Dear All,
I have set two bilayers:
1. 400 DOPC
2. 320DOPC and 80 Cardiolipin
Second one show significant curvature during NPT equilibrium and MD run
(not in NVT eq.). Is it normal?
For the first bilayer, after adding the protein to the system, here also I
can see big curvature in the membrane.
D
Hi,
Is there any difference between confout.gro file and last frame which we
can extract from trajectory? I am thinking they are different!!
When I see the trajectory I can see the edge of the well-shaped box, but
when I see confout.gro it is not well-shaped and some atoms looks went out
out of th
ers for the polar head and the lipidic tail, so
> it is worth trying to merge them
> to have the correct representation!
>
> Francesco
>
> 2012/5/21 Dariush Mohammadyani
>
>> Have you checked MARTINI website?
>> http://md.chem.rug.nl/cgmartini/index.
Have you checked MARTINI website?
http://md.chem.rug.nl/cgmartini/index.php/downloads/force-field-parameters
Dariush
Kind Regards,
Dariush Mohammadyani
Department of Structural Biology
University of Pittsburgh School of Medicine
Biomedical Science Tower 3
3501 Fifth Avenue
Pittsburgh, PA
cardiolipin) fly away from bilayer and come inside the water.
Does anybody know what is the problem? How should I fix my system?
I am using Coarse grained model using MARTINI force field.
Thanks,
Dariush
--
Kind Regards,
Dariush Mohammadyani
Department of Structural Biology
University of
:
>
>
> On 4/26/12 1:35 PM, Dariush Mohammadyani wrote:
>
>> Dear All,
>> I am using CG-MD using MARTINI forcefield. The system contains Protein
>> and lipid
>> bilayer. Although I used:
>> define = -DPOSRES
>> components in system were moving around and i
Dear All,
I am using CG-MD using MARTINI forcefield. The system contains Protein and
lipid bilayer. Although I used:
define = -DPOSRES
components in system were moving around and interact with each other. Then,
I cannot do NVT or NPT equilibration.
Could you please let me know how can I control thi
I have gotten this error previously. I changed the address of the g_dist
(e.g. /user/gromacs/bin/g_dist) in distances.pl file and it works.
Dariush
On Thu, Mar 29, 2012 at 11:51 AM, vidhya sankar wrote:
> Dear justin , Thank you for your previous reply
> When i Download and run Distance.pl scri
As far as I concern, the minimum size is that cove all parts of your
molecules or system. In case you should use solvent it is up to you to add
how many molecules and in this case you should make decision by experience
or according to literature.
Dariush
--
Kind Regards,
Dariush Mohammadyani
ation"?
Thanks,
Dariush
On Wed, Mar 14, 2012 at 10:08 AM, Justin A. Lemkul wrote:
>
>
> Dariush Mohammadyani wrote:
>
>> Dear user,
>> When I am using:
>> genbox -cp confout.gro -cs water-1bar-303K.gro -vdwd 0.21 -o solvated.gro
>> to add water in
figure it out?
Or actually if we have some clashes in system how we can correct them?
Thanks,
Dariush Mohammadyani
Department of Structural Biology
University of Pittsburgh School of Medicine
Biomedical Science Tower 3
3501 Fifth Avenue
Pittsburgh, PA 15261
USA
--
gmx-users mailing list
--
> *From:* Dariush Mohammadyani
> *To:* dina dusti ; Discussion list for GROMACS users
>
> *Sent:* Thursday, March 8, 2012 11:24 PM
> *Subject:* Re: [gmx-users] Martini
>
> SC5 does not work?
> Dariush
>
> --
> Kind Regards,
> Dariush Mohammadyani
SC5 does not work?
Dariush
--
Kind Regards,
Dariush Mohammadyani
Department of Structural Biology
University of Pittsburgh School of Medicine
Biomedical Science Tower 3
3501 Fifth Avenue
Pittsburgh, PA 15261
USA
On Thu, Mar 8, 2012 at 2:34 PM, dina dusti wrote:
> Dear Gromacs Speciali
Thanks Justin!
