Hi!
I need a small QM/MM gromacs input data with a well known result (and
preferably the output too) to compare to the gromacs/gamess-uk setup i'm
testing.
Does anyone have something i can use?
--
Ake Sandgren, HPC2N, Umea University, S-90187 Umea, Sweden
Internet: a...@hpc2n.umu.se Phone: +4
Hi,
This error message in incorrect, it is probably not a software inconsistency.
Looking at the code, it seems the problem is that the topology file
you provided does not have enough SOL molecules in the [molecules ] section.
I'll fix this error message for the next release.
Berk
From: iitd...
Hi,
Could it be that you have multiple SOL entries in the [ molecules ] section,
a first one for the crystal waters, with less than 48 molecules and then
one with the rest of the waters?
In that case genion should subtract the water molecules from the last SOL entry,
the current version takes the
Dear all,
I am simulating a protein along with a ligand molecule.
The ligand molecule is modeled as per the literature. The
ligand molecule consists of FE and S alone and in addition
to that it is covalently bonded with the enzyme's cys
residue. So I have modeled my ligand FE4S4 with SG and
011013021-Jyotsna wrote:
Dear all,
I am simulating a protein along with a ligand molecule. The ligand
molecule is modeled as per the literature. The ligand molecule consists
of FE and S alone and in addition to that it is covalently bonded with
the enzyme's cys residue. So I have modeled m
Thanks berk.
By the way, if I dont give -p topol.top as input to genion, then genion
executes. In this case, I manually edit the topology file and add the ion
information.
[ molecules ]
; Compound#mols
Protein_A 1
Protein_B 1
Protein_C 1
Protein_D 1
Hi,
genion in future Gromacs versions will only use the last SOL block
and give a proper error message when there is not enough water.
Berk
From: iitd...@gmail.com
Date: Thu, 11 Feb 2010 16:45:06 +0530
Subject: Re: [gmx-users] Software inconsistency error: Not enough water
To: gmx-users@gromacs
Hi,
Is it desirable that genion only considers a single SOL block? Why not
use them all if there are many?
Regards,
Erik
Berk Hess skrev:
Hi,
genion in future Gromacs versions will only use the last SOL block
and give a proper error message when there is not enough water.
Berk
--
Hi,
We are getting to much detail now.
In principle yes, but since you get a clear error message now, I wouldn't worry
about this.
The chance that the last water block is willingly smaller than the number of
ions is about zero.
Berk
> Date: Thu, 11 Feb 2010 13:34:59 +0100
> From: er...@xray.b
Plus I suppose that if you have kept the crystal waters you would not
want them to be replaced by genion.
Tom
Berk Hess wrote:
Hi,
We are getting to much detail now.
In principle yes, but since you get a clear error message now, I
wouldn't worry about this.
The chance that the last water blo
Hi,
Yes, but genion is not smart enough (yet) to see the difference between crystal
water and normal water.
Berk
> Date: Thu, 11 Feb 2010 13:07:41 +
> From: t.pig...@bristol.ac.uk
> To: gmx-users@gromacs.org
> Subject: Re: [gmx-users] Software inconsistency error: Not enough water
>
> Plu
Sure, that's why I think it is a good idea to do what you said and just
have genion use the final SOL block (normally added through genbox, so
not containing the crystal waters) rather than use all of the SOL blocks.
Tom
Berk Hess wrote:
Hi,
Yes, but genion is not smart enough (yet) to see t
Hi Ake,
you can download two files at
wwwuser.gwdg.de/~ggroenh/ffamber03.tar.gz and
wwwuser.gwdg.de/~ggroenh/qmmm_input.tar.gz
First is the forcefield files (GMXLIB shoul point there)
second is qmmm input files for a QM/MM simulation.
Hope it helps.
Gerrit
>
> Message: 1
> Date: Thu, 11 Fe
Hi,
Yes, but there are (currently) two independent steps in genion.
First water is replaced using the index group that the users selected
and then the top file is edited. They two steps are independent.
There are no checks that the index group actually matches the topology
molecule sections (and
On Thu, 2010-02-11 at 14:41 +0100, Gerrit Groenhof wrote:
> Hi Ake,
> you can download two files at
>
> wwwuser.gwdg.de/~ggroenh/ffamber03.tar.gz and
> wwwuser.gwdg.de/~ggroenh/qmmm_input.tar.gz
>
> First is the forcefield files (GMXLIB shoul point there)
> second is qmmm input files for a QM/
Dear All
I would like to perform MD simulations with benzene as a solvent and
am observing some strange behaviour when I use Lincs to constrain all
the bonds. When I run a fully flexible NPT MD of a box of 320 benzene
molecules simulation at 298K and 1bar, the density comes out at 841
g/l, not to
Dear Mike,
It's hard to know what's going on from your input. Did you check the
thermodynamic components with g_energy (especially the pressure bond, LJ
and Coulomb energies)? This may give you a hint. Also, I would do a test
run with PME - you're anyway not following the parametrisation of
Jorgen
Hi everybody,
I am doing some analysis of the interpeptidique hbonds (INTRHB) during the
aggregation in beta fuof 4 heptapeptides in water
I have defined in a index file the Acceptor-Donor-Hydrogen atoms list for the
28 INTRHB like this
NH--CO
[intra_hbds]
4 17 5
18 26 19
27 43 28
44 52 4
ABEL Stephane 175950 wrote:
Hi everybody,
I am doing some analysis of the interpeptidique hbonds (INTRHB) during the aggregation in beta fuof 4 heptapeptides in water
I have defined in a index file the Acceptor-Donor-Hydrogen atoms list for the 28 INTRHB like this
NH--CO
[intra_hbds]
4
Hi Stephane,
The map shows weather a certain hydrogen bond exists at a certain time.
