mdp file is parameter file for md simulations.
You need to copy if you want to use the parameters used in the tutorial.
You can also change that parameter according to your use and need.
On Sat, Feb 17, 2018 at 7:34 AM, neelam wafa wrote:
> -- Forwarded message
-- Forwarded message --
From: "neelam wafa"
Date: 17 Feb 2018 00:57
Subject: how to get .mdp files
To:
Cc:
Hi
I am new to this list. I have run the gromacs tutorial ' lysosime in
water'. now i have to run a
Hi,
I am trying to output the neighbor list calculated during a simulation. I
consulted the manual which says that DUMPNL is the env variable suited for
this purpose.
In my bash script I first set up:
export DUMPNL=10
and then run the simulation (GROMACS version 4.5.4).
I do not see any
Hi all!
I have a question concerning immersion of the ion channel (four subunits
with extracellular domains and a bundles of helixes) into the lipid
bilayer. 6 years ago I used some tutorial or mailing lists, which described
the way from KALP15 tutor. With CCR5 model there were no problems at
On 2/16/18 3:00 PM, Poncho Arvayo Zatarain wrote:
Where shud i see the answer Justin? Please tell me
Like any other post, in your email.
-Justin
De: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
en
Hi,
You can upload a log file to a file-sharing service and share the link :-)
Mark
On Fri, Feb 16, 2018 at 8:22 PM Osmany Guirola Cruz <
osmany.guir...@biocomp.cigb.edu.cu> wrote:
> Hi,
> When I send the full log I received this mail from the list.
>
> -
>
>
>
On 2/16/18 2:35 PM, Poncho Arvayo Zatarain wrote:
Hello Gomacs users: I have a problem with a lipid bilayer. The bilayers is
inverted, the water is in the middle and the lipid tails are outside. How can i
flip it to a correct way? I´m trying with gmx trjconv -f file.gro -s file.tpr
-n
Hello Gomacs users: I have a problem with a lipid bilayer. The bilayers is
inverted, the water is in the middle and the lipid tails are outside. How can i
flip it to a correct way? I´m trying with gmx trjconv -f file.gro -s file.tpr
-n index -o file.gro -pbc whole but nothing happens. In
Hi,
When I send the full log I received this mail from the list.
-
Your mail to 'gromacs.org_gmx-users' with the subject
Re: [gmx-users] GPU problem with running gromacs.2018
Is being held until the list moderator can review it for approval.
The reason it
Hi,
Indeed, this is an issue introduced in the 2018 release which aborts
mdrun if an error is encountered during GPU detection; My first guess
is that one of your GPUs is in exclusive or prohibited mode. You can
use mdrun by skipping that GPU, i.e. setting the CUDA_VISIBLE_DEVICES
environment
Hi GROMACS users,
The official release of GROMACS 2016.5 is available!
This release fixes several minor issues found since 2016.4. It incorporates
all the fixes found in the 5.1.5 release. We encourage all users of the
2016 series to update to 2016.5. Please see the link to the release notes
This is the output with gromacs 2018 and cuda 9
---Program: gmx
mdrun, version 2018Source file: src/gromacs/gpu_utils/gpu_utils.cu
(line 735)Function:void findGpus(gmx_gpu_info_t*)
Assertion failed:Condition: cudaSuccess ==
On 2/15/18 12:38 PM, Poncho Arvayo Zatarain wrote:
Hello Gromacs users: I have a problem with a lipid bilayer, when i watch in
vmd, is inverted, the water is in the middle and the lipid tails are outside.
How can i flip it to a correct way? I´m trying with gmx trjconv -f file.gro -s
On 2/16/18 3:40 AM, Subhomoi Borkotoky wrote:
Hello,
I believe *do_dssp* will do the trick. Generate the *.xpm* matrix file , it
contains the required information.
Only indirectly, but scount.xvg has all that is needed, the number of
residues in a given secondary structure as a function of
hi
just installed gmx-2018 on a x86_64 PC with a Geforce GTX 780 and the
cudasoftware directly from the nvidia webpage (didn't work using the debian
nvidia packages)
output of lscpu is included below.
i find that:
1) 2018 is slightly faster (~5%) than 2016.2) both 2016 and 2018 use the GPU,
Hello,
I believe *do_dssp* will do the trick. Generate the *.xpm* matrix file , it
contains the required information.
Regards,
S. Borkotoky
On Fri, Feb 16, 2018 at 1:30 PM, Sundari wrote:
> Dear gromacs users,
>
> can any one please tell me that how we get the secondary
Dear gromacs users,
can any one please tell me that how we get the secondary structure
propensity or secondary structure content(%) as a function of simulation
time.
I used "gmx do_dssp" but it gives me number of residues forming the
secondary structure vs simulation time. is it same thing or
Dear gromacs users,
can any one please tell me that how we get the secondary structure
propensity or secondary structure content(%) as a function of simulation
time.
I used "gmx do_dssp" but it gives me number of residues forming the
secondary structure vs simulation time. is it same thing or
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