There is one script in User Contributions page, but it does not work.
I totally changed my way, I will use NAMD in this case...
On Fri, Jan 27, 2012 at 2:11 PM, Justin A. Lemkul wrote:
>
>
> Dariush Mohammadyani wrote:
>
>> Is there any similar script to
Is there any similar script to change it for this reason?
On Fri, Jan 27, 2012 at 11:26 AM, Justin A. Lemkul wrote:
>
>
> Dariush Mohammadyani wrote:
>
>> Hi all,
>>
>> I have two files (Topology and Parameter files) in NAMD format (*.inp). I
>> am going to
Hi all,
I have two files (Topology and Parameter files) in NAMD format (*.inp). I
am going to use them in GROMACS.
Can you help me how can I use them?
Kind Regards,
Dariush Mohammadyani
Department of Structural Biology
University of Pittsburgh School of Medicine
Biomedical Science Tower 3
3501
GROMACS 4.5.3
and charmm27.ff.
Cytochrome C is a difficult protein to simulate :(
Thanks,
Dariush
On Tue, Jan 17, 2012 at 10:33 AM, Justin A. Lemkul wrote:
>
>
> Dariush Mohammadyani wrote:
>
>> According your help and "pdb2gmx -his -missing" I could create input
g 'HIS' names and interactive setup is that bonds to
> heme
> iron will be generated based on the 'specbond.dat' entries, if HIS NE2
> nitrogens are close enough to the FE.
>
> Krzysztof
>
>
>
> On 1/10/12 2:40 PM, Dariush Mohammadyani wrote:
>
Hi all,
Has anybody used Coarse grained model for Cytochrome C? I could create a
model using MARTINI forcefiels (using martinize.py script and 1HRC.pdb
file), but it does not have HEM and HOH groups. Can anybody help me?
Kind Regards,
Dariush Mohammadyani
Department of Structural Biology
Dear Justin,
I could not find HIS in CHARMM and GROMOS53a6. Somebodies offer to rename
it to HSE or HSD, but I do not know why? and which one is correct. I am
working on Cytochorom c.
Thanks,
Dariush
On Tue, Jan 10, 2012 at 4:22 PM, Justin A. Lemkul wrote:
>
>
> Dariush Mohammady
Does anybody know where can I find [ HIS ] parameters?
Thanks,
Dariush
On Sat, Jan 7, 2012 at 3:58 AM, Dariush Mohammadyani <
d.mohammady...@gmail.com> wrote:
> Dear Peter and Krzyszto,
>
> Thank you. I am following your comments. If I get any problem I will come
> back.
>
(un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
--
Kind Regards,
Dariush Mohammadyani
Department of Structural Biology
University of Pittsburgh Sch
gt; > > OO -0.515
> > >[ bonds ]
> > > CH3HH31
> > > CH3HH32
> > > CH3HH33
> > > CH3C
> > > C O
> > >
> > > Surprisingly, an .hdb entry for
t; bob h.
>
>
>
>
> On 1/5/2012 12:00 PM, Dariush Mohammadyani wrote:
>
> Yes, I have PDB file (1HRC.pdb). However, when I try to use "pdb2gmx" I
> get this error:
>
> Residue 'HEM' not found in residue topology database
>
> and HEM is Iron
e umbrella mdp files.
> >>>>
> >>>> pull= umbrella
> >>>> pull_geometry = distance
> >>>> pull_dim = Y Y Y
> >>>> pull_start = no
> >>>> pull_ngroups = 1
> >>>> pull_group0 = cage
heir website; I
used martinize.py script; Again I got error.
Regards,
Dariush
On Thu, Jan 5, 2012 at 11:51 AM, Justin A. Lemkul wrote:
>
>
> Dariush Mohammadyani wrote:
>
>>
>> Hi all,
>>
>> Has anybody made initial configuration for Cytochrom C? Can it be
Hi all,
Has anybody made initial configuration for Cytochrom C? Can it be shared
with me?
Thanks,
Dariush
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