, Jul 18, 2013 at 2:05 PM, Justin Lemkul wrote:
>
>
> On 7/18/13 8:04 AM, Rasoul Nasiri wrote:
>
>> Justin,
>>
>> I just ran this calculations on "VERSION 4.6-GPU-dev-20120501-ec56c" and I
>> will let you know about the outcomes.
>>
>>
> Th
Justin,
I just ran this calculations on "VERSION 4.6-GPU-dev-20120501-ec56c" and I
will let you know about the outcomes.
Rasoul
On Thu, Jul 18, 2013 at 1:09 PM, Rasoul Nasiri wrote:
> Bellow are commands and error message:
>
> 1- trjconv_d -f traj.xtc -n maxclust.ndx -o
, Justin Lemkul wrote:
>
>
> On 7/18/13 6:52 AM, Rasoul Nasiri wrote:
>
>> Hello all,
>>
>> I'm trying to know how the surface area of a nano-drop changes during the
>> evaporation in the vacuum.
>>
>> When I filter the trajectory of non-ev
Hello all,
I'm trying to know how the surface area of a nano-drop changes during the
evaporation in the vacuum.
When I filter the trajectory of non-evaporated molecules by trjconv and use
g_sas for calculation of their surface, it usually crash (I'm using version
of 4.5.5).
Is there still this i
Hello all,
Is it possible one can calculate molecular diffusion of multi-component
systems in the gas phase by GROMACS?
This quantity is very important in evaporation of fluids when liquid and
vapour phases are in quasi-equilibrium state.
Any help would be highly appreciated?
Best
Rasoul
--
gm
Are you sure lattice cell set up in f.c.c structure has been explained
there for the positions of molecules?
On Thu, May 16, 2013 at 3:28 PM, Mark Abraham wrote:
> Does manual 2.3 help?
>
>
> On Thu, May 16, 2013 at 2:51 PM, Rasoul Nasiri
> wrote:
>
> > Hi All,
>
Hi All,
Has anyone performed MD simulation on fluids in reduced units with GROMACS?
I just wandering how the obtained density values through the box should be
converted in the SI unit (Kg/m3).
Thanks
Rasoul
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listi
conditions for MD simulations
> of droplets.
>
> There will be many papers discussing it and I'd be shocked if there aren't
> several review articles as well.
>
> Richard
>
>
> On 07/05/13 14:50, Rasoul Nasiri wrote:
>
>> Dear All,
>>
>>
Dear All,
I just had a question regarding using the PBC for evaporation of clusters.
Due to PBC the evaporated molecules again come back to drop
(re-condensation). For me such a process is physically meaning less.
Shall I ask a question from GMX users about this issue.
How we can eliminated this
estimate the temperature as well.
Is it correct?
Rasoul
On Mon, Apr 8, 2013 at 2:30 PM, Justin Lemkul wrote:
> On Mon, Apr 8, 2013 at 9:24 AM, Rasoul Nasiri
> wrote:
>
> > Justin,
> > Thanks for your comment.
> >
> > Instead of .xtc, I just used .trr in wh
Justin,
Thanks for your comment.
Instead of .xtc, I just used .trr in which nstvout isn’t zero. I'm still
encountering to empty file for temperature.
Rasoul
On Mon, Apr 8, 2013 at 2:10 PM, Justin Lemkul wrote:
> On Mon, Apr 8, 2013 at 9:08 AM, Rasoul Nasiri
> wrote:
>
&g
Bellow is my command which I used:
g_clustsize_d -f traj.xtc -s topol.tpr -n n.ndx -nc nclust.xvg -mc maxclust
.xvg -ac avclust.xvg -mcn maxclust.ndx -cut 0.516 -temp Tempe.xvg
Rasoul
On Mon, Apr 8, 2013 at 2:04 PM, Justin Lemkul wrote:
> On Mon, Apr 8, 2013 at 9:01 AM, Rasoul Nas
Dear All,
I tried to use g_clustsize_d program for estimation of temperature of
cluster/nanodroplet but the temperature output file is empty. Could you
comment where is the problem?
