Hello
I use a charmm force field in gromacs. I almost finished my parametrization
except for Lennard-Jones parameters. For this parameters I want to adopt the
values in the charmm force field for the basic atom types.
In gromacs I have to put this parameters in the ffnonbonded.itp file in the
Hi
I have three questions:
1.)
If you create a .rtp file in your force field folder (I use charmm27) you have
a block [ dihedrals ] with the structure
[ dihedrals ]
atom1 atom2 atom3 atom4 phi0 cp mult
What is cp and what is mult?
2.)
In the [ impropers ] block y
Hi
If you have a good parametrization of a molecule and it's pdb file and you use
pdb2gmx for getting a topology, will the topology alway be finished?
It is usual to fix something in the topology file after pdb2gmx or are
necessary additions in the topology a hint for a bad or even wrong
par
Hello
I got this error:
Fatal error:
Atom ON1 is used in an interaction of type improper in the topology
database, but an atom of that name was not found in residue
number 1.
What do this mean? How to fix it?
The Atom ON1 is declared in atomtypes.atp file.
In my .rtp file I used [ imprope
Hi
In a supporting Information of a paper is written:
"The description of the LF radical force fields is complete, as soon as also
the parameters of the Lennard-Jones potentials are given. For these parameters
we adopt the values specified in the CHARMM22 force field for the basic atom
types"
Hi
The first part in a .rtp file is the [ bondedtypes ] with syntax
[ bondedtypes ]
; bonds angles dihedrals impropers
1 1 1 2
1.)
What do this numbers mean? I found nothing in the manual to that.
2.)
If you have improper dihedrals, d
Please help :-(
Greetings
Lara
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Thanks for your help. :-)
I did not realize that table 5.5 corresponds to [ bondedtypes ]
Greetings
Lara
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Hello
I wrote an email to the mailing list with the subject [ bondedtypes ] and I got
answers that helped me. I wanted to answer to this by a new email with same
subject and the mailing list create a new question out of it.
How do I answer in this mailing list to a topic?
Thanks
Greetings
La
Hi
Thanks for answer. This is also a test if it work :-)
Greetings
Lara
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Hello
Is this em.mdp file correct for a simple MD simulation?
integrator = steep
nsteps = 200
nstlist = 10
rlist = 1.0
coulombtype = pme
rcoulomb = 1.0
vdw-type = cut-off
rvdw = 1.0
nstenergy = 10
Thanks for help
Greetings
Lara
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Hi
I used the command
grompp -f em.mdp -p topol.top -c solvated.gro -o em.tpr
and get this errors:
ERROR 1 [file flavin.rtp, line 1]:
Invalid directive bondedtypes
ERROR 2 [file flavin.rtp, line 7]:
Not enough parameters
I know where this error occurs from but I don't know what is fa
Hi
I used the command
grompp -f em.mdp -p topol.top -c solvated.gro -o em.tpr
and got the error
Source code file: /home/adrian/src/gromacs-4.5.5/src/gmxlib/statutil.c, line:
819
Invalid command line argument:
em.tpr
What is the problem here?
Greetings
Lara
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gmx-users mailing listgm
Hi
My topology file which I get after pdb2gmx has in one section following section:
[ pairs ]
; ai aj funct c0 c1 c2 c3
1 5 1
1 6 1
1 9 1
1 17 1
Is it correct that there are no entries in c0, c1, c2 a
Hi
After pdb2gmx I got two [ dihedrals ] sections in the topology file.
[ dihedrals ]
ai aj ak al funct c0 c1
c2 c3 c4 c5
2 1 19 8 5
6 8 9 10 5
6 8 19 1 5
[ di
Hi
After pdb2gmx are in the [ angles ] section some lines missing and I am pretty
sure that they are defined in my .rtp file in my force field folder. There are
also just a few lines mission, most of the angles are in topology. I know the
parameters so I can add it by hand to topology but what
Hi
After I used
grompp -f em.mdp -p topol.top -c solvated.gro -o em.tpr
to collect my files into one em.tpr file (which is the meaning of gromp as fas
as I understand it)
Then I start mdrun for energy minimization with the command
mdrun -nt 1 deffnm em
and got the error
Can not open file:
Hi
I create a file pr.mdp for equilibrating the water around my molecule and used
after that the command
grompp -f pr.mdp -p topol.top -c em.gro -o pr.tpr
And I got tthe error:
Fatal error:
Group protein not found in index file.
