On Sep 4, 2013 7:59 AM, "James" wrote:
>
> Dear all,
>
> I'm trying to run Gromacs on a Fujitsu supercomputer but the software is
> crashing.
>
> I run grompp:
>
> grompp_mpi_d -f parameters.mdp -c system.pdb -p overthe.top
>
> and it produces the error:
>
> jwe1050i-w The hardware barrier couldn'
Seems like a bug. Please open an issue at redmine.gromacs.org, and be sure
to mention the GROMACS version.
Why are you using -pd?
On Sep 4, 2013 2:20 AM, "Nilesh Dhumal" wrote:
> Hello
>
> I am running a simulation with charge and without charge for 128 pairs of
> bmim-tf2n ioinc liquids.
> This
I am facing a problem while simulating the tRNA molecule
while converting pdb to gro,
Fatal error:
Atom OP3 in residue A 1 was not found in rtp entry RA5 with 31 atoms
while sorting atoms.
force field used 3 (AMBER96 protein, nucleic AMBER94), water model TIP3P.
i checked in gromacs error list,
On 9/4/13 6:04 AM, Prajisha Sujaya wrote:
I am facing a problem while simulating the tRNA molecule
while converting pdb to gro,
Fatal error:
Atom OP3 in residue A 1 was not found in rtp entry RA5 with 31 atoms
while sorting atoms.
force field used 3 (AMBER96 protein, nucleic AMBER94), water
Hello,
Does anyone know if there is a tool called g_saxs available in the latest
version of Gromacs or planned for any future version. It is supposed to compute
small-angle x-ray scattering profiles from trajectories.
Many thanks
Andreas
--
gmx-users mailing listgmx-users@gromacs.org
http:/
On 9/4/13 8:55 AM, Kukol, Andreas wrote:
Hello,
Does anyone know if there is a tool called g_saxs available in the latest
version of Gromacs or planned for any future version. It is supposed to compute
small-angle x-ray scattering profiles from trajectories.
It is in the master branch in
Thanks Justin, for your quick response, albeit what does it mean ('master
branch' and 'git repro') ? Can it be used ?
Many thanks
Andreas
> -Original Message-
> From: gmx-users-boun...@gromacs.org [mailto:gmx-users-
> boun...@gromacs.org] On Behalf Of Justin Lemkul
> Sent: 04 September
On 9/4/13 9:23 AM, Kukol, Andreas wrote:
Thanks Justin, for your quick response, albeit what does it mean ('master
branch' and 'git repro') ? Can it be used ?
It means that it's in the development code (the git repository) in the master
branch, which is the one in which new features are
DEa Users,
My system involves protein in vacuum - 80 atoms in box of 9x9x9 nm3. I want
to use PME in my mdp:
rcoulomb = 2.0
coulombtype = PME
pme_order= 4
fourierspacing = 0.12
The cutoff needs to stay like this, I have my own tables with VDW, bonds,
angles and
Thank you! Would you suggest just a cut-off for coulmb?
Steven
On Wed, Sep 4, 2013 at 3:09 PM, Justin Lemkul wrote:
>
>
> On 9/4/13 10:03 AM, Steven Neumann wrote:
>
>> DEa Users,
>>
>> My system involves protein in vacuum - 80 atoms in box of 9x9x9 nm3. I
>> want
>> to use PME in my mdp:
>>
>
I was following
http://www.gromacs.org/Documentation/Installation_Instructions. The link to
4.6.3 regression test set isn't obvious. Following the pattern, I
downloaded the 4.6.3 regression test tarball (which apparently unpacks to a
folder named for 4.6.2). Now, GMX_CPU_ACCELERATION=None passes al
Hi,
I was wondering if there is a documentation of all the source code
variables is available or not.
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Thank you. i am using my own vdw tables so need a cut off.
On Wed, Sep 4, 2013 at 3:13 PM, Justin Lemkul wrote:
>
>
> On 9/4/13 10:11 AM, Steven Neumann wrote:
>
>> Thank you! Would you suggest just a cut-off for coulmb?
>>
>>
> Not a finite one. The best in vacuo settings are:
>
> pbc = no
On 9/4/13 10:15 AM, HANNIBAL LECTER wrote:
Hi,
I was wondering if there is a documentation of all the source code
variables is available or not.
No.
-Justin
--
==
Justin A. Lemkul, Ph.D.
Postdoctoral Fellow
Department of Pharmaceutical Sci
On 9/4/13 10:20 AM, Steven Neumann wrote:
Sorry it is a vacuum but I included implicit solvent in vdw parameters...So
I need pbc as well.
Sorry, this doesn't make much sense to me. If you're using implicit solvent
(GB), then it's by definition not vacuum. I also find the same to be true
On 9/4/13 10:11 AM, Steven Neumann wrote:
Thank you! Would you suggest just a cut-off for coulmb?
