Why can't it be called 2017?
*How it is different from Gromacs 5.1.4 *
*Is there any need to upgrade from **Gromacs 5.1.4 to *GROMACS 2016.4
On Fri, Sep 15, 2017 at 9:00 PM, <
gromacs.org_gmx-users-requ...@maillist.sys.kth.se> wrote:
>
>
> Message: 4
> Date: Fri, 15 Sep 2017 15:15:18 +
> From
Hi All,
Though am naive, and much appreciate the efforts required to put things
altogether but I think I found few things confusing or wrong by mistake or
repeated here:
http://manual.gromacs.org/documentation/2016/user-guide/mdrun-performance.html
The replaced corrections are in [CAPITAL] (plea
Hi,
They do somewhat different things. See parts of
http://manual.gromacs.org/documentation/2016.4/user-guide/mdrun-performance.html#running-mdrun-on-more-than-one-node
Mark
On Fri, Sep 15, 2017 at 5:50 PM Peter Stern
wrote:
> http://manual.gromacs.org/programs/gmx-tune_pme.html
>
>
> -Ori
http://manual.gromacs.org/programs/gmx-tune_pme.html
-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Vidya R
Sent: Friday, September 15, 2017 6:42 PM
To: gmx-us...@gromacs.org
Subject: [gmx
Hi gromacs users,
What is the difference between gmx mdrun and gmx tune_pme? Which is better
to use in a cluster (especially when we submit our jobs through qsub
command?)
Also, what is the purpose of -np option in gmx tune_pme? Can someone
elucidate?
Thanks,
Viday.R
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On 9/15/17 11:14 AM, sp...@iacs.res.in wrote:
- Message from Justin Lemkul -
Date: Fri, 15 Sep 2017 11:12:37 -0400
From: Justin Lemkul
Reply-To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Binary mixture
To: gmx-us...@gromacs.org
On 9/15/17 10:59 AM, sp...@
- Message from Justin Lemkul -
Date: Fri, 15 Sep 2017 11:12:37 -0400
From: Justin Lemkul
Reply-To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Binary mixture
To: gmx-us...@gromacs.org
On 9/15/17 10:59 AM, sp...@iacs.res.in wrote:
Hi all
I want to prepare a cubic
Hi GROMACS users,
The official release of GROMACS 2016.4 is available!
This release fixes several issues found since 2016.3, including disabling
the broken support for automatic PME tuning in mdrun for group-scheme
simulations, and various other fixes. It also implements production-ready
support
On 9/15/17 10:59 AM, sp...@iacs.res.in wrote:
Hi all
I want to prepare a cubic box of 6M urea. How many molecules of urea and
how many water molecules should be added to the simulation box? How to
calculate these numbers? Please help me to solve this.
Everything depends on the size of the b
On 9/15/17 10:57 AM, Elisa Pieri wrote:
Dear Gromacs users,
I'm trying to simulate a system in a membrane. My protein is a rhodopsin
(which contains the RET chromophore); I already have a forcefield to treat
the retinal, i.e. a modified version of an Amber94 forcefield.
Now, I added the membr
Dear Gromacs users,
I'm trying to simulate a system in a membrane. My protein is a rhodopsin
(which contains the RET chromophore); I already have a forcefield to treat
the retinal, i.e. a modified version of an Amber94 forcefield.
Now, I added the membrane in my initial PDB file. I chose Charmm27
Hi all
I want to prepare a cubic box of 6M urea. How many molecules of urea and
how many water molecules should be added to the simulation box? How to
calculate these numbers? Please help me to solve this.
Thanks
Sunipa
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Sounds complex!
Thanks Justin
Sergio Manzetti
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Midtun
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On 9/15/17 4:14 AM, Sergio Manzetti wrote:
Hi, has anyone experience with changing position restrains for DNA in GMX? In case, is it only to
change the figure "1" to "0.75" for instance in the itp file?
If you want to change the magnitude of the restraints, you need to generate a
new file.
I answered this the other day:
https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2017-September/115865.html
-Justin
On 9/14/17 9:55 AM, Agatha Faria wrote:
Dear GROMACS Community,
I am very new with GROMACS I am trying to run a simulation of an ionic liquid
(1-butyl-3-methyl-im
Hi,
I can't tell what you think the error is
Mark
On Fri, 15 Sep 2017 13:46 Rana Rehan Khalid wrote:
> Hi everybody
>
> I am facing this error kindly guide me
>
> hecking for duplicate atoms
> Generating any missing hydrogen atoms and/or adding termini.
> Now there are 324 residues with 51
Hi everybody
I am facing this error kindly guide me
hecking for duplicate atoms
Generating any missing hydrogen atoms and/or adding termini.
Now there are 324 residues with 5193 atoms
Chain time...
Making bonds...
Number of bonds was 5261, now 5260
Generating angles, dihedrals and pairs...
Be
Hi gromacs users,
When i tried using,
gmx tune_pme -np 8 -s eql2.tpr -launch
Got this error..
How to fix it?
[compute-0-3.local:28193] [[20294,1],0] ORTE_ERROR_LOG: A message is
attempting to be sent to a process whose contact information is unknown in
file rml_oob_send.c at line 105
[compute-
Hi gromacs users,
In this command,
gmx mdrun -ntmpi 1 -ntomp 8 -v -deffnm eql2
how to determine the value of pme..
I want to include -npme...
Please help
Thanks,
Vidya.R
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Hi,
This approach to dihedral restraints was removed in 4.6, and removed from
the documentation in 5.0. In such versions, you need to implement such
restraints wholly in the topology file. See PDF reference manual for
details.
Mark
On Fri, Sep 15, 2017 at 7:22 AM minky son wrote:
>
> Hello,
>
Hi, has anyone experience with changing position restrains for DNA in GMX? In
case, is it only to change the figure "1" to "0.75" for instance in the itp
file?
Thanks
Sergio
Sergio Manzetti
[ http://www.fjordforsk.no/logo_hr2.jpg ]
[ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://
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