Group names must match either [moleculetype] names
or custom inde
, 6.März 2012
Betreff: Re: [gmx-users] Missing Interactions in [ angles ] Section in Topology
Lara Bunte wrote:
> Hi
>
> In some lines the equilibrium angle and the force constant is missing.I give
> you an example:
>
>
> The [ angles ] section is build like
>
> [ a
s do not.
-Justin
> On 2012-03-07 05:19:19PM +, Lara Bunte wrote:
>> Hi Justin
>>
>>
>> I am using a CHARMM27 force field. I create a pdb file with the coordinates
>> of my molecule and I create a .rtp and a .hdb file for this. I also edit
>> atomtyp
t;protein,"
* copy $GMXLIB/residuetypes.dat to your working directory and add your protein
residues to allow the default generated groups to understand your knowledge
about what is a protein,
* name your [moleculetype] the same as your references to it in your .mdp file
and [molecules] secti
Hello
I want to learn how to create a .mdp file and learn what I can write in such a
file and learn what the entries in this file are meaning.
I did not find this in the manual. Could you please give me link or some source
where I can find this information?
Thanks and best greetings
Lara
--
g
Hi
in a topology file in the section [ moleculetypes ] is standing
; nrexcl
3
What do this mean?
Thanks for help
Greetings
Lara
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your knowledge
about what is a protein,
* name your [moleculetype] the same as your references to it in your .mdp file
and [molecules] section.
Mark
>
>
> On 2012-03-07 05:13:11PM +, Lara Bunte wrote:
>> Hi
>>
>> I create a file pr.mdp for equilibratin
Hello
I want to use the command
grompp -n index.ndx -f pr.mdp -p topol.top -c em.gro -o pr.tpr
and I got the error:
Fatal error:
Group protein not found in index file.
Group names must match either [moleculetype] names
or custom index group names,in which case you
must supply an index file
Hello
What size should a box have in that you do your MD? I always read that for
short Lennard Jones interactions one should do a cut off with the half of the
box size but what how to know a good box size?
Thanks for help
Greetings
Lara
--
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Hello
I want to equilibrate the water around my (small) molecule. In the tutorials I
found and in the manual is not enough information how to do that if you have an
own parametrization of a molecule.
Here is my situation:
I have a pdb file and I have a parametrization for this molecule out o
AM, Lara Bunte wrote:
> Hello
>
> I want to equilibrate the water around my (small) molecule. In the tutorials
> I found and in the manual is not enough information how to do that if you
> have an own parametrization of a molecule.
>
>
> Here is my situation:
>
>
he Message -
Von: Mark Abraham
An: Discussion list for GROMACS users
CC:
Gesendet: 14:45 Montag, 26.März 2012
Betreff: Re: [gmx-users] Equilibrate the water around my molecule
On 26/03/2012 11:21 PM, Lara Bunte wrote:
> Hi
>
> I changed in my residuetypes.dat file ISO Isoalloxazi
has to do with this termini? Thanks
Greetings
Lara
- Ursprüngliche Message -
Von: Mark Abraham
An: Discussion list for GROMACS users
CC:
Gesendet: 15:28 Montag, 26.März 2012
Betreff: Re: [gmx-users] Equilibrate the water around my molecule
On 26/03/2012 11:55 PM, Lara Bunte wro
Hello
If gromacs gives the warning that the system could explode, what could be the
reason for that?
Greetings
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Hello
If you add solvent water around your protein you have to generate a box with
the editconf command. How to know what shape that box should have? In my
tutorial is a dodecahedron used. What other boxes exist and how to know which
box one has to use?
Thanks
Greetings
Lara
--
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Hello
I have a question about editing a pdb file.
I have a molecule in a box of water as a pdb file. I want to remove all water
except of ONE layer around he molecule. How to do that?