Please note that I can get Temperature of system using g_energy_d but I'm
interest to know cooling effect of nano-d
ecule is n-alkane that have (2n+2) C-H bond. Is that
make sense that I put the virtual sites there?
Best
Rasoul
On Mon, Feb 11, 2013 at 5:33 PM, Erik Marklund wrote:
> Try virtual sites constructions.
>
>
> On Feb 11, 2013, at 6:01 PM, Rasoul Nasiri wrote:
>
>> Dear A
Dear All,
I need to define interaction sites on the center of C-H bonds instead
of nuclei of each atom. The main reason was that non-bonding
parameters (sigma and epsilon) have been parametrized in these centers
and those are only available for the center of C-H.
So, I just wanted to know how ca
Dear all,
I would like to ask you that using PBC for evaporation of droplets is necessary?
Please note that the MD simulations are to be performed in vacuum.
I checked the relevant references but in some of them PBC has been
taken into account but in others not [for instance please see J.chem.
p
Dear GMX users,
I just wanted to know that it's possible one estimates Gibbs free
energy of evaporation via following the solvation free energy scheme?
I'm trying to obtain evaporation rate with using the value of G(evap.)
for different hydrocarbon molecules at different temperatures.
Any advice
tance between solute and co-solvents and co-solvents with themselves
cause to rise of pressure.
Rasoul
.
On Sat, Apr 17, 2010 at 6:03 PM, Justin A. Lemkul wrote:
>
>
> rasoul nasiri wrote:
>
>> Hi,
>> Thanks for the replies.
>> Since I want to increase distance am
appropriate distances. Is it OK?
Rasoul
On Sat, Apr 17, 2010 at 5:43 PM, Justin A. Lemkul wrote:
>
>
> Justin A. Lemkul wrote:
>
>
>>
>> rasoul nasiri wrote:
>>
>>> Dear Justin,
>>> Hello again
>>>
>>> Thanks for the message. I want to
Dear Justin,
Hello again
Thanks for the message. I want to increase the distance between solutes in
simulation box before MD simulation. How can I do it?
Rasoul
On Sat, Apr 17, 2010 at 5:16 PM, Justin A. Lemkul wrote:
>
>
> rasoul nasiri wrote:
>
>> Dear All,
>> Hell
Dear All,
Hello
I understand one can adjust distance of between solvent molecules by genbox
command and -vdwd but I don't know, how do it between the solutes?
Thanks for helping!
Rasoul
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Pleas
P.S,
You can E-mail your request to cgmart...@rug.nl.
Rasoul
On Fri, Jan 29, 2010 at 10:18 AM, rasoul nasiri wrote:
> Hi,
>
> It is better you plan this question in MARtini forum, there are experts
> that can answer this question!
> Please register in:
> http://md.che
Hi,
It is better you plan this question in MARtini forum, there are experts that
can answer this question!
Please register in:
http://md.chem.rug.nl/cgmartini/index.php/user-platform/login
Rasoul
On Thu, Jan 28, 2010 at 1:43 PM, Emanuel Peter <
emanuel.pe...@chemie.uni-regensburg.de> wrote:
> D
Hi,
please see: http://tfy.tkk.fi/soft/levi2010/
Rasoul
On Thu, Jan 28, 2010 at 12:42 PM, oguz gurbulak wrote:
> Dear Gromacs Developers,
>
> I'm intested in a workshop for Gromacs. Is there a workshop planned in
> 2010 ?
>
> Kind Regards,
>
>
> --
> gmx-users mailing listgmx-users@gromacs
Hi
I want to use a solvent with two types molecules (for example linear and
cyclic Glucose form).
How can I fill box with them?
I highly appreciate for advice given me!
