when I first run enery minimization in vacuum, then add water model,
(I use GROMOS96 53a6 force field, and spce water model)
EM in water model:
Steepest Descents:
Tolerance (Fmax) = 1.0e+03
Number of steps= 2000
Step=0, Dmax= 5.0e-03 nm, Epot= -3.51690e+05 Fmax= 2.16
Hi, all
when I use:
grompp -f em_constrain.mdp -c provin_solv_ion.pdb -p provin_1dxo.top -o
bovin_em.tpr
mdrun -v -s bovin_em.tpr -nt 2 -deffnm em_constrain
get the result:
Steepest Descents:
Tolerance (Fmax) = 1.0e+03
Number of steps= 2000
Step=0, Dmax= 1.0
Dear Justin,
Thank you very much for your quick response
Cheers,
Safa
On 8 June 2013 12:07, Justin Lemkul wrote:
>
>
> On 6/7/13 11:05 PM, Souilem Safa wrote:
>
>> Dear Gromacs users,
>>
>> I'm aiming to extract a frame file from a reduced trajectory, i did the
>> simulation on gromacs version
On 6/7/13 11:05 PM, Souilem Safa wrote:
Dear Gromacs users,
I'm aiming to extract a frame file from a reduced trajectory, i did the
simulation on gromacs version 4.6.1 and I would like to do my analysis in
gromacs 4.5.6 for availability reasons.
When I entered my command , I got this error :
Dear Gromacs users,
I'm aiming to extract a frame file from a reduced trajectory, i did the
simulation on gromacs version 4.6.1 and I would like to do my analysis in
gromacs 4.5.6 for availability reasons.
When I entered my command , I got this error :
reading tpx file (md.tpr) version 83 with ve
On 6/7/13 8:43 PM, Sanku M wrote:
Hi,
I have a pair of polypeptides which are generated as ideal helix. I want to
carry out their assembly/dis-assembly simulation by maintaining the helicity of
them.
I wonder which of the methods for retaining helicity is better :
1. use a harmonic restrai
Hi,
I have a pair of polypeptides which are generated as ideal helix. I want to
carry out their assembly/dis-assembly simulation by maintaining the helicity of
them.
I wonder which of the methods for retaining helicity is better :
1. use a harmonic restraints using [bonds] directive using type
Thank you for your answers,
I finally added "l" at the end of the names of the atoms, which seemed to
be the easiest solution. For most of the computation, having these
[bondtypes] like entries was not mandatory, but I wanted to import the
topologies in pDynamo, which requires such a "database".
I may not got the question properly but when I designed ACPYPE, I had
similar issues and for that reason I created this option:
-g, --disambiguatedisambiguate lower and uppercase atomtypes in GMX top
file
So try your usual acpype command with "-g" option.
BTW, acpype
On Fri, Jun 7, 2013 at 2:06 PM, Mark Abraham wrote:
> Running Amil's .tpr, the next output is from our CPU detection machinery.
> While the Xeon 5500 is not exactly new, AFAIK there should be no reason for
> the detection to fail. But the stack trace will tell.
Good point. Amil, please post the cm
On 6/7/13 10:33 AM, Steven Neumann wrote:
It is stated in manual that tables must always contain 7 columns with a
meaningful data (i.e. no zeros). must be entered in all columns.
That may be an erroneous statement. Within very short distances, you will have
nearly infinite forces, so zeroes
Running Amil's .tpr, the next output is from our CPU detection machinery.
While the Xeon 5500 is not exactly new, AFAIK there should be no reason for
the detection to fail. But the stack trace will tell.
Mark
On Fri, Jun 7, 2013 at 7:23 PM, Roland Schulz wrote:
> Amil,
>
> would it be possible
Amil,
would it be possible for you to compile with a different compiler?
Ideally gcc 4.7.3. Alternative could you send us the stack for when it
crashes?
For that you need to:
- compile with debug -DCMAKE_BUILD_TYPE=Debug
- run under gdb "gdb --arg /path/to/mdrun {your mdrun arguments}"
- enter "bt
Roland,
I have now run the regression test on my installation and it all fails for
runmd (segmentation fault). Don't see that anything else is being tested.
