> Hi!
> I would like to simulate halkali halides in GROMACS by using the Tosi-Fumi
> potential.
>
> The potential is of this kind (Born Mayer Huggins), with an exponential, a
> 6th, 8th powers and the coulomb term:
>
> U(r) = Ae^(-r/rho) - C/r^6 -D/r^8 + (q1 q2)/(4 pi eps r)
>
> Did somebody used
Hi
To be more clear I have .xtc file for a disulfide linked complex of
two chains. From this trajectory I can extract .xtc file for
individual chains. But when I generate .top file from individual chain
pdb I get one atom extra in .top file i.e. protonated SG of Cys which
I dont need in order to ma
On 3/18/13 10:49 PM, shahid nayeem wrote:
I am using Gromacs-4.5.4 and this does not have -cys option in pdb2gmx.
shahid
My apologies. For some reason I always think there is a -cys option, when in
fact it is -ss. In any case, if you're trying to treat some strange form of
cysteine, some
I am using Gromacs-4.5.4 and this does not have -cys option in pdb2gmx.
shahid
On Tue, Mar 19, 2013 at 2:06 AM, Justin Lemkul wrote:
>
>
> On 3/18/13 10:39 AM, shahid nayeem wrote:
>>
>> Hi All
>> How can I get a topology file using pdb2gmx from a single chain
>> polypeptide with one of the CYS
On 3/18/13 9:59 PM, Kieu Thu Nguyen wrote:
Thank Justin !
I made this rectangular box from merging two cubic boxes. And i carry out
equilibrate this box. Do you mean that i should run NVT, and next step run
NPT, to keep box shape fixed ?
I'm not making any recommendation. You haven't provid
On 3/18/13 7:49 PM, Gabriele Lanaro wrote:
Hi!
I would like to simulate halkali halides in GROMACS by using the Tosi-Fumi
potential.
The potential is of this kind (Born Mayer Huggins), with an exponential, a
6th, 8th powers and the coulomb term:
U(r) = Ae^(-r/rho) - C/r^6 -D/r^8 + (q1 q2)/(
As noted by your rtp entry:
> [ bonds ]
> C1-C4
> C1H11
> C1H12
> C1C2
> C2F21
> C2F22
> C2+C3
> C3F31
> C3F32
> C3C4
> C4F4
> C4Cl4
> C4+C1
One end of the residue bonds via the C1 to a C4 in
Thank Justin !
I made this rectangular box from merging two cubic boxes. And i carry out
equilibrate this box. Do you mean that i should run NVT, and next step run
NPT, to keep box shape fixed ?
Regards,
~Thu
On Tue, Mar 19, 2013 at 3:39 AM, Justin Lemkul wrote:
>
>
> On 3/18/13 1:36 PM, Kieu
I have successfully construct the polymer chain of length 1 using the OPLS
force field. The rtp file as follow:
; F2311 - this is an internal residue
[ Fre ]
[ atoms ]
C1opls_135 -0.5681
H11 opls_1400.2741
H12 opls_1400.2731
C
Hi!
I would like to simulate halkali halides in GROMACS by using the Tosi-Fumi
potential.
The potential is of this kind (Born Mayer Huggins), with an exponential, a
6th, 8th powers and the coulomb term:
U(r) = Ae^(-r/rho) - C/r^6 -D/r^8 + (q1 q2)/(4 pi eps r)
Did somebody used anything of this
On 3/18/13 6:14 PM, Steven Neumann wrote:
On Mon, Mar 18, 2013 at 8:40 PM, Justin Lemkul wrote:
On 3/18/13 2:56 PM, Steven Neumann wrote:
Dear Gmx Users,
I am trying to obtain given density for my system for a given molecule
- its a cubic box of 5 nm in dimension.
I calculated that I ne
On Mon, Mar 18, 2013 at 8:40 PM, Justin Lemkul wrote:
>
>
> On 3/18/13 2:56 PM, Steven Neumann wrote:
>>
>> Dear Gmx Users,
>>
>> I am trying to obtain given density for my system for a given molecule
>> - its a cubic box of 5 nm in dimension.
>>
>> I calculated that I need 850 molecules to get th
On 3/18/13 2:56 PM, Steven Neumann wrote:
Dear Gmx Users,
I am trying to obtain given density for my system for a given molecule
- its a cubic box of 5 nm in dimension.
I calculated that I need 850 molecules to get the density of 500 g/mol
In my box there is already 1 molecule so I try:
genb
On 3/18/13 1:36 PM, Kieu Thu Nguyen wrote:
Dear All,
I want to equilibrate a rectangular box. But after running MD 60 ns, the
system become to be a cubic box mostly. I do not want this happens. Can
anyone tell me how to constrain the boxsize. In that case, the boxsize has
fluctuations but rema
On 3/18/13 12:47 PM, Parshvika Sharma wrote:
Dear gromacs users,
I want to run a protein ligand MD in Gromacs 4.6 using CHARMM forcefield.
