Dear all,
While running mdrun using following mdpparameters:
title= Model MD
; Run parameters
integrator= md
nsteps= 500
dt= 0.002
; Output control
nstxout= 500
nstvout= 500
nstxtcout= 500
nstenergy= 500
nstlog= 500
nstcomm
Dears,
I changed the coordinates of overlapping atoms and got a normal potential
energy. Then when I go to the next step ( NVT equilibrium ), it doesn't run and
I just get some pdb files. How is it possible to find the problem?
It might be clashes in the system but How can I find the overlappi
On 12/16/12 11:55 PM, Shine A wrote:
Sir,
I studying the dynamics of membrane proteins.First I did a 20 ns
simulation using GROMOS96 53a6.This force field cause some problems in the
helical part of the protein.Now I am trying to do the same simulation with
opls-aa force field.Is the chan
On 12/17/12 5:57 AM, ananyachatterjee wrote:
Dear all,
While running mdrun using following mdpparameters:
title= Model MD
; Run parameters
integrator= md
nsteps= 500
dt= 0.002
; Output control
nstxout= 500
nstvout= 500
nstxtcout= 500
nstene
Hi,
I'm setting my system but when I run grompp I get a warning and the program
terminates. It says the following:
You are using pressure coupling with absolute position restraints, this will
give artifacts. Use refcoord_scaling option.
I want to try it but i don't know where to change thi
On 12/17/12 8:53 AM, Kieu Thu Nguyen wrote:
Dear All,
I'm practising the tutorial 2a (protein in water) in the MARTINI tutorial.
After doing step 6 (Do a short energy minimization and position restrained
simulation),i carry out running NVT equilibrium. But it appears the error
in the terminal
On 12/17/12 8:55 AM, Eduardo Oliveira wrote:
Hi,
I'm setting my system but when I run grompp I get a warning and the program
terminates. It says the following:
You are using pressure coupling with absolute position restraints, this will
give artifacts. Use refcoord_scaling option.
I wan
OK, so if i got this right all I have to do is add another line in the mdp file
with refcoord_scaling = com? I thought that i had to make a substitution in
one of the existing terms.
Thanks.
De: Justin Lemkul
Para: Eduardo Oliveira ; Discussion list for GROM
On 12/17/12 9:06 AM, Eduardo Oliveira wrote:
OK, so if i got this right all I have to do is add another line in the mdp file
with refcoord_scaling = com? I thought that i had to make a substitution in one
of the existing terms.
Right, it's a new term entirely (see the manual). All keywords
Dear Justin,
The nvt.mdp file is:
define= -DPOSRES; position restrain the protein
; Run parameters
integrator= md; leap-frog integrator
nsteps= 5; 2 * 5 = 100 ps
dt= 0.002; 2 fs
; Output control
nstxout= 100; save coo
On 12/17/12 9:14 AM, Kieu Thu Nguyen wrote:
Dear Justin,
The nvt.mdp file is:
define= -DPOSRES; position restrain the protein
; Run parameters
integrator= md; leap-frog integrator
nsteps= 5; 2 * 5 = 100 ps
dt= 0.002; 2 fs
; Outpu
Ok,
Thanks a lot!
De: Justin Lemkul
Para: Discussion list for GROMACS users
Enviadas: Segunda-feira, 17 de Dezembro de 2012 12:08
Assunto: Re: [gmx-users] mdp file warnings
On 12/17/12 9:06 AM, Eduardo Oliveira wrote:
> OK, so if i got this right all I ha
On 12/17/12 9:24 AM, Kieu Thu Nguyen wrote:
Dear All,
When i do the "Step Four: Adding Ions"in the tutorial "KALP-15 in DPPC", it
appears the error:
Fatal error:
No such moleculetype W
I checked .top file and included.itp files, they have definded water
molecule type name is "W".
What happe
Hi,
I am trying to simulate alanine dipeptide with the CHARMM27 force field
I have downloaded the ALAD file provided here:
http://www.charmm-gui.org/?doc=archive&lib=csml
And the run pdb2gmx, solvation, minimization and nvt equilibration
Everything worked fine, but when I want to use g_rama to ex
Hi all,
I try to generate a topology using pdb2gmx of a protein that contains a
non-native amino acid, that is "lysine with some more atoms", which is
treated a one amino acid RETK.