Not a finite one. The best in vacuo settings are:
pbc = no
rlist = 0
rvdw = 0
rcoulomb = 0
nstlist = 0
vdwtype = cutoff
coulombtype = cutoff
-Justin
On Wed, Sep 4, 2013 at 3:09 PM, Justin L
On 9/4/13 10:18 AM, Steven Neumann wrote:
Thank you. i am using my own vdw tables so need a cut off.
Then I guess you have your answer. Finite cutoffs in vacuo can lead to serious
artifacts if you're not careful. Tread lightly.
-Justin
On Wed, Sep 4, 2013 at 3:13 PM, Justin Lemkul
On 9/4/13 10:03 AM, Steven Neumann wrote:
DEa Users,
My system involves protein in vacuum - 80 atoms in box of 9x9x9 nm3. I want
to use PME in my mdp:
rcoulomb = 2.0
coulombtype = PME
pme_order= 4
fourierspacing = 0.12
The cutoff needs to stay like this, I
Sorry it is a vacuum but I included implicit solvent in vdw parameters...So
I need pbc as well.
On Wed, Sep 4, 2013 at 3:18 PM, Steven Neumann wrote:
> Thank you. i am using my own vdw tables so need a cut off.
>
>
>
>
> On Wed, Sep 4, 2013 at 3:13 PM, Justin Lemkul wrote:
>
>>
>>
>> On 9/4/13
Thanks a lot!
On Wed, Sep 4, 2013 at 3:46 PM, Justin Lemkul wrote:
>
>
> On 9/4/13 10:44 AM, Steven Neumann wrote:
>
>> Thank you. But with rwdv = 0 and vdw_type =User the vdw parameters will be
>> taken into account at infinite cutoff or omitted?
>>
>>
> As I said, setting the cutoffs to zero
On 9/4/13 10:44 AM, Steven Neumann wrote:
Thank you. But with rwdv = 0 and vdw_type =User the vdw parameters will be
taken into account at infinite cutoff or omitted?
As I said, setting the cutoffs to zero does not omit interactions. The zero is
used to trigger infinite cutoffs.
-Justin
Thank you. But with rwdv = 0 and vdw_type =User the vdw parameters will be
taken into account at infinite cutoff or omitted?
On Wed, Sep 4, 2013 at 3:37 PM, Justin Lemkul wrote:
>
>
> On 9/4/13 10:35 AM, Steven Neumann wrote:
>
>> I am not using any solvent. I mimic the presence of water by vdw
On 9/4/13 10:35 AM, Steven Neumann wrote:
I am not using any solvent. I mimic the presence of water by vdw tabulated
potentials. I wish to see what electrostatics will change. And the coulomb
cutoff = 0 will completely remove the electrostatic, right?
No, it does the opposite. Setting all
I am not using any solvent. I mimic the presence of water by vdw tabulated
potentials. I wish to see what electrostatics will change. And the coulomb
cutoff = 0 will completely remove the electrostatic, right?
On Wed, Sep 4, 2013 at 3:23 PM, Justin Lemkul wrote:
>
>
> On 9/4/13 10:20 AM, Steve
Hi everyone,
I am simulating a system of paracetamol crystal in ethanol solvent. I used
pdb2gmx to generate the topology and gro file and I minimized the system using
steepest decent. As long as I perform NVT simulations at any temperature, the
simulations goes on! But as soon as I switch from
Hi all,
I just want to ask you which is about REMD..I just understanding about
the MD simulation which is the basic one..If i have a several models
that i need to see the interaction between them is it okay to use
MD?Or i need to use REMD instead?
Thanks in advance,
--
Best Regards,
Nur Syafiq
Did you follow the link in the error message?
On Wed, Sep 4, 2013 at 7:17 PM, Golshan Hejazi wrote:
> Hi everyone,
>
> I am simulating a system of paracetamol crystal in ethanol solvent. I used
> pdb2gmx to generate the topology and gro file and I minimized the system
> using steepest decent. As
Going through the GROMOS53a6 parameters, found that there appears to be an
inconsistency between what is present within the ffnonbonded.itp file and that
quoted within the paper (Ooostenbrink et al 2004
http://dx.doi.org/10.1002/Jcc.20090) for the c12 LJ values for CH2 and CH3 in
the [ pairtype
Hi,
I have run my MD till 13 ns extending it by 500 ps simulations. But while
shifting the data from a system, accidentally I lost my tpr files. My
backup contains trr files till 13 ns (i.e. all trr files) and tpr files
till 6.5ns. How could I regenerate the tpr files now if I have to extend
the s
Hi,
well I guess it depends on what models you mean...
REMD is a technique to enhance the conformational sampling. So if you have a
e.g. a protein that is disordered or has large
disordered parts. Using REMD several copies of the same system are simulated,
each replica at a
different temperatu
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