In principle you can get the information by integrating this data, but
I'm not sure it can be done without changing the code. A possible
solution is to use a script and run g_hbond -num 28 times with two
relevant
Justin A. Lemkul skrev:
ABEL Stephane 175950 wrote:
Hi everybody,
I am doing some analysis of the interpeptidique hbonds (INTRHB)
during the aggregation in beta fuof 4 heptapeptides in water
I have defined in a index file the Acceptor-Donor-Hydrogen atoms list
for the 28 INTRHB like this
NH
Hi all,
Please, can someone shed more light on how to set up reduced units in
an .mdp file? I have tried to this but it does not work. I set epsilon,
sigma and mass to 1 in my force field file as stated in section 2.3 of the
manual. I multiplied 300K temperature by 0.00831451 and divided by
Hi,
I am doing PMF calculations using Gromacs 3.3.3, and I have found very
different results using 2 different machines. Attached you can see that the
graphics are really different for both cases (about 10 KJ/mol!!). The version
of Gromacs (3.3.3) and number of processors used (2) is the same fo
On 2/11/10 7:40 PM, Rebeca García Fandiño wrote:
Hi,
I am doing PMF calculations using Gromacs 3.3.3, and I have found very
different results using 2 different machines. Attached you can see
that the graphics are really different for both cases (about 10
KJ/mol!!). The version of Gromacs (3.3
n reduced units as shown on Table 2.4 of the manual to get
a value of 0.0431 and included all of these in the .mdp file but this did
not work for me in the mdrun.
Is this the right way to set up reduced units in gromacs? Please, help
me out.
Thanks,
Lum
-- next part --
On Feb 11, 2010, at 7:40 PM, Rebeca García Fandiño wrote:
Hi,
I am doing PMF calculations using Gromacs 3.3.3, and I have found
very different results using 2 different machines. Attached you can
see that the graphics are really different for both cases (about 10
KJ/mol!!). The version o
Thank you very much for the suggestions. I will look carefully for the
convergence of my PMF to see if it is the problem.
Cheers,
Rebeca.
From: x.peri...@rug.nl
To: gmx-users@gromacs.org
Subject: Re: [gmx-users] different results in different machines
Date: Thu, 11 Feb 2010 20:00:32 +0100
On F
Dear All,
I have retrieved the latest version of the gmxtest regression tests
from git and run them against a newly installed GROMACS 4.0.7
installation. Most of the tests pass, but there are a few problems
--- I know from the wiki that some problems are expected, but as a
sysadmin rather than a
Thanks Justin,
On Wed, Feb 10, 2010 at 8:49 PM, Justin A. Lemkul wrote:
>
>
> Segun Jung wrote:
>
>> Dear gromacs users,
>>
>> I am trying to collect trajectories corresponding to each temperature by
>> using trjcat with demux.
>>
>> There were similar issues posted earlier, but I do not see th
Dear all,
I face some problem during run grompp (see below), the command is
"grompp -f em.mdp -c ../2add_lipw/b4ion.gro -p ../topol.top -o b4ion.tpr"
-Before this process, i've changed the ffG53a6nb.itp & ff53Ga6bon.itp
according to the tutorial
(http://www.bevanlab.biochem.vt.edu/Pages/Personal/
On 12/02/10 12:16, chiloo777 777 wrote:
Dear all,
I face some problem during run grompp (see below), the command is
"grompp -f em.mdp -c ../2add_lipw/b4ion.gro -p ../topol.top -o b4ion.tpr"
-Before this process, i've changed the ffG53a6nb.itp& ff53Ga6bon.itp
according to the tutorial
(http://w
Do you mean i should change the order of #include thing in file.top or
something involving pope.itp?
I try to change order of #include thing, there is the same error.
Do i need to define something like "proper dihedral types" in pope.itp
& popg.itp?
Thanks
Jit
On Fri, Feb 12, 2010 at 8:24 AM, Ma
chiloo777 777 wrote:
Do you mean i should change the order of #include thing in file.top or
something involving pope.itp?
I try to change order of #include thing, there is the same error.
Do i need to define something like "proper dihedral types" in pope.itp
& popg.itp?
Without seeing your
chiloo777 777 wrote:
To see topology, please see the attached files
You're using ffG53a6, per my tutorial, but then if you look within popg.itp,
you'll find atom type HO, which is not a recognized type within 53a6 (it is for
ffgmx). The proper type is H. The other warnings are probably d
On 12/02/10 09:45, Jess Bromley wrote:
Dear All,
I have retrieved the latest version of the gmxtest regression tests
from git and run them against a newly installed GROMACS 4.0.7
installation. Most of the tests pass, but there are a few problems
--- I know from the wiki that some problems are e
If this problem comes from the mismatch forcefield, That mean i should
change forcefield from ffG53a6 to ffgmx, or find popg.itp (which is
matched with ffG53a6), right?
Thanks
Jit
On Fri, Feb 12, 2010 at 9:06 AM, Justin A. Lemkul wrote:
>
>
> chiloo777 777 wrote:
>>
>> To see topology, please se
On 12/02/10 18:17, chiloo777 777 wrote:
If this problem comes from the mismatch forcefield, That mean i should
change forcefield from ffG53a6 to ffgmx, or find popg.itp (which is
matched with ffG53a6), right?
Standard procedure is to choose a forcefield that is known to be able to
model the ki
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