Justin Lemkul wrote
> So the initial equilibration was NPT?
Yes.
Justin Lemkul wrote
> Did you ever try simply running NVT with
> either Berendsen or V-rescale before applying any type of pressure
> coupling?
No, I haven't, and I don't remember seeing that described in any work flow.
Justin
Could you tell me what is the procedure to cut the bond to produce
the photodissociation?
On Thu, Sep 20, 2012 at 3:12 PM, Mark Abraham wrote:
> On 20/09/2012 1:08 PM, Rajiv Gandhi wrote:
>
>> Dear all,
>>
>> Why all people cut the protein ligand bond to produce the
>> photodissociation?
>>
>
> B
Thanks Mark.
I was using the following command as I got it in the manual.
g_dist -f traj.xtc -s topol.tpr -n index.ndx -o dist.xvg
But I could not able to find the way how to specify the indices of the
two desired atoms.
( suppose I want to plot the distance between atom no. 500 (protein
backbone)
On 20/09/2012 1:08 PM, Rajiv Gandhi wrote:
Dear all,
Why all people cut the protein ligand bond to produce the photodissociation?
Because MM forcefields typically assume bonds do not break or form.
Electronic degrees of freedom are not directly considered in the model.
For instances, In my
On 20/09/2012 2:05 PM, tarak karmakar wrote:
Thanks Justin.
But in my case I want to plot the distance between one atom in the
backbone of the protein and other atom present in the ligand. Then how
can I specify these two atoms I need for plotting the distance between
them.
g_dist treats the
Thanks Justin.
But in my case I want to plot the distance between one atom in the
backbone of the protein and other atom present in the ligand. Then how
can I specify these two atoms I need for plotting the distance between
them.
On Thu, Sep 20, 2012 at 12:26 AM, Justin Lemkul wrote:
>
>
> On
On 20/09/2012 7:10 AM, Ladasky wrote:
After weeks of trying various conditions, I found my problem. Here, from my
position-restrained MDP file, are the two relevant lines:
; Temperature coupling is on
tcoupl= V-rescale ; Weak coupling for initial equilibration
[snip]
; Pressure coup
On 9/19/12 5:10 PM, Ladasky wrote:
After weeks of trying various conditions, I found my problem. Here, from my
position-restrained MDP file, are the two relevant lines:
; Temperature coupling is on
tcoupl= V-rescale ; Weak coupling for initial equilibration
[snip]
; Pressure coupl
I am not sure where the idea of using berendsen barostat with the v-rescale
thermostat for equilibration came from, however. Doesn't the typical
equilibration begin with v-rescale for temperature equilibration then
adding parinello-rahman barostat then switching to nose-hoover for production
ru
Dear Sara,
I just had a problem with my simulations that I traced to the use of the
V-rescale temperature algorithm. Here is my recent post:
http://gromacs.5086.n6.nabble.com/Re-Water-molecules-cannot-be-settled-why-td4999302.html;cid=1348087067061-71#a5001121
V-rescale may be appropriate in ce
After weeks of trying various conditions, I found my problem. Here, from my
position-restrained MDP file, are the two relevant lines:
; Temperature coupling is on
tcoupl= V-rescale ; Weak coupling for initial equilibration
[snip]
; Pressure coupling is on
pcoupl= Berendsen
On 9/19/12 4:10 PM, Eduardo Oliveira wrote:
As i suspected. But I still don't know how to set this thing up. Should i repeat
the values on the same line? I don't care about accuracy this time as it is
just a test for further analysis
Yes, it is standard (and most logical) to set all values
On 9/19/12 2:55 PM, tarak karmakar wrote:
Dear All,
I want to calculate the distance between the nitrogen atom present in
the ligand and the H- attached to the backbone of the protein along a
long trajectory. So can anyone suggest me how to consider these two
atoms to calculate and plot the di
Dear All,
I want to calculate the distance between the nitrogen atom present in
the ligand and the H- attached to the backbone of the protein along a
long trajectory. So can anyone suggest me how to consider these two
atoms to calculate and plot the distance along with the time ?
--
Tarak
--
gm
On 9/19/12 1:41 PM, Eduardo Oliveira wrote:
Hi all,
I was preparing my system for a simulation and after using grompp i got the
following message:
Fatal error:
Invalid T coupling input: 2 groups, 1 ref_t values and 1 tau_t values
For more information and tips for troubleshooting, please chec
On 9/19/12 12:54 PM, Lara Bunte wrote:
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
Thanks for your time and help as usual.