Do you know a software that is able to do that? Do you know how it could work
with programs like PyMol or o
Lara
- Ursprüngliche Message -
Von: Mark Abraham
An: Discussion list for GROMACS users
CC:
Gesendet: 14:27 Mittwoch, 4.April 2012
Betreff: Re: [gmx-users] File editing - only one layer of water around a
molecule
On 4/04/2012 7:27 PM, Lara Bunte wrote:
> Hello
>
> I h
a
molecule
Please leave the discussion on the mailing list, so that others can contribute
and benefit now and via the archives.
On 11/04/2012 10:53 PM, Lara Bunte wrote:
Hi
>
>
>How to do that? I searched the manual for "layer" and I don't find something
>that
Re: [gmx-users] File editing - only one layer of water around a
molecule
On 12/04/2012 3:24 AM, Justin A. Lemkul wrote:
>
>
> Lara Bunte wrote:
>> Could you please give how g_select is used?
Reading g_select -h might have led you to try g_select -select 'help'
>&
Gesendet: 11:51 Freitag, 13.April 2012
Betreff: Re: [gmx-users] File editing - only one layer of water around a
molecule
On 13/04/2012 7:29 PM, Lara Bunte wrote:
I read g_select -select 'help all' and I understand nothing of that.
>
>
>
>In general one have a molecule (vale
Hi Justin
What is a box vector? I read that the CHARMM force field that I am using has a
cut-off of 1 (is this Angstrom or nano-meters?). So should I use a box size of
3 nano-meters?
Greetings
Lara
Von: Justin A. Lemkul
An: Lara Bunte ; Discussion list
Betreff: Re: [gmx-users] File editing - only one layer of water around a
molecule
On 13/04/2012 8:01 PM, Lara Bunte wrote:
Hi Mark
>
>
>Could you please give me for that the prompt how to write this in the console.
>
>
>
>"All atoms of a residue LIG within 0.5 nm o
users] File editing - only one layer of water around a
molecule
On 13/04/2012 8:17 PM, Lara Bunte wrote:
Thanks for that but where in this do I give Gromacs my pdb. file. From where do
g_select use this information?
>
>
>
>What I have is a pdb file.
>
Look at g_select -h fo
cked. I don't get it. :-(
Greetings
Lara
p.s.
Here in this email if I got to answer (like always) is only Justins mail
adress, not the gromacs user list. I do it in cc
____
Von: Justin A. Lemkul
An: Lara Bunte ; Discussion list for GROMACS users
Ges
[gmx-users] File editing - only one layer of water around a
molecule
Lara Bunte wrote:
> Hi Justin
>
> Okay, after
>
> g_select -f mol_in_water.pdb -select '"Close to ISO" resname SOL and within
> 0.5 of group "ISO"'
>
> I got:
>
>
Please help
Greetings
Lara
Von: Teemu Murtola
An: Discussion list for GROMACS users
Gesendet: 18:20 Freitag, 13.April 2012
Betreff: Re: [gmx-users] File editing - only one layer of water around a
molecule
On Fri, Apr 13, 2012 at 18:30, Lara Bunte wrote:
> Is there no way only to use the
Hello
I want and need a tutorial especially for g_select but I found nothing. Do you
know a tutorial for g_select? Manual and help are here not enough to understand
how to use g_select.
Thanks
Lara
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http://lists.gromacs.org/mailman/listinfo/g
Greetings
Lara
p.s.
I use yahoo. I tried to find an "answer to all" option or something like that.
Again after pressing answer the mail should go only to Justin. I put the
mailing list in cc. Is here someone using yahoo also and know how to fix this?
