ZHANG Cheng wrote:
> Dear martini friends,
>
>
> By default, the "martinize.py" will
>
I got an answer :)
> The GLU0 is good indeed. For the termini, it depends on the secondary
structure. Coil is the most likely for a terminus, so P5 should be OK.
Note that there is a -nt option in martinize that sets neutral termini.
> Jonathan
Peter
On 29-01-19 10:44, Peter Kroon wrote:
> Hi
Re: Radius of gyration and moment of inertia (Dallas Warren)
Yes of course the ratios are similar. The shapes are similar
But when I measure the distance of the two agrregates in VMD , the length
of the aggregates and the width of the aggregates are more or less of the
same dimensions. Which mean
Hi,
Yes of course the ratios are similar. The shapes are similar
But when I measure the distance of the two agrregates in VMD , the length
of the aggregates and the width of the aggregates are more or less of the
same dimensions. Which means that the size of the aggregates are
comparable and there
Dear Peter,
Thank you very much! I will use GLU0 and -nt.
Yours sincerely
Cheng
-- Original --
From: "ZHANG Cheng"<272699...@qq.com>;
Date: Tue, Jan 29, 2019 08:38 AM
To: "gromacs.org_gmx-users";
Subject: How to adjust the default protonation states in m
Dear Martini friends,
My protein has 10 Cys with 5 disulfind bonds in light chain (LC) and heavy
chain (HC):
) Interchain disulfide bond: LC214 ?C HC220
) Intrachain disulfide of LC: LC23 ?C LC88, LC134 ?C LC194
) Intrachain disulfide of HC: HC144 ?C HC200, HC96 ?C HC22
Using this command will
Hi Cheng,
What’s the distance between the two interchain SG atoms? You can either tune
the distance used for autodetecting cys bonds, or just specify all of them
using the command line. Try `python martinize.py -h`
Peter
PS. The cgmartini.nl forum is also back online, which might be a better me
Dear Peter,
Thank you, I find the answer now. Sorry I was using a pdb that the SS length is
too long to form the SS bond. After changing to a correct one, I got the
solution.
I think, if we have more than one chain, we MUST use "-merge" option, so that
the interchain SS bond can shown in the
Dear gromacs users
I am working on molecular simulation using gromacs 2018.4, we have a new
gpu machine which has two GPU cards.
I have new workstation with 20 cores (Intel I9 processors) with 3.3 GHz
Nvidia Getforce X1080 Ti cards(2 nos)
I have tried running simulation using the command gmx
I am not expert on this subject but have recently gone through the
exercise...
Firstly, does nvidia-smi indicate both cards are active ?
Secondly, for the nvt or npt runs have you tried mdrun commands similar to
:
mdrun -deffnm file -nb gpu -gpu_id 01
or
mdrun -deffnm file -nb gpu -pme
Dear Users,
I am trying to understand a model of water evaporation and am asking for a
few of suggestions or just point to a link.
So far I have modeled 1 molecules of spce water and equilibrated to a
density near 1 gm/cc. I then double the size of the box and then using
p-coupl
Dear all,
I am using gromacs 5.1.2 and I am doing simulation with lysin and
surfactant.
Now in the same box I want two lys30 (two identical lysin) oriented once
in parallel and once in orthogonal each other.
I tried using gmx insert-molecules ... but it's a random orientation.
I also tri
Giuseppe,
Use Avogadro, import or construct the four ( if I understand your model )
molecules in the desired orientations. Save as a pdb. Used editconf to
construct the box.
Paul
-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
On Behalf Of Giuseppe R
Del Sor
Hello GMX users
I'm simulating a complex system. I started with energy minimization step
which went fine then followed by a short NPT for equilibration then
followed by energy minimization for more minimization and its output as
below
Steepest Descents converged to Fmax < 10 in 3783 steps
Potential
Hey everyone! I need help, please. When I try to run MD with GPU I get the next error: Command line:gmx_mpi mdrun -deffnm md -nb autoBack Off! I just backed up md.log to ./#md.log.4#NOTE: Detection of GPUs failed. The API reported:GROMACS cannot run tasks on a GPU.Reading file md.tpr, VERSION 2018.
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