I've placed the output of the make check (Make_check.out) at
https://www.dropbox.com/sh/h6867f7ivl5pcl9/j9gt9CsVdP
I'll copy the first
On Fri, Jun 7, 2013 at 5:22 PM, Colin Bannister <
colin.bannis...@nottingham.ac.uk> wrote:
> Mark,
>
> Thanks for the response. We use MKL for a lot of applications, and have
> had no problems, except with gromacs.
Because of the historical pain of specifying the MKL link configuration,
the eas
Mark,
Thanks for the response. We use MKL for a lot of applications, and have had no
problems, except with gromacs. I wonder if there is a bug in cmake, as surely
getting a segmentation fault can never be right ?
If anyone else has any ideas, I'd be grateful for them - I will try a build
wit
On Tue, Jun 4, 2013 at 12:51 PM, suhani nagpal wrote:
> Hi all !
>
> well, I'm working on REMD with 96 replicas, with temperature range 280K to
> 425.04K.
>
> The NVT equilibration works well and graphs plotted show almost the
> required temperature after equilibration.
>
> Then, after 3 ns of rem
On Wed, Jun 5, 2013 at 11:27 AM, Baptiste Demoulin
wrote:
> Hello GMX users,
>
> I have some troubles with overriding parameters. I have generated
> parameters for lipids using Lipid11 forcefield for AMBER, based on GAFF,
> and Acpype. This forcefield contains atomtypes cA, cB for instance. When I
Don't know, but re-interpreting the old velocities at a new time might not
be fully integrated with things calculated from the old velocities, such as
temperature-coupling quantities. For switching integrators, you will need
to re-equilibrate, so you may as well generate new velocities and avoid th
On Thu, Jun 6, 2013 at 5:14 PM, Neha wrote:
> Hi again!
>
> At the moment, the only way I know how to access .edr files is through the
> use of g_energy. However g_energy only outputs .xvg files which is fine for
> routine analysis. However if I want to get into further processing, it
> would
> b
Can't say On the information given, something about the protocol might be
too aggressive.
Mark
On Fri, Jun 7, 2013 at 7:56 AM, Venkat Reddy wrote:
> Dear gmx-users,
> I am experiencing some strange things while performing mdrun. I am running
> a CG simulation and it is terminating with LINCS w
They're fine now. Perhaps the FTP server was offline briefly.
Mark
On Fri, Jun 7, 2013 at 7:41 AM, Bhamy Maithry Shenoy <
bhamymait...@aero.iisc.ernet.in> wrote:
>
> Hi,
> I would like to use Gromacs for MD simulation of biomolecules. But I am
> not able to download any of the source files from
On Fri, Jun 7, 2013 at 12:20 PM, colinbannister <
colin.bannis...@nottingham.ac.uk> wrote:
> I am trying to build Gromacs 4.6 on a Linux machine, running Scientific
> Linux
> 6.2. I am doing an MPI build with Intel-MPI, and Intel compilers, and MKL.
>
> Commands I issue to set environment, and ru
It is stated in manual that tables must always contain 7 columns with a
meaningful data (i.e. no zeros). must be entered in all columns.
The example of table6-12.xvg involves xeros until 0.04. How come?
I want to cut my potential at some point to zero - can I put zeros or shall
I specify some value
That is all that is possible.
Mark
On Fri, Jun 7, 2013 at 4:31 AM, Dallas Warren wrote:
> Easiest, naïve way that I can see is to do the simulation in blocks, and
> change the output settings within the mdp file used as required for each
> block.
>
> Catch ya,
>
> Dr. Dallas Warren
> Drug Disco
On Fri, Jun 7, 2013 at 1:53 PM, Justin Lemkul wrote:
>
>
> On 6/7/13 8:21 AM, Steven Neumann wrote:
>
>> Thank you.
>> Another question... I specify in my table functions e.g. g(x) and h(x) and
>> it is written that I need to setup parameters C6 and C12. But where I
>> should specify them? In :
>
On 6/7/13 8:21 AM, Steven Neumann wrote:
Thank you.