Best Regards
Rasoul
On Sat, Jan 16, 2010 at 11:42 AM, David van der Spoel
wrote:
> leila karami wrote:
>
>> Dear David
>> in
OK. you are right!
Rasoul
On Wed, Jan 6, 2010 at 1:09 PM, Justin A. Lemkul wrote:
>
>
> On 1/6/10 7:05 AM, leila karami wrote:
>
>> dear Rasoul
>> I put executable DSSP in /usr/local/bin and gromacs is
>> in /usr/local/gromacs.
>> is it true?
>>
>>
> Is the executable named DSSP, or dssp? Case
yes. Could you perform do_dssp properly?
Rasoul
On Wed, Jan 6, 2010 at 1:05 PM, leila karami wrote:
> dear Rasoul
>
> I put executable DSSP in /usr/local/bin and gromacs is
> in /usr/local/gromacs.
>
> is it true?
>
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.o
Then your executable has problem. Gromacs tool can not find DSSP for doing
d_dssp. Do you put executable DSSP in the path of gromacs is installed?
Rasoul.
On Wed, Jan 6, 2010 at 11:58 AM, leila karami wrote:
> dear Rasoul
>
> I had executable dssp program, already.
>
> leila karami
>
> --
> gmx-
Do you have a DSSP program on your system? If no, please install executable
DSSP program from http://swift.cmbi.kun.nl/gv/dssp/ website.
Rasoul
On Wed, Jan 6, 2010 at 11:34 AM, leila karami wrote:
> Hi
>
> I apply following command:
>
> do_dssp -f rrr.xtc -s .tpr -n n.ndx -map ss.map
>
> but
Hi,
Thank you for your quick reply.
Is there another CGFF for this purpose that Gromacs can read it? What is
your opinion about CG GO model?
Kind regards
Rasoul
On Mon, Dec 21, 2009 at 8:23 PM, Justin A. Lemkul wrote:
>
>
> rasoul nasiri wrote:
>
>> Dear Justin,
>> Th
and %Random coil) of the protein at
different time of reaction.
Could I perform CGMD simulation with MArtini force field for finding the
denaturation mechanism of the protein properly?
Best regards
Rasoul
On Fri, Dec 18, 2009 at 10:04 PM, Justin A. Lemkul wrote:
>
>
> rasoul nas
and a vdw distance of 0.19.
>
> Regards
> Cesar
>
> 2009/12/17 rasoul nasiri
>
>> yes, I know there will be limitation for modeling of Folding/Unfolding
>> proteins with MARtini CGFF if I want to look at complete folding/unfolding
>> mechanism of proteins but I want to
Rasoul
On Thu, Dec 17, 2009 at 5:03 PM, César Ávila wrote:
> I suggest you read the original paper for Martini Protein FF. I think it is
> not suitable for your purpouse.
>
> 2009/12/17 rasoul nasiri
>
>> Hi,
>>
>> My purpose is finding of denaturation mechanism
smaller radius of van
der waals of the water beads, then I will continue CGMD simulation. Is it
possible I reduce this radius? Which commands of Gromacs suit can do it?
Rasoul
On Thu, Dec 17, 2009 at 1:42 PM, Mark Abraham wrote:
> rasoul nasiri wrote:
>
>> greetings GMX users,
>
greetings GMX users,
When I use genbox command for filling solvent in CGMD simulation with
Gromacs suit, I must use a larger van der Waals distance to avoid crashes.
when I use default value (0.105nm), system will crash. Which distance is
suitable for performing CGMD simulation. I used 0.15 or 0.
Dear GMX users,
Hi
I'm working on denaturation of proteins with MARTINI CGFF by Gromacs suit.
according to this paper (J. Chem. Theory and Comput. 2008, 4, 819–834) I
undestand there is a limitation for modeling of folding and unfolding with
MARITI CGFF for systems in which the folding and unfoldi
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