Elie
> Date: Wed, 19 Sep 2012 13:47:26 -0400
> From: jalem...@vt.edu
> To: gmx-users@gromacs.org
> Subject: Re: [gmx-users] use of PRODRG
>
>
>
> On 9/19/12 11:40 AM, Elie M wrote:
> >
> >> I don't understand this. PRODRG will be of no use here since you
On 9/19/12 11:40 AM, Elie M wrote:
I don't understand this. PRODRG will be of no use here since you are using
OPLS-AA, and if there is no ligand, then why do you need some external program
to build a topology?
- The "LIG" residue only appears in the pdb version of the file. I tried to
use
On 9/19/12 11:47 AM, 이종화 wrote:
Greetings all,
I am trying to compare the stability of two protein-ligand systems where
ligands differ. I am trying to observe the difference of interaction energy
between the ligands. Would it be correct to make energy groups of Protein,
Solvent, Ligand, and
Hi all,
I was preparing my system for a simulation and after using grompp i got the
following message:
Fatal error:
Invalid T coupling input: 2 groups, 1 ref_t values and 1 tau_t values
For more information and tips for troubleshooting, please check the GROMACS
for more information here goes th
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
On 9/19/12 12:27 PM, Lara Bunte wrote:
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. A
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
Hi
Thanks for the help. I changed this cut-off parameters and increased the
distance between my box und the solute from 0.5 to 1.5. I got no error and no
note. :-)
Greetings
Lara
- Ursprüngliche Message -
Von: Peter C. Lai
An: Discussion list for GROMACS users
CC:
Gesendet: 12:
Greetings all,
I am trying to compare the stability of two protein-ligand systems where
ligands differ. I am trying to observe the difference of interaction energy
between the ligands. Would it be correct to make energy groups of Protein,
Solvent, Ligand, and compare the energy obtainable by g_
> I don't understand this. PRODRG will be of no use here since you are using
> OPLS-AA, and if there is no ligand, then why do you need some external
> program
> to build a topology?
- The "LIG" residue only appears in the pdb version of the file. I tried to
use editconf on the .mol type of
On 19/09/2012 11:22 PM, Ali Alizadeh wrote:
Dear Justin
I prepare a .top file with a combination of input #include and pdb2gmx,
How can i generate a .gro file from this .top file?
You can't - they have radically different kinds of information. Also,
see
http://www.gromacs.org/Documentation/
Dear Justin
I prepare a .top file with a combination of input #include and pdb2gmx,
How can i generate a .gro file from this .top file?
Sincerely
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at
http://www.gro
On 9/19/12 8:31 AM, naga sundar wrote:
Dear simone
I think so u r using the same pr.mdp and md.mdp files
what u created initially. So open both the mdp files replace DRG with UNK
and the try sure it will work out.
The error is from pdb2gmx, so .mdp alterations will have
Dear simone
I think so u r using the same pr.mdp and md.mdp files
what u created initially. So open both the mdp files replace DRG with UNK
and the try sure it will work out.
On Tue, Sep 18, 2012 at 9:44 AM, Justin Lemkul wrote:
>
>
> On 9/18/12 12:42 PM, SIMONE BROGI wrote:
Dear Mark Thank you for your previous help
With your Help I Have successfully
Constructed .top and .gro for my cyclic peptide After That i Have solvated
and added ions . . But when I do Energy Minimization My Molecule after Energy
Minimiz
for EM you can probably ignore this, but note that these are the wrong
cutoffs for CHARMM27. (rlist=1.2 rlistlong=1.4 rcoulomb=1.2 rvdw=1.2
rvdw_switch=0.8 and vdwtype=switch).
On 2012-09-19 11:04:47AM +0100, Lara Bunte wrote:
> Hello
>
> I want to do md simulations with the amino acid alanin fo
On 9/19/12 6:04 AM, 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 with dis
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
On 9/19/12 3:26 AM, Ali Alizadeh wrote:
Dear All users
Is it possible adding new atomtype to force fields?
Yes.
Can i prepare a .top file with a combination of input #include and pdb2gmx?
Yes.
-Justin
--
Justin A. Lemkul, Ph.D.
Research Scie
On 9/18/12 10:35 PM, Elie M wrote:
Dear all,
I have been reading about PRODRG that takes a PDB file as an input and produces
topologies compatible with GROMACS as an output. Can this program be then
considered as a solution to the problem of missing residues in GROMACS like LIG?
PRODRG pro
g_hbond does.
19 sep 2012 kl. 05.49 skrev Mark Abraham:
> On 19/09/2012 12:49 PM, Amit Shavit wrote:
>> Hello,
>>
>> I'm relatively new to GROMACS, and I need to write some of my own analysis
>> tools using the template.c file.
>> I have been able to figure out most of the structure of it, and h
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