Another question... I specify in my table functions e.g. g(x) and h(x) and
it is written that I need to setup parameters C6 and C12. But where I
should specify them? In :
[ atomtypes ]
;name at.num mass charge ptype V(c6) W(c12)
O 8 15.99940
Thank you.
Another question... I specify in my table functions e.g. g(x) and h(x) and
it is written that I need to setup parameters C6 and C12. But where I
should specify them? In :
[ atomtypes ]
;name at.num mass charge ptype V(c6) W(c12)
O 8 15.99940 0.000 A 0.22617E-02 0.74158E-06
or
[ nonbon
On 6/7/13 7:36 AM, Steven Neumann wrote:
Thank you, just getting into this. I just dont understand why they start
from x=0.04? Why not 0.02 or sth else?
You can start the table from whatever value of x that you like, but at a certain
point, it is unlikely that particles ever come that close
On 6/7/13 7:41 AM, gromacs query wrote:
Dear All,
Please any suggestion?
I think you should be able to set whatever value you like for pull_init1 and the
code should take care of it.
-Justin
On Mon, Jun 3, 2013 at 4:53 PM, gromacs query wrote:
Dear All,
(Sorry for long mail!)
(Tha
Dear All,
Please any suggestion?
regards,
On Mon, Jun 3, 2013 at 4:53 PM, gromacs query wrote:
> Dear All,
>
> (Sorry for long mail!)
>
> (Thanks Thomas Schlesier for clarifying previous umbrella queries)
>
> I wish to run umbrella samplings using restart file of previous window.
> e.g. initia
Thank you, just getting into this. I just dont understand why they start
from x=0.04? Why not 0.02 or sth else?
Steven
On Fri, Jun 7, 2013 at 11:36 AM, Mohan maruthi sena
wrote:
> Hi Neumann,
> You can use tabulated potential option in
> gromacs. Please check the s
Hi Neumann,
You can use tabulated potential option in
gromacs. Please check the site given below:
http://www.gromacs.org/Documentation/How-tos/Tabulated_Potentials
Thanks,
Mohan
On Fri, Jun 7, 2013 at 3:38 PM, Steven Neumann wrote:
> Dear Gmx Users,
>
> I want to
I am trying to build Gromacs 4.6 on a Linux machine, running Scientific Linux
6.2. I am doing an MPI build with Intel-MPI, and Intel compilers, and MKL.
Commands I issue to set environment, and run cmake (available as cmake28)
are:
[cczcb@login02 gromacs-build-nocuda]$ module load intel/compiler
Dear Gmx Users,
I want to specify a table to mdrun for non bonded parameters. I wish to set
it up for all atoms with same potential. Is there any example of the table
like this? I want use my specific potential so table should have two
columns: X distance [nm] and Y Potential energy {kJ/mol]. Is t
Hi,
It may very well be. Here's the red mine issue
http://redmine.gromacs.org/issues/891. If there's a -ver option for do_dssp
then it's capable of the new syntax. If not then it assumes the old syntax. If
you can't install a newer version of gromacs there is the option to install
old_dssp whi
Hi Eric,
I'm using gromacs 4.5.5.
Is it the version is different for dssp?
Thanks
On Fri, Jun 7, 2013 at 3:41 AM, Erik Marklund [via GROMACS]
wrote:
> HI,
>
> What version of gromacs is this? DSSP changed its syntax a while back and we
> had to adjust do_dssp accordingly. You may have a mismatc
HI,
What version of gromacs is this? DSSP changed its syntax a while back and we
had to adjust do_dssp accordingly. You may have a mismatch between gromacs and
dssp versions.
Erik
On 7 Jun 2013, at 08:42, Nur Syafiqah Abdul Ghani wrote:
> Hi All,
>
> I already done the MD production so I wa
On 2013-06-07 04:12, Justin Lemkul wrote:
On 6/6/13 10:00 PM, Badamkhatan wrote:
Dear GMX-users
Recently i got this error and note from my MD2 simulation. I'm solvating
1-octanol to 1-octanol and calculating free energy differences. This
is the
last step of my calculation and previous steps a
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