__
Von: Justin A. Lemkul
An: Discussion list for GROMACS users
Gesendet: 17:27 Samstag, 14.April 2012
Betreff: Re: [gmx-users] File editing - only one layer of water around a
molecule
Lara Bunte wrote:
> Hi Justin
>
> The difference in my
>
> g_select
s for helping
Greetings
Lara
Von: Justin A. Lemkul
An: Discussion list for GROMACS users
Gesendet: 22:37 Sonntag, 22.April 2012
Betreff: Re: [gmx-users] File editing - only one layer of water around a
molecule
On 4/22/12 3:55 PM, Lara Bunte wrote:
> H
l
An: Discussion list for GROMACS users
Gesendet: 23:10 Sonntag, 22.April 2012
Betreff: Re: [gmx-users] File editing - only one layer of water around a
molecule
On 4/22/12 5:07 PM, Lara Bunte wrote:
> Hi
>
> I got always the same error. I tried
>
> trjconv -n index.ndx -s molecule_in
An: Discussion list for GROMACS users
CC:
Gesendet: 13:02 Montag, 23.April 2012
Betreff: Re: [gmx-users] File editing - only one layer of water around a
molecule
On 4/23/12 3:46 AM, Lara Bunte wrote:
>
>
> Hi
>
> that worked. I used
>
> trjconv -n index.ndx -f my_molecule.pdb -o o
.April 2012
Betreff: Re: [gmx-users] File editing - only one layer of water around a
molecule
On 4/23/12 11:01 AM, Lara Bunte wrote:
> Hi
>
> What do you mean with
>
>
>> Specify a .pdb file as the output of your original command.
>
> I wrote in
>
>
> tr
Hi
In this case my problem is not solvable with gromacs?
All I have is the my_molecule.pdb which is a small molecule in a water box and
my generated index.ndx file, size.xvg file and output.xtc file.
Greetings
Lara
- Ursprüngliche Message -
Von: Justin A. Lemkul
An: Lara Bunte
üngliche Message -
Von: Justin A. Lemkul
An: Discussion list for GROMACS users
CC:
Gesendet: 19:44 Montag, 23.April 2012
Betreff: Re: [gmx-users] File editing - only one layer of water around a
molecule
On 4/23/12 1:27 PM, Lara Bunte wrote:
> Hi
>
> In this case my problem is
Hi
Just out of curiosity: When will be the next release for a new version of
Gromacs with extended manual?
Greetings
Lara
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helping me.
Lara
- Ursprüngliche Message -
Von: Justin A. Lemkul
An: Lara Bunte ; Discussion list for GROMACS users
CC:
Gesendet: 18:07 Montag, 30.April 2012
Betreff: Re: [gmx-users] File editing - only one layer of water around a
molecule
On 4/30/12 11:41 AM, Lara Bunte wrote
or being such patient with me.
Greetings
Lara
- Ursprüngliche Message -
Von: Justin A. Lemkul
An: Discussion list for GROMACS users
CC:
Gesendet: 18:35 Montag, 30.April 2012
Betreff: Re: [gmx-users] File editing - only one layer of water around a
molecule
On 4/30/12 12:29 PM, Lara Bunte wrote
Hello
After I understand how to select a
molecule with water layers out of a molecule in a box filled with water
(again thanks to Justin and Mark for lots of help), I want to
understand more about choosing good parameters in g_select.
I have the command
g_select -s molecule_in_water.pdb -
Hi
There is a new problem :-(
If I used the commands
g_select -s molecule.pdb -select '"Close to ISO" resname SOL and within 1.2 of
resname ISO'
and
trjconv -n index.ndx -f molecule.pdb -s molecule.pdb -o output.pdb
I got only water in my output.pdb
Than I tried all 8 possible permutations
h "Close to ISO"?
Greetings
Lara
- Ursprüngliche Message -
Von: Justin A. Lemkul
An: Discussion list for GROMACS users
CC:
Gesendet: 20:55 Dienstag, 1.Mai 2012
Betreff: Re: [gmx-users] File editing - only one layer of water around a
molecule
On 5/1/12 2:40 PM, L
Hi
I need a little help in using Linux. I wrote this script for the bash, that I
called g_select_script.sh:
#!/bin/bash
g_select -s mol_in_water.pdb -select '"Close to ISO" resname SOL and within 0.4
of resname ISO' -on
make_ndx -f mol_in_water.pdb -o index2.ndx
cat index2.ndx index.ndx > ind
etings
Lara
- Ursprüngliche Message -
Von: Justin A. Lemkul
An: Discussion list for GROMACS users
CC:
Gesendet: 20:34 Dienstag, 6.März 2012
Betreff: Re: [gmx-users] Missing Interactions in [ angles ] Section in Topology
Lara Bunte wrote:
> Hi
>
> In some lines the equili
ssage -
Von: Justin A. Lemkul
An: Discussion list for GROMACS users
CC:
Gesendet: 21:59 Sonntag, 6.Mai 2012
Betreff: Re: [gmx-users] Missing Interactions in [ angles ] Section in Topology
On 5/6/12 3:45 PM, Lara Bunte wrote:
> Hi
>
> You said:
>
>> The blank lines will be
Hello
I read the mdp options more than once but I don't understand how to make a good
em.mdp file for the first energy minimization, if you plug your molecule in a
water box. In my tutorial is this example given.
integrator = steep
nsteps = 200
nstlist = 10
rlist = 1.0
coulombtype = pme
rcoulom
Hello
I saw that in my force field parametrization I wrote the atom names and not the
atom types in the blocks like bonds, angles and so on.
Could this be a problem? Should I write the atom types in the blocks?
Greetings
Lara
--
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http://lists.
Hi Justin
In my flamol.rtp file that I create in my force field order CHARMM27
Greetings
Lara
- Ursprüngliche Message -
Von: Justin A. Lemkul
An: Lara Bunte ; Discussion list for GROMACS users
CC:
Gesendet: 20:32 Montag, 14.Mai 2012
Betreff: Re: [gmx-users] Atom Names or Atom
Hello
I want to write my parameters in the ffbonded.itp file in the CHARMM27 force
field folder. I wrote my atom types in this file. This atom types are defined
by me in atomtypes.dat
grompp gives me an error
Fatal error:
Unknown bond_atomtype
for all my atom types. Do I have to declare that
ng me
Greetings
Lara
- Ursprüngliche Message -
Von: Justin A. Lemkul
An: Discussion list for GROMACS users
CC:
Gesendet: 20:59 Montag, 7.Mai 2012
Betreff: Re: [gmx-users] Missing Interactions in [ angles ] Section in Topology
On 5/7/12 2:54 PM, Lara Bunte wrote:
> Hi
>
>
] for using CHARMM27
force field?
Thanks
Greetings
Lara
- Ursprüngliche Message -
Von: Mark Abraham
An: Discussion list for GROMACS users
CC:
Gesendet: 12:57 Dienstag, 15.Mai 2012
Betreff: Re: [gmx-users] Two [ dihedrals ] sections in topology
On 15/05/2012 8:47 PM, Lara Bunt
Hi
After pdb2gmx I have two [ dihedrals ] sections in my topology. The first block
is empty, the second block is correct with my parameters.
An an example:
First block:
[ dihedrals ]
; ai aj ak al funct c0 c1
c2 c3 c4
Hello
To make better energy minimization procedures I read about thermostats and
barostats. I understand the physical concepts and differences between global
and local thermostats and the difference between Berendsen and Nose-Hoover
thermostat.
1.)
Maybe this question is a little bit hairspl
-- Ursprüngliche Message -
Von: Justin A. Lemkul
An: Lara Bunte ; Discussion list for GROMACS users
CC:
Gesendet: 17:02 Dienstag, 15.Mai 2012
Betreff: Re: [gmx-users] Two [ dihedrals ] sections in topology
On 5/15/12 10:43 AM, Lara Bunte wrote:
> Hi
>
> You wrote:
>
>>
Hi
If I use pdb2gmx -f mymol.pdb -water tip3p (CHARMM27 force field) I got
warnings like this:
Making bonds...
Warning: Long Bond (1-2 = 0.261872 nm)
Warning: Long Bond (2-4 = 0.267812 nm)
Warning: Long Bond (6-4 = 0.260531 nm)
and so on
For what problem tries GROMACS to warn me? Should I
Hi
After:
pdb2gmx -f mymol.pdb -water tip3p
editconf -f conf.gro -bt dodecahedron -d 1.3 -o box.gro
genbox -cp box.gro -cs spc216.gro -p topol.top -o solvated.gro
I typed:
grompp -f em.mdp -p topol.top -c solvated.gro -o em.tpr
where em.mdp is my energy minimization file and I got:
Fata
n A. Lemkul
An: Lara Bunte ; Discussion list for GROMACS users
CC:
Gesendet: 13:22 Mittwoch, 16.Mai 2012
Betreff: Re: [gmx-users] grompp Unkown bond_atomtype C2
On 5/16/12 3:56 AM, Lara Bunte wrote:
> Hi
>
> After:
>
> pdb2gmx -f mymol.pdb -water tip3p
> editconf -f co
Hello
After
grompp -f em.mdp -p topol.top -c solvated.gro -o em.tpr
I got the error:
Incorrect number of parameters - found 2, expected 4 or 4 for U-B.
I thought that this could be an inconsistency be declaring the functions, but
in my topology I have function 4 (for improper dihedrals)
f the
topol.top file.
Greetings
Lara
- Ursprüngliche Message -
Von: Mark Abraham
An: Discussion list for GROMACS users
CC:
Gesendet: 2:35 Mittwoch, 16.Mai 2012
Betreff: Re: [gmx-users] Two [ dihedrals ] sections in topology
On 16/05/2012 4:53 AM, Lara Bunte wrote:
> Hi
>
>&
-
Von: Justin A. Lemkul
An: Lara Bunte ; Discussion list for GROMACS users
CC:
Gesendet: 17:02 Donnerstag, 17.Mai 2012
Betreff: Re: [gmx-users] Two [ dihedrals ] sections in topology
On 5/17/12 10:48 AM, Lara Bunte wrote:
> Hi
>
> grompp -f em.mdp -p topol.top -c solvated.gro -o em.
Hello
I never had contact with such units. Could you please help me and explain me
how to transform following units:
1.)
kcal / mol --> kJ / (mol * nm^2)
2.)
kcal / (mol * rad^2) --> kJ / (mol * rad^2)
I have additionally some question to that: Both should be units of a force
constant. From
trization I have this values. Could you please explain this?
Greetings and really thanks for your help
Lara
- Ursprüngliche Message -
Von: Justin A. Lemkul
An: Lara Bunte ; Discussion list for GROMACS users
CC:
Gesendet: 18:52 Donnerstag, 17.Mai 2012
Betreff: Re: [gmx-users] For
that means probably, that the writers of the paper did an error. Could such
an error ruin my hole MD? My complete force field parametrization is out of
this paper.
Thanks for helping me
Greetings
Lara
- Ursprüngliche Message -
Von: Richard Broadbent
An: Lara Bunte ; Discussi
g=AFQjCNFOxi8Cf2eUshmA9rzPfLPra5u-gw&sig2=79QqmWk3b8LSFlVjey4FFg
Do you think it is a typo?
Greetings
Lara
- Ursprüngliche Message -
Von: Justin A. Lemkul
An: Lara Bunte ; Discussion list for GROMACS users
CC:
Gesendet: 20:37 Donnerstag, 17.Mai 2012
Betreff: Re: [gmx-users] Force Con
ant is divided by mol. What is the reason for this? In example
Energy/length^2 is the force constant, why do we consider Energy/(mol *
lenght^2) ?
Thanks for helping me
Greetings
Lara
- Ursprüngliche Message -
Von: Justin A. Lemkul
An: Lara Bunte ; Discussion list for GROMACS user
That helps a lot. Thank you, I guess I got it now :-)
Greetings
Lara
- Ursprüngliche Message -
Von: Richard Broadbent
An: Lara Bunte ; Discussion list for GROMACS users
CC: "jalem...@vt.edu"
Gesendet: 11:21 Freitag, 18.Mai 2012
Betreff: Re: [gmx-users] Force Constant
Hello
I want to equilibrate the water around my molecule. For doing this I created a
pr.mdp file that makes most sense for me. Sadly I am a beginner with less
knowledge, so could you please take a look on this pr.mdp file and say me if
this is good or if not, what would you suggest to me? My Sy
Hello
After equilibrating the water around my molecule I want to run the MD
simulation. In my tutorial this is primed with:
grompp -f run.mdp -p topol.top -c pr.gro -o run.tpr
I don't have this pr.gro file but I have a pr.tpr file. Could I use this one?
It seems GROMACS accepts this but I don'
Hello
If I have a force constant 287 kcal/(mol * A^2), the A stands for Angstrom and
I want to calculate this to kJ/(mol * nm^2), is it correct that I have to
multiply 4.19/0.01 = 419 to the force constant?
Is ithis true: 287 kcal/(mol * A^2) = 120253 kJ/(mol * nm^2)
Could this be a physica
Hi
>Monte Carlo methods in GROMACS 5.0.
