k you to help me, Please?
Best Regards
Sara
____
From: Tsjerk Wassenaar
To: mohammad agha ; Discussion list for GROMACS users
Sent: Saturday, December 31, 2011 3:41 PM
Subject: Re: Fw: [gmx-users] trjconv in martini
Hi Sara,
> # Extract the first part of the trajector
- Forwarded Message -
From: mohammad agha
To: "gmx-users@gromacs.org"
Sent: Tuesday, January 10, 2012 9:08 PM
Subject: Re: Fw: [gmx-users] trjconv in martini
Hi Tsjerk,
I know that my question is silly but please help me.
I installed python2.5 on my system,
Dear prof.
I used a piece of python code that reverses a trajectory named xtcrev.py
((c)2011 Tsjerk A. Wassenaar), I have one problem when I ran it as following:
./xtcrev.py 1a.xtc > 1a-rev.xtc
it's error is:
Traceback (most recent call last):
File "./xtcrev.py", line 54, in
n = 92 + i(
to help me, please?
Best Regards
Sara
From: Tsjerk Wassenaar
To: mohammad agha ; Discussion list for GROMACS users
Sent: Wednesday, January 11, 2012 12:54 PM
Subject: Re: Fw: [gmx-users] trjconv in martini
Hi Sara,
That can only happen if the input file is
much and thank you very much but may I ask you any
suggestion about my problem, please?
Best Regards
Sara
rom: Tsjerk Wassenaar
To: mohammad agha ; Discussion list for GROMACS users
Sent: Wednesday, January 11, 2012 1:38 PM
Subject: Re: Fw: [gmx-users] tr
Hi Tsjerk,
I have a good news!!! That was corrected!!!
Thank you very much from your help.
Best Regards
Sara
From: Tsjerk Wassenaar
To: mohammad agha ; Discussion list for GROMACS users
Sent: Wednesday, January 11, 2012 2:12 PM
Subject: Re: Fw: [gmx
Dear Gromacs users,
I defined tree beads for aniline consists of SC4, SC4 and SNd as following:
[moleculetype]
; molname nrexcl
DRG 1
[atoms]
; id type resnr residu atom cgnr charge
1 SNd 1 DRG NH2 1 0
2 SC4 1 DRG
Dear Prof.
I don't know about definition of sulfuric acid in Martini Corse-Grained, May I
ask you to help me, Please?
And Please say me about my definition of aniline as SC4, SC4, SNd that is
correct?
Best Regards
Sara
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Dear Prof.
I want to use walls (in z=0 and z=z_box) for my simulation with martini
coarse-grained force field, but always it give me error!
Do the martini force field support walls? Should I use just 12-6 for wall_type?
May I ask your help about this, Please?
Best regards
Sara--
gmx-users mai
Dear Gromacs users,
May I ask you to help me about use of walls in martini coarse-grained, please?
I defined two walls for my system as following:
pbc = xy
nwall = 2
wall_type = 12_6
wall_r_linpot = 1
wall_atomtype = W W
I sel
Dear Gromacs users,
I want to work by walls as table with martini coarse-grained.
Is there anyone to help me for building table.xvg for bonds, angles and
dihedrals in martini when I change vdw_type from shift to user?
Thank you in advance.
Best Regards
Sara
--
gmx-users mailing listgmx-user
Dear Prof.
I am confused about generation a radial density graph (density vs distance from
center of mass), I know that I should use g_rdf. Then I count the number of
atoms in the shells around the COM of special group by " trjorder -com -nshell
-r " , next I use from this formula for compute t
- Forwarded Message -
From: mohammad agha
To: "gmx-users@gromacs.org"
Sent: Tuesday, January 31, 2012 11:56 AM
Subject: g_rdf
Dear Prof.
I am confused about generation a radial density graph (density vs distance from
center of mass), I know that I should use g_rdf. Th
Behalf Of mohammad agha
Sent: Tuesday, 31 January 2012 7:26 PM
To: gmx-users@gromacs.org
Subject: [gmx-users] g_rdf
Dear Prof.