Without vsites, everything works fine. With pdb2gmx -vsite hydrogen, a
constraint is generated between the bac
hello:
I am running GMX-4.6 beta2 GPU work in a 24 CPU core workstation with
two GTX590, it stacked there without any output i.e the .xtc file size
is always 0 after hours of running. Here is the md.log file I found:
Using CUDA 8x8x8 non-bonded kernels
Potential shift: LJ r^-12: 0.112 r^-6
Thank Justin ! I found my mistake. But when i type the next command line
genion -s ions.tpr -o system_solv_ions.gro -p topol.top -pname NA -nname
CL -nn 4
and choose group 0 (system), the error is
Fatal error:
No line with moleculetype 'System' found the [ molecules ] section of file
'topol.top
Hi,
That unfortunately tell exactly about the reason why mdrun is stuck. Can
you reproduce the issue on another machines or with different launch
configurations? At which step does it get stuck (-stepout 1 can help)?
Please try the following:
- try running on a single GPU;
- try running on CPUs o
On 12/17/12 11:38 AM, Kieu Thu Nguyen wrote:
Thank Justin ! I found my mistake. But when i type the next command line
genion -s ions.tpr -o system_solv_ions.gro -p topol.top -pname NA -nname
CL -nn 4
and choose group 0 (system), the error is
Fatal error:
No line with moleculetype 'System'
I have just found the right group is 15 (SOL) :-)
Thanks so much and sorry about my stupid question !
On Mon, Dec 17, 2012 at 11:40 PM, Justin Lemkul wrote:
>
>
> On 12/17/12 11:38 AM, Kieu Thu Nguyen wrote:
>
>> Thank Justin ! I found my mistake. But when i type the next command line
>>
>>
hello:
I reduced the GPU to two, and it said:
Back Off! I just backed up nvt.log to ./#nvt.log.1#
Reading file nvt.tpr, VERSION 4.6-dev-20121004-5d6c49d (single precision)
NOTE: GPU(s) found, but the current simulation can not use GPUs
To use a GPU, set the mdp option: cutoff-scheme = Ve
Hi,
How about GPU emulation or CPU-only runs? Also, please try setting the
number of therads to 1 (-ntomp 1).
--
Szilárd
On Mon, Dec 17, 2012 at 6:01 PM, Albert wrote:
> hello:
>
> I reduced the GPU to two, and it said:
>
> Back Off! I just backed up nvt.log to ./#nvt.log.1#
> Reading file
On 12/17/2012 06:08 PM, Szilárd Páll wrote:
Hi,
How about GPU emulation or CPU-only runs? Also, please try setting the
number of therads to 1 (-ntomp 1).
--
Szilárd
hello:
I am running in GPU emulation mode with the GMX_EMULATE_GPU=1 env. var
set (and to match closer the GPU setup with -nt
sir,
I am studying dynamics of a membrane protein using oplsaa force field.
Energy minimization during nvt equilibration getting error like this.
Fatal error:
1 particles communicated to PME node 1 are more than 2/3 times the cut-off
out of the domain decomposition cell of their charge group
On 12/17/12 12:53 PM, Shine A wrote:
sir,
I am studying dynamics of a membrane protein using oplsaa force field.
Energy minimization during nvt equilibration getting error like this.
Fatal error:
1 particles communicated to PME node 1 are more than 2/3 times the cut-off
out of the doma
Hi Albert,
Thanks for the testing.
Last questions.
- What version are you using? Is it beta2 release or latest git? if it's
the former, getting the latest git might help if...
- (do) you happen to be using GMX_GPU_ACCELERATION=None (you shouldn't!)?
A bug triggered only with this setting has bee
Hi,
I want to simulate a water soluble protein of approx. 160aa size and its
shape from a .pdb looks a little elongated (if rotated around the longest
axis, it roughly occupies a cylinder with length to diameter ratio 1.8 -
1.9). Would it be considered globular enough to try dodecahedron box?
Out
On 12/17/12 1:48 PM, zugunder wrote:
Hi,
I want to simulate a water soluble protein of approx. 160aa size and its
shape from a .pdb looks a little elongated (if rotated around the longest
axis, it roughly occupies a cylinder with length to diameter ratio 1.8 -
1.9). Would it be considered glob
On Mon, Dec 17, 2012 at 6:01 PM, Albert wrote:
> hello:
>
> I reduced the GPU to two, and it said:
>
> Back Off! I just backed up nvt.log to ./#nvt.log.1#
> Reading file nvt.tpr, VERSION 4.6-dev-20121004-5d6c49d (single precision)
>
This is a development version from October 1. Please use the m
On Mon, Dec 17, 2012 at 7:56 PM, Mark Abraham wrote:
> On Mon, Dec 17, 2012 at 6:01 PM, Albert wrote:
>
> > hello:
> >
> > I reduced the GPU to two, and it said:
> >
> > Back Off! I just backed up nvt.log to ./#nvt.log.1#
> > Reading file nvt.tpr, VERSION 4.6-dev-20121004-5d6c49d (single precisi
well, that's one of the log files.