Thats cool, when will GROMACS 5.0 be released?
Greetings
Lara
- Ursprüngliche Message -
Von: Michael Shirts
An: Discussion list for GROMACS users
CC:
Gesendet: 18:24 Freitag, 1.Juni 2012
Betreff: Re: [gmx-users] Configurational bias Mo
Hello
In all my tutorials for md they investigate a molecule in solution. I want to
do md simulations in vacuum and I did not find a good tutorial. So I want to
ask you what should I do for a md simulation in vaccum?
I take a molecule, optimize the structure, generate a topology with gromacs an
Hello
I read about Gromacs building blocks (
http://www.gromacs.org/Documentation/File_Formats/Gromacs_Building_Blocks ) and
there is written following table. How to do a MD Smiluation with this building
blocks?
Greetings
Abbrev. Source 2 Full Name
FAD ffgmx.rtp O flavin adenine dinucleot
Hi
Is it possible to convert a .pdb file to a .xyz file with GROMACS?
At this point there shouldn't be a force field or final topology, I just want
to convert this formats to each other. Is it possible with GROMACS?
Greetings
Lara
--
gmx-users mailing listgmx-users@gromacs.org
http://lis
Hello
I use a CHARMM27 force field and my system is lumiflavin in water. I use the
spc216 water model, a dodecahedral box with 1.3 nm. I want to make a structure
minimization. I made a file pr.mdp. Could you please tell me, what I could do
better in this file, or what is wrong? I guess there ha
same problem. The water could not be settled.
What is wrong with this file for my system?
Greetings
Lara
- Ursprüngliche Message -
Von: Justin A. Lemkul
An: Lara Bunte ; Discussion list for GROMACS users
CC:
Gesendet: 12:23 Freitag, 29.Juni 2012
Betreff: Re: [gmx-users] Structure
Hello
Is it possible with GROMACS to convert a given .pdb structure file to a .xyz
structure file?
Thanks for help
Greetings
Lara
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at
http://www.gromacs.org/Suppo
Hi Justin
I really forgot this old mail. I am sorry for that.
editconf worked :)
Greetings
Lara
- Ursprüngliche Message -
Von: Justin Lemkul
An: Lara Bunte ; Discussion list for GROMACS users
CC:
Gesendet: 16:04 Dienstag, 18.September 2012
Betreff: Re: [gmx-users] PDB and XYZ
Hello
I want to do md simulations with the amino acid alanin for practice. I choose
alanin because it is parametrized in my forcefield. I use charmm27.
I created with pdb2gmx my topology and I use water model tip3p. I choosed a
dodecahedron box with distance of 0.5 between the solute and this b
, Lara Bunte wrote:
> Hello
>
> I want to do md simulations with the amino acid alanin for practice. I choose
> alanin because it is parametrized in my forcefield. I use charmm27.
>
> I created with pdb2gmx my topology and I use water model tip3p. I choosed a
> dodecahedron box
Hello
I want to equilibrate water around the amino acid alanin. I guess I have no
further errors up to here.
In my pdb file of alanin stands in the first line COMPND Alanin
In my topology in the [ moleculetype ] block stands at name:
Protein_chain_A. At the end of the topology file stands in
Hello
In my practice calculation I made wrong cut-offs in an energy minimization.
After the help of Justin and Peter (thanks a lot) it works and now I have some
theoretical question about this. I read about cut-offs in the manual but I
don't understand it really.
Could you please explain me
Hello
Could you please take a look on my new pr.mdp file that I created for
equilibrating water around lumiflavin. grompp works but I guess there must be
something wrong because after grompp I am using mdrun and get this warning:
Warning: 1-4 interaction between 1 and 5 at distance 2.429 which
Hello
In my former questions I got some answers that leads me to following question
(I am really thankful for that. This mailing list and the people here are great
:-) ).
I am using a CHARMM27 force field and it seems that I often used wrong settings
in equilibrating and energy minimization. So
Hello
My equilibration of water around lumiflavin works (I got no error, no warning
and no note). Sadly the mdrun fails with following error:
step 886: Water molecule starting at atom 7596 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.
What does GROMACS me
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