I am confused about generation a radial density graph (density vs distance from
center of mass), I know that I should use g_rdf. Then I count the number of
atoms in
-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On
Behalf Of mohammad agha
Sent: Thursday, 2 February 2012 3:48 AM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] g_rdf
Dear Prof.
Thank you very much from your reply.
Is your mean that "density=(N/V)*g(r)"
Dear Specialist Gromacs,
I want to compare properties of two micelles of different surfactants by
MARTINI coarse-grained force field.
The difference of these surfactants is in their counterion, one of them has
bromide (Br-) ion and another has Chloride (Cl-). I know that I should show
this part
Dear Gromacs Specialists,
I want to make a system consists of one box of solvent (for example water) that
there is 100 surfactant molecules in it and water is in contact with air in
surface as same as we do in laboratory in beaker. But I don't know how should I
define this air-water interface f
Dear Gromacs Specialists,
I made a box consists of water with box lengths: 6nm * 6nm * 6nm , then I
equilibrated it with NPT ensemble, box size increased to 6.66176, then I kept
the x- and y-dimensions fixed, and double the system size in z as following:
editconf -f pr1.gro -o newbox1.gro -bo
mohammad agha
Sent: Wednesday, 22 February 2012 3:12 AM
To: Discussion list for GROMACS users
Subject: [gmx-users] interface
Dear Gromacs Specialists,
I made a box consists of water with box lengths: 6nm * 6nm * 6nm , then I
equilibrated it with NPT ensemble, box size increased to 6.66176, then
Can you help me to construct the air/water interface, Please?
Best Regards
Sara
From: Mark Abraham
To: Discussion list for GROMACS users
Sent: Wednesday, February 22, 2012 12:59 AM
Subject: Re: [gmx-users] interface
On 22/02/2012 3:11 AM, mohammad agha
Dear Mark,
Thank you very much from your reply.
Best Regards
Sara
From: Mark Abraham
To: Discussion list for GROMACS users
Sent: Thursday, February 23, 2012 5:24 AM
Subject: Re: [gmx-users] interface
On 22/02/2012 10:34 PM, mohammad agha wrote:
Dear
Dear Gromacs users,
I work with Gromacs in Linux, I want prepare a copy of snapshots by ngmx with
jpg or pdf format or whatever that be open in Windows.
May I ask you to help me,Please?
Best Regards
Sara
--
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http://lists.gromacs.org/mailman/listinf
From: Justin A. Lemkul
To: mohammad agha ; Discussion list for GROMACS users
Sent: Monday, May 7, 2012 10:28 PM
Subject: Re: [gmx-users] ngmx
On 5/7/12 1:50 PM, mohammad agha wrote:
> Dear Gromacs users,
>
> I work with Gromacs in Linux, I want
Dear Justin,
Thank you very much from your response.
Best Regards
Sara
From: Justin A. Lemkul
To: mohammad agha ; Discussion list for GROMACS users
Sent: Tuesday, May 8, 2012 6:15 AM
Subject: Re: [gmx-users] ngmx
On 5/7/12 9:42 PM, mohammad agha wrote
Dea GROMACS Users,
I want to calculate the free energy for my system, for example (Gibbs and
Helmholtz), but I didn't define the free_energy in the md.mdp and my simulation
has been finished!!!
May I ask you that say me is there a solution fro this problem?
Best Regards
Sara
--
gmx-users mai
Dear GROMACS Specialists,
We know that one system is at equilibrium state when the variation of Helmholtz
or Gibbs free energy be zero.
May I ask you say me that how I can understand that my system has reached to
equilibrium state in the end of simulation, Please?
Best Regards
Sara
--
gmx-user
Dear GROMACS Users,
I work with NPT ensemble. Is the total energy equal to Gibbs free energy?
Thanks in advance.
Sara
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* Please search the archive at
http://www.gromacs.org/Support/Mailing_Li
I know that "delta S
= (internal energy + P*delta V- delta G)/T" but here has been written: Delta
S(N,p,T) = S(N,p,T) - S idgas(N,p,T) = ( + pV - Delta G)/T.
