Unfortunately not
Mark
On Fri, Feb 9, 2018, 17:56 Nick Johans wrote:
> Hi,
>
> I deleted the pullf.xvg file unintentionally. Is there anyway to restore
> and reproduce it from other outputs?
>
> Best regards
> -Nick
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://
Hi,
On Fri, Feb 9, 2018, 17:15 Kevin C Chan wrote:
> Dear Users,
>
> I have encountered the problem of "There is no domain decomposition for n
> nodes that is compatible with the given box and a minimum cell size of x
> nm" and by reading through the gromacs website and some threads I
> understa
Hi,
On Fri, Feb 9, 2018, 18:05 Alex wrote:
> Just to quickly jump in, because Mark suggested taken a look at the
> latest doc and unfortunately I must admit that I didn't understand what
> I read. I appear to be especially struggling with the idea of gputasks.
>
Szilard's link specifically targ
On Fri, Feb 9, 2018, 16:57 Daniel Kozuch wrote:
> Szilárd,
>
> If I may jump in on this conversation, I am having the reverse problem
> (which I assume others may encounter also) where I am attempting a large
> REMD run (84 replicas) and I have access to say 12 GPUs and 84 CPUs.
>
> Basically I h
Hi,
That's always your call. You perform equilibration to swap between MM
(energy minimization) and MD (kinetic energy). In the other word you slowly
start MD and prevent unwanted and unrealistic rearrangement in your system.
If initial positions are important - you restrain the interesting
molecul
Hello Elton,
Thanks a lot for your help! I just tried to load a binutils library (it
was installed on the cluster) and install Gromacs 2018 again,
it works now!
All the best,
Qinghua
On 02/09/2018 11:33 PM, Elton Carvalho wrote:
If you are in a hurry, you can download the binutils package
If you are in a hurry, you can download the binutils package from here
https://www.gnu.org/software/binutils/ and compile it on your own, setting
the PREFIX to a directory in your home, then use $PATH to make your binary
the highest priority.
Cheers,
Elton
On Fri, Feb 9, 2018 at 8:17 PM, Qinghua
Hello Elton,
Thanks a lot for your information, I already sent an e-mail to the
administrator,
hopefully they will fix it.
All the best,
Qinghua
On 02/09/2018 08:03 PM, Elton Carvalho wrote:
Hello, Qinghua,
The error message refers to the standard library. I believe the package
that provid
Hello, Qinghua,
The error message refers to the standard library. I believe the package
that provides this in ubuntu is glibc. Check that it's a current enough
version.
Another thing is that the liker (ld) needs to support C++11. That's the
binutils package. I've had success with version 2.29. No
Hi,
Thanks for the report!
Did you build with or without hwloc? There is a known issue with the
automatic pin stride when not using hwloc which will lead to a "compact"
pinning (using half of the cores with 2 threads/core) when <=half of the
threads are launched (instead of using all cores 1 thre
Just to quickly jump in, because Mark suggested taken a look at the
latest doc and unfortunately I must admit that I didn't understand what
I read. I appear to be especially struggling with the idea of gputasks.
Can you please explain what is happening in this line?
-pme gpu -nb gpu -ntmpi 8
Hi,
I deleted the pullf.xvg file unintentionally. Is there anyway to restore
and reproduce it from other outputs?
Best regards
-Nick
--
Gromacs Users mailing list
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
* Can't post? Read htt
Dear Users,
I have encountered the problem of "There is no domain decomposition for n
nodes that is compatible with the given box and a minimum cell size of x
nm" and by reading through the gromacs website and some threads I
understand that the problem might be caused by breaking the system into t
Szilárd,
If I may jump in on this conversation, I am having the reverse problem
(which I assume others may encounter also) where I am attempting a large
REMD run (84 replicas) and I have access to say 12 GPUs and 84 CPUs.
Basically I have less GPUs than simulations. Is there a logical approach to
On Thu, Feb 8, 2018 at 10:20 PM, Mark Abraham
wrote:
> Hi,
>
> On Thu, Feb 8, 2018 at 8:50 PM Alex wrote:
>
> > Got it, thanks. Even with the old style input I now have a 42% speed up
> > with PME on GPU. How, how can I express my enormous gratitude?!
> >
>
> Do the science, cite the papers, spr
On Fri, Feb 9, 2018 at 4:25 PM, Szilárd Páll wrote:
> Hi,
>
> First of all,have you read the docs (admittedly somewhat brief):
> http://manual.gromacs.org/documentation/2018/user-guide/
> mdrun-performance.html#types-of-gpu-tasks
>
> The current PME GPU was optimized for single-GPU runs. Using mu
Hi,
First of all,have you read the docs (admittedly somewhat brief):
http://manual.gromacs.org/documentation/2018/user-guide/mdrun-performance.html#types-of-gpu-tasks
The current PME GPU was optimized for single-GPU runs. Using multiple GPUs
with PME offloaded works, but this mode hasn't been an
Great to hear!
(Also note that one thing we have explicitly focused on is not only peak
performance, but to get as close to peak as possible with just a few CPU
cores! You should be able to get >75% perf with just 3-5 Xeon or 2-3
desktop cores rather than needing a full fast CPU.)
--
Szilárd
On
Hello,
does anybody know of a software (with gui!) that allows to draw and
assign residue names atom per atom? For example display a molecule with
the gui and clicking on the atoms to define the residue name.
Thanks in advance,
Momin
--
Momin Ahmad
Karlsruhe Institute of Technology (KIT)
S
Dear GMX developers,
I am trying to install Gromacs2018 with cuda on clusters, the
installation was successful on one cluster,
but failed on the other cluster. I guess there might be some library
missing on the other cluster.
For the succeeded one, the operating system is openSUSE 42.2 (GNU/L
Dear all
I have carried out a protein ligand simulation for 50ns and performed a
PBSA calculation for 10-20ns trajectory. I get a positive binding energy.
How can I tackle it..?
Thank you
--
*Regards,*
*Rahul Suresh*
*Research Scholar*
*Bharathiar University*
*Coimbatore*
--
Gromacs Users ma
Hi list,
I am preparing an amorphous sample using GROMACS but i am in doubt that
during the equilibration stage ( NVT & NPT ) do i need to put position
restraint on my polymer as there are no solvent in my system and if i have
to use position restraint then why i should do that?
THANKS,
SK
--
Gr
Hello,
I have got the zwitterion structure of beta-alanine from ChEBI website, and
the ChEBI Id is *CHEBI:57966.*
I downloaded in mol2 format and tried with the CGenFF and swissparam servers
to get the charmm FF. but i have got two different charges for each of the
case.
In case of CGenFF the char
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