I've tried both
VERSION 4.6-dev-20121004-5d6c49d
VERSION 4.6-beta1
VERSION 4.6-beta2
and the latest 5.0 by git.
the problems are the same.:-(
On 12/17/2012 07:56 PM, Mark Abraham wrote:
On Mon, Dec 17, 2012 at 6:01 PM, Albert wrote:
>hello:
>
> I r
On 12/17/12 2:03 PM, Albert wrote:
well, that's one of the log files.
I've tried both
VERSION 4.6-dev-20121004-5d6c49d
VERSION 4.6-beta1
VERSION 4.6-beta2
and the latest 5.0 by git.
the problems are the same.:-(
It seems to me that the system is simply crashing like any other that beco
Thank you, Justin, for the prompt answer!
Justin Lemkul wrote
> In almost all cases, a dodecahedral box is the optimal choice. A cubic
> box with the same periodic distance for an elongated protein would be much
> larger.
OK, got it.
Justin Lemkul wrote
> In the absence of the actual editcon
On 12/17/12 2:14 PM, zugunder wrote:
Thank you, Justin, for the prompt answer!
Justin Lemkul wrote
In almost all cases, a dodecahedral box is the optimal choice. A cubic
box with the same periodic distance for an elongated protein would be much
larger.
OK, got it.
Justin Lemkul wrote
I
Justin Lemkul wrote
> It is calculated correctly, the math is just a bit more complex (see the
> manual for the equations). The distance to the box edge is defined the
> same way, but the two approaches don't necessarily give equally suitable
> results. Consider the first case, which produces a r
On 12/17/12 3:04 PM, zugunder wrote:
Justin Lemkul wrote
It is calculated correctly, the math is just a bit more complex (see the
manual for the equations). The distance to the box edge is defined the
same way, but the two approaches don't necessarily give equally suitable
results. Consider
Dear Justin
According to papers, I expect gold atom interacts with the sulfur atom of amino
acid cysteine covalently. But in last email you said in the case of protein-Au
This will not be true to add these parameters
in topology file. Then in which file should I add the parameters between
On 12/17/12 4:01 PM, fatemeh ramezani wrote:
Dear Justin
According to papers, I expect gold atom interacts with the sulfur atom of amino
acid cysteine covalently. But in last email you said in the case of protein-Au
This will not be true to add these parameters
in topology file. Then
On 12/17/12 5:51 PM, Tom wrote:
Dear Gromacs Users,
I created a new residue on aminoacids.rtp file
and assigned improper dihedral after [ bonds ], for example
[ impropers ]
C2H C3 S1
Then I want to add the parameters of this dihedral angle potential
onto ffbonded.itp
I k
On 12/17/12 7:17 PM, Kieu Thu Nguyen wrote:
Dear All,
When i do step EM, the output file .gro is separated into many step.pdb
files . And many errors "Water molecule starting at atom XXX can not be
settled" appears. And the potential energy is positive !
What should i do to solve it ?
Pl
Thank Justin !
On Tue, Dec 18, 2012 at 7:20 AM, Justin Lemkul wrote:
>
>
> On 12/17/12 7:17 PM, Kieu Thu Nguyen wrote:
>
>> Dear All,
>>
>> When i do step EM, the output file .gro is separated into many step.pdb
>> files . And many errors "Water molecule starting at atom XXX can not be
>> sett
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1
On 17/12/12 21:57, ananyachatterjee wrote:
> [ganga:04205] *** Process received signal *** [ganga:04205] Signal:
> Segmentation fault (11) [ganga:04205] Signal code: Address not
> mapped (1) [ganga:04205] Failing at address: 0x201a01c20
Segmentation
On 12/17/12 8:47 PM, Christopher Samuel wrote:
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1
On 17/12/12 21:57, ananyachatterjee wrote:
[ganga:04205] *** Process received signal *** [ganga:04205] Signal:
Segmentation fault (11) [ganga:04205] Signal code: Address not
mapped (1) [ganga:04205]
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