Dear all,
There is an inconsistency in the truncated octahedron entry in table 3.1
of the reference manual (version 2018 and all previous ones I checked).
The value indicated for the bc and ab angles is 71.53 degrees, but the
vectors a, b and c indicated in the table give the value 70.53 degre
Hi,
You have a bonded interaction at a distance of 10 nm. I assume that's not
your intention. Perhaps you should give a configuration to grompp that has
whole molecules. IIRC less ancient versions of GROMACS do a better job of
this.
Mark
On Thu, Feb 15, 2018 at 5:39 PM Iman Ahmadabadi
wrote:
>
Hi,
There's not enough information to say. What makes you think your molecules
will fit in the spaces you say are there? What radii did you suggest for
the atoms in your molecules?
Mark
On Thu, Feb 15, 2018 at 6:54 PM Joydeep Munshi wrote:
> Hello,
>
> I have a system of polymer(P3HT)-fulleren
Szilárd wrote:> Option A) Get a gcc 5.x (e.g. compile from source)
> Option B) Install CUDA 9.1 (and required driver) which is compatible
> with gcc 6.3
> (http://docs.nvidia.com/cuda/cuda-installation-guide-linux/index.html)
didn't try A (there might be a good reason why stretch does not have gcc
Hello,
I have a system of polymer(P3HT)-fullerene system. I am using initially
Insert-molecule command to insert N number of P3HT molecules followed by
PCBM molecules. Finally I am solvating the system using Solvate command.
While I am trying to insert N=300 atoms it is successfully inserting all
Yes, it is true, sorry, but I have problems with both. With version
2018 the error it's diferent. that's why i compiled an older version.
Osmany
-Original Message-
From: Szilárd Páll
Reply-to: gmx-us...@gromacs.org
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] GPU pr
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
file.tpr -n index -o file.gro -pbc whole but nothing happens.
PS: Also, what you pasted in here states "2016.4", but your subject
claims version 2018
--
Szilárd
On Thu, Feb 15, 2018 at 6:23 PM, Szilárd Páll wrote:
> Please provide a full log file output.
> --
> Szilárd
>
>
> On Thu, Feb 15, 2018 at 6:11 PM, Osmany Guirola Cruz
> wrote:
>> Hi
>>
>> I am ha
Please provide a full log file output.
--
Szilárd
On Thu, Feb 15, 2018 at 6:11 PM, Osmany Guirola Cruz
wrote:
> Hi
>
> I am having problems running mdrun command compiled with GPU
> support(cuda 9.0).
> here is the output of the mdrun command
>
>
> Using 1 MPI thread
> Using 4 Open
Hi
I am having problems running mdrun command compiled with GPU
support(cuda 9.0).
here is the output of the mdrun command
Using 1 MPI thread
Using 4 OpenMP threads
1 compatible GPU is present, with ID 0
1 GPU auto-selected for this run.
Mapping of GPU ID to the 1 PP rank in this
Dear Gromacs Users,
In one job, I always get in (any number of nodes) the domain decomposition
error as following and I don't know what should I do. I have to use the
-dds or -rdd setting for my problem?
Sincerely
Iman
Initializing Domain Decomposition on 56 nodes
Dynamic load balancing: auto
Wi
as compilation of gmx-2018 idn't work for me i went back to 2016.4
after some google-ing i found that the following commands work, and gmx
compiles without any complaints...
> cmake .. -DGMX_GPU=on -DNVML_FOUND=1
> -DNVML_LIBRARY=/usr/lib/x86_64-linux-gnu/libnvidia-ml.so.1
> -DNVML_INCLUDE_DIR=
Hi Dr.Lemkul
Thank you very much for your answer, it was very great help for me
Thank you
Regards
Azadeh
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http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List befor
Option A) Get a gcc 5.x (e.g. compile from source)
Option B) Install CUDA 9.1 (and required driver) which is compatible
with gcc 6.3
(http://docs.nvidia.com/cuda/cuda-installation-guide-linux/index.html)
--
Szilárd
On Thu, Feb 15, 2018 at 2:34 PM, Michael Brunsteiner wrote:
>
> Hi,
> I have prob
Hi,
I have problems compiling gromacs-2018 (January 10 release) on debian stretch
(vanilla)
my specs: Linux 4.9.0-4-amd64 #1 SMP Debian 4.9.65-3+deb9u1 (2017-12-23) x86_64
GNU/Linux
gcc-6.3.0,Cuda compilation tools, release 8.0, V8.0.44
graphics: Geforce GTX 780.
I do:
> cmake .. -DGMX_GPU=on
w
On 2/15/18 4:13 AM, Rakesh Mishra wrote:
Dear Justin thanks for your advise.
I will check for longer run for getting response according to you.
I would like to explain my system,which is siRNA of chain A and B.
Here, after doing all formalities, I had run 10 ns then try to apply the
pull pro
On 2/15/18 4:17 AM, kordza...@aut.ac.ir wrote:
Hi Dr.Lemkul
you said, the breaking molecule occured because of period boudary condition,
isn't it a problem?
because before your answer I thought I must select bigger box in order to the breaking
won't occur. but now I understand the beaking i
On 2/14/18 11:16 PM, kordza...@aut.ac.ir wrote:
Hi Dr.Lemkul
Thank you very much for your answer and your time
I 'm using Gromos 54a7 force field, How can I find my force field is
parametrized in such a way that the nonbonded energy decomposition has some
physical meaning?
In your case,
Hi Justin,
That makes sense, I've found where the parameters are
Thanks for your help
James
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
on behalf of Justin Lemkul
Sent: 14 February 2018 22:31:07
To: gmx-us...@gromacs.org
Subject: Re: [gmx-user
Hi Dr.Lemkul
you said, the breaking molecule occured because of period boudary condition,
isn't it a problem?
because before your answer I thought I must select bigger box in order to the
breaking won't occur. but now I understand the beaking isn't a problem.
I have another question, what is d
Dear Justin thanks for your advise.
I will check for longer run for getting response according to you.
I would like to explain my system,which is siRNA of chain A and B.
Here, after doing all formalities, I had run 10 ns then try to apply the
pull protocol.
See, here for pulling this system, I
Dear Justin and Mark,
The define = -DPOSRES -DFLEXIBLE is correct and thank you so much for your
help.
Respectfully,
Iman
On Wed, Feb 14, 2018 at 11:17 PM, Iman Ahmadabadi <
imanahmadabad...@gmail.com> wrote:
> Dear Justin,
>
> Because there is a movement on atoms that posres should act on them
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