Dear Chris,
Thanks again for investing your valuable time on my problem.
I forgot to mention in my previous mail that, I have made total
two changes in the parameters. First I changed x/y compressibility from 0
(zero) to 4.5e-5 and second x/y ref_t from zero to 1.0 as you have
suggested.
OLD PA
>>* I am trying to simulate my own structure based simulation using 3.3.2.
*
>What sort of structure?
RNA with a ligand (the ligand is the trouble)
>>* I
*>>* have developed the forcefield and it works fine without periodic boundary
*>*> conditions. When I use pbc=xyz atoms that are connected in
> Hi
>
> I seem to be doing something wrong here, but cannot figure out what.
>
> - I have run a 200 ps NVT simulation for a lipid bilayer on 4
> processors using the gromacs-3.3.1 build.
>
> - The last frame from the NVT simulation was used in conjunction with
> a newly written .mdp file to resta
> I am trying to simulate my own structure based simulation using 3.3.2.
What sort of structure?
> I
> have developed the forcefield and it works fine without periodic boundary
> conditions. When I use pbc=xyz atoms that are connected in the [bonds]
> section of the topology get broken. What ha
> Hi Alok,
>
>Thanks for your email.
>
>Could you please explain in more detail? What do you mean by chain
> identifier?
See http://wiki.gromacs.org/index.php/Multiple_Chains
Mark
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> Hi All,
>
>I am trying to put 2 identical peptide chains in a simulation box.
> However, gromacs tends to see both separate peptide chains as one.
>
>The following is the method that I used, please comment and correct me
> if
> I'm wrong.
>
>First, I translate the peptide to a certain
Hi Alok,
Thanks for your email.
Could you please explain in more detail? What do you mean by chain
identifier?
Many thanks.
Best regards,
Huey Ling
On 26/10/2007, [EMAIL PROTECTED] <[EMAIL PROTECTED]> wrote:
>
> Hello Huey Ling,
>
> Use different chain identifiers for different peptid
>
> This is my first post to this list, so a warm hello to everybody!
>
> I want to constrain the distance between two atoms in different
> molecules (two diff proteins, in complex). So, I defined both molecules
> in the same [ moleculetype ] and added an extra [ bonds ] line:
> 216 6465 6 0.
I am trying to simulate my own structure based simulation using 3.3.2. I
have developed the forcefield and it works fine without periodic boundary
conditions. When I use pbc=xyz atoms that are connected in the [bonds]
section of the topology get broken. What happens is 1 of the two atoms will
cr
Hello Huey Ling,
Use different chain identifiers for different peptides.
Then pdb2gmx will not create any bond between them.
Regards,
Alok
> Hi All,
>
>I am trying to put 2 identical peptide chains in a simulation box.
> However, gromacs tends to see both separate peptide chains as one.
>
Dear Chris,
I have ran the equilibration run till 225ps but water molecule are not ready
to stay at my desirable place :-( , I mean to say still I am getting uneven
distribution of water moleculers over lipid head groups. Even after changing
0 to 4.5e-5.
I also suggested that you change ref_p t
Hi
I seem to be doing something wrong here, but cannot figure out what.
- I have run a 200 ps NVT simulation for a lipid bilayer on 4
processors using the gromacs-3.3.1 build.
- The last frame from the NVT simulation was used in conjunction with
a newly written .mdp file to restart the simulati
Quoting Huey Ling Tan <[EMAIL PROTECTED]>:
> Hi All,
>
>I am trying to put 2 identical peptide chains in a simulation box.
> However, gromacs tends to see both separate peptide chains as one.
>
>The following is the method that I used, please comment and correct me if
> I'm wrong.
>
>F
Hi All,
I am trying to put 2 identical peptide chains in a simulation box.
However, gromacs tends to see both separate peptide chains as one.
The following is the method that I used, please comment and correct me if
I'm wrong.
First, I translate the peptide to a certain distance. Then I
This is my first post to this list, so a warm hello to everybody!
I want to constrain the distance between two atoms in different
molecules (two diff proteins, in complex). So, I defined both molecules
in the same [ moleculetype ] and added an extra [ bonds ] line:
216 6465 6 0.400 300.00
sarbani chattopadhyay wrote:
hi,
I had run MD simulations where the output control parameters were
nstxout=250
nstvout= 1000
nstenergy=100
Due to this the '.trr' file is very large. I want to compress this file
so that
xyz coordinates are stored every 1000 steps,
velo
Check out ffoplsaanb.itp
Tom
--On Friday, October 26, 2007 01:05:46 -0700 huan
<[EMAIL PROTECTED]> wrote:
i checked it but the what is the atomtype for opls_064
for?
thanks
--- David van der Spoel <[EMAIL PROTECTED]> wrote:
huan wrote:
> i am a new user of Gromacs and i would lik
Note: Forwarded message attached
-- Original Message --
From: "sarbani chattopadhyay" <[EMAIL PROTECTED]>
To: [EMAIL PROTECTED]
Subject: trjconv help
--- Begin Message ---
hi,
I had run MD simulations where the output control parameters were
nstxout=250
nstvout= 1000
huan wrote:
i checked it but the what is the atomtype for opls_064
for?
Check the paper that describes the force field. Reference in the GROMACS
manual.
Mark
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gmx-users mailing listgmx-users@gromacs.org
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i checked it but the what is the atomtype for opls_064
for?
thanks
--- David van der Spoel <[EMAIL PROTECTED]> wrote:
> huan wrote:
> > i am a new user of Gromacs and i would like to
> knoe
> > the opls for C, =O, and -O in RCOOR'. i tried it
> many
> > times but i still fail to get the prop
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