My system consists of 2 non-covalently bound ligands (FAD and NADPH) in the
active site. I generated the topology files (*.itp) of ligands using
SWISSPARAM
On 3/18/13 12:35 PM, shahid nayeem wrote:
Hi
Is it possible to write .top file from .xtc and .tpr using index.ndx
so that .top is available for tailormade components of simulated
protein.
All topology information is in the .tpr, but not in .top format. You may be
able to post-process the o
On 3/18/13 10:39 AM, shahid nayeem wrote:
Hi All
How can I get a topology file using pdb2gmx from a single chain
polypeptide with one of the CYS, SH in the form of SG as if it is
involved in disulfide linkage, while the other chain with which I
expect it to form disulfide link is not in the i
Dear gromacs users,
I want to run a protein ligand MD in Gromacs 4.6 using CHARMM forcefield.
My system consists of 2 non-covalently bound ligands (FAD and NADPH) in the
active site. I generated the topology files (*.itp) of ligands using
SWISSPARAM. Before running the energy minimization, I added
Hi,
I believe there is no force output for constraint pulling. Try umbrella.
Erik
On Mar 18, 2013, at 3:28 PM, raghav singh wrote:
Hello Fellow Users,
I am trying to pull a DNA molecule. I have fixed one end and trying
to pull
the other one using this .mdp file.. force output is all zeros
Hi All
How can I get a topology file using pdb2gmx from a single chain
polypeptide with one of the CYS, SH in the form of SG as if it is
involved in disulfide linkage, while the other chain with which I
expect it to form disulfide link is not in the input pdb file. or can
I use pdb2gmx command and
Hello Fellow Users,
I am trying to pull a DNA molecule. I have fixed one end and trying to pull
the other one using this .mdp file.. force output is all zeros.
I have tried going through the user-list but have not found any solution
yet. I am using gmx-version 4.5.5.
Any idea why is it happening.
Thanks - I have filed issue #1194 and assigned it to David.
http://redmine.gromacs.org/issues/1194
Let me know if there is anything else that is needed. I could take a shot at
myself, and will play around with it, but I don't know the details of the
symtab in any detail, unfortunately.
15 mar
On Mon, Mar 18, 2013 at 8:24 AM, Shima Arasteh
wrote:
> Yes, I overcome the last problems and I could see the pos.rest energy term
> in my log file.
> In order to create the itp files to include in top file, I opened the gro
> file which I entered as an input in my mdrun command. How might I check
Yes, I overcome the last problems and I could see the pos.rest energy term in
my log file.
In order to create the itp files to include in top file, I opened the gro file
which I entered as an input in my mdrun command. How might I check this issue
that all the atoms in itp groups are involved i
On Mon, Mar 18, 2013 at 1:15 PM, Justin Lemkul wrote:
>
>
> On 3/18/13 3:42 AM, Shima Arasteh wrote:
>
>> Thanks for all your replies.
>> But I' d like to know what the meanings of S and D are? Why sometimes we
>> should write DPOSRE, sometimes POSRE, and sometimes DPOSRES?
>>
>>
> I already expl
On 3/18/13 6:02 AM, Shima Arasteh wrote:
With position restraints I got a new RMSD with the Min 0.05 and Max 0.11. I
don't know if this range of deviation with position restraints is sensible or
not! I can't believe with such a force of 10 I still see deviations!
I'd prefer to get less d
On 3/18/13 3:42 AM, Shima Arasteh wrote:
Thanks for all your replies.
But I' d like to know what the meanings of S and D are? Why sometimes we should
write DPOSRE, sometimes POSRE, and sometimes DPOSRES?
I already explained what the "D" prefix means. If this is unclear to you,
please read
On 3/18/13 3:05 AM, Shima Arasteh wrote:
To solve the problem, I changed all DPOSREs in if statments to POSRE. Again I get the
fatal error. This error states that I have inserted topology section
"position_restraints" in a wrong place. I checked again the itp files included
in my top file. T
On 3/18/13 1:36 AM, preetichoudh...@iisermohali.ac.in wrote:
Original Message
Subject: implicit solvation
From:preetichoudh...@iisermohali.ac.in
Date:Fri, March 15, 2013 1:58 pm
To: gmx-users@gromacs.org
-
With position restraints I got a new RMSD with the Min 0.05 and Max 0.11. I
don't know if this range of deviation with position restraints is sensible or
not! I can't believe with such a force of 10 I still see deviations!
I'd prefer to get less deviation. Would it be possible by using a gre
Thanks for all your replies.
But I' d like to know what the meanings of S and D are? Why sometimes we should
write DPOSRE, sometimes POSRE, and sometimes DPOSRES?
Sincerely,
Shima
From: Shima Arasteh
To: Justin Lemkul ; Discussion list for GROMACS users
Se
To solve the problem, I changed all DPOSREs in if statments to POSRE. Again I
get the fatal error. This error states that I have inserted topology section
"position_restraints" in a wrong place. I checked again the itp files included
in my top file. They are matched correctly! Did I modified th
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