May I ask you to answer me about this and the equation of delta G, Please?
Best Regards
Sara
- Original Message -
From: St
Dear Steven,
Many thanks from your help. In the manual at the
section g_energy has been written that the gromacs calculate the delta G
as is follows:
"Delta G = G(N,p,T) - G idgas(N,p,T) = kT ln < eˆ(Upot/kT) >"
But
I don't understand why Upot? to calculate of delta S, I know that
"delta S = (
Dear GROMACS Specialists,
I have one system consists of many surfactant molecules that they create
several micelles. How should I know that time of simulation is enough or not?
that means where is the enough time for equilibrium of system?
To creation of micelles, the small oligomers are merged
Dear Gromacs Specialists,
I want to find information about RDF of some components in my system but when I
do the g_rdf command, I find true answers about RDF diagrams but my system type
below note in several times:
"There were 2 inconsistent shifts. Check your topology"
May I know that this mess
Dear GROMACS Specialist,
I want to plot probability (nm^-1) distribution of micelle selected atoms with
respect to COM of the micelle (nm).
with respect to this definition, "Probability was defined as the number of
instances the selected atom was found within a spherical shell of width 0.02 nm
Dear GROMACS Specialists,
Thank you very much from your answer, but I want to know plotting this curve
from g_rdf.
May I ask you to give me one formula by this command, Please?
Best Regards
Sara
On 2013-05-09 20:15, Justin Lemkul wrote:
>
>
> On 5/9/13 10:15 AM, mohammad a
f (i.e. surfactant headgroup, alkyl tail, etc?)
Do not forget to take into account the (average) volume of the simulation cell
and the mass of the atom group to obtain the rho(r) (g.cm-3) as function of the
Micelle COM otherwise, you will obtain the N(r) as function of Micelle COM (in
nm-1)
HT
f (i.e. surfactant headgroup, alkyl tail, etc?)
Do not forget to take into account the (average) volume of the simulation cell
and the mass of the atom group to obtain the rho(r) (g.cm-3) as function of the
Micelle COM otherwise, you will obtain the N(r) as function of Micelle COM (in
nm-1)
HT
Dear GROMACS Specialists,
I have one problem with g_dist. When I use g_dist along with option -dist, the
output is printed on the terminal, but I want them into a file as separately.
May I ask you to help me, Please?
Thank you in advance
Best Regards
Sara
--
gmx-users mailing listgmx-users@
Dear Justin,
Thank you very much from your answer.
May I ask you to help me more, Please?
I work with UBUNTU, I don't know how should I do it!
Best Regards
Sara
On 5/10/13 11:27 AM, mohammad agha wrote:
> Dear GROMACS Specialists,
> I have one problem with g_dist. When I use g
Dear Justin,
Thank you very much from your help.
Best Regards
Sara
On 5/10/13 11:27 AM, mohammad agha wrote:
> Dear GROMACS Specialists,
> I have one problem with g_dist. When I use g_dist along with option -dist,
> the output is printed on the terminal, but I want them into
Dear GROMACS Specialists,
I want to obtain number of instances the different atoms was found within a
spherical shell of width 0.02 nm at a distance r
from the micelle COM. For this, I use g_dist -dist, but when I select for
example 0.04, it also result all instances in 0-0.02, whereas I want on
- Forwarded Message -
From: Justin Lemkul
To: mohammad agha
Cc:
Sent: Monday, May 13, 2013 4:11 PM
Subject: Re: probability from COM of micelle
It is much better to post this information to the list so that others can
benefit from it.
-Justin
On 5/13/13 5:25 AM, mohammad agha
Dear Gromacs Users,
I have several questions about g_clustsize, Please help me.
I have several micelles in my system and I want to calculate: the number of
monomers in micelles and cluster number and monomer number during the time of
simulation, I used from this command as is follows:
g_clustsiz
Dear Gromacs Users,
I have several questions about g_clustsize, Please help me.
I have several micelles in my system and I want to calculate: the number of
monomers in micelles and cluster number and monomer number during the time of
simulation, I used from this command as is follows:
g_clus
Dear Justin,
Thank you very much from your response.
according you said I should set -cut with less than 0.7, but this doesn't
answer me!
for 0.6:
0.00e+00 115
6.00e+01 107
1.20e+02 114
1.80e+02 105
2.40e+02 100
3.00e+02
Dear Justin,
Thank you very much from your help.
I think that I should work more on this command and will ask you next.
I don't know why does it bother me for it's .xvg and -tu !!!
Thank you very much again.
Best Regards
Sara
On 7/19/12 9:42 AM, mohammad agha wrote:
>
Dear Gromacs Users,
I don't know what is the quantity of -cut in g_clustsize for different systems,
exactly!
May I ask you to help me, Please?
Best Regards
Sara
--
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http://lists.gromacs.org/mailman/listinfo/gmx-users
* Only plain text messages a
Dear Gromacs Users:
When I want to place 12000 solvent molecule in the box (15*15*15) it say:
number of coordinates in coordinate file (ctacyc.gro, 28794)
does not match topology (topol.top, 37950)
it means that I should enlarge the box to place all of solvent molecules into
that.
Dear Gromacs Users:
When I want to place 12000 solvent molecule in the box (15*15*15) it say:
number of coordinates in coordinate file (ctacyc.gro, 28794)
does not match topology (topol.top, 37950)
it means that I should enlarge the box to place all of solvent molecules into
th
Hi Emanuel,
Thank you very much from your response.
It means that it isn't one problem and it is natural.yes?
Best Regards
Sara
- Original Message -
From: Emanuel Birru
To: 'mohammad agha' ; 'Discussion list for GROMACS users'
Cc:
Sent: Tuesday, August
Sara
- Original Message -
From: Emanuel Birru
To: 'mohammad agha' ; 'Discussion list for GROMACS users'
Cc:
Sent: Tuesday, August 14, 2012 12:06 PM
Subject: RE: [gmx-users] box of simulation
Hi Sara,
The number of molecules in your .gro file and .top file should
Thank you very much.
Best Regards
Sara
- Original Message -
From: Emanuel Birru
To: 'mohammad agha' ; Discussion list for GROMACS users
Cc:
Sent: Tuesday, August 14, 2012 12:46 PM
Subject: RE: [gmx-users] Fw: box of simulation
I am not sure whether a pressur
www.gromacs.org/Documentation/Terminology/Equilibration?highlight=equilibration
>
> http://www.gromacs.org/Documentation/Terminology/Pressure_Coupling
>
> Cheers,
> EB
>
> -Original Message-
> From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On
> B
Dear Mark,
Thank you very much from your help.
Best Regards
Sara
- Original Message -
From: Mark Abraham
To: Discussion list for GROMACS users
Cc:
Sent: Tuesday, August 14, 2012 2:44 PM
Subject: Re: [gmx-users] box of simulation
On 14/08/2012 6:55 PM, mohammad agha wrote:
> D
Dear Mark,
Unfortunately, my problem about box of simulation has not been solved!
My command lines are as follow:
1- genbox -ci solute.gro -nmol 150 -box 12 12 12 -o solute150.gro
2- editconf -f solute150.gro -o solute1501.gro -c -d 1.0 -bt cubic -box 13.6
13.6 13.6 -center 6.8 6.8 6.8
3- grompp
Dear Mark,
Unfortunately, my problem about box of simulation has not been solved!
My command lines are as follow:
1- genbox -ci solute.gro -nmol 150 -box 12 12 12 -o solute150.gro
2- editconf -f solute150.gro -o solute1501.gro -c -d 1.0 -bt cubic -box 13.6
13.6 13.6 -center 6.8 6.8 6.8
3- gr
Dear Mark,
Thank you very much from your help.
Best Regards
Sara
- Original Message -
From: Mark Abraham
To: Discussion list for GROMACS users
Cc:
Sent: Wednesday, August 15, 2012 5:23 PM
Subject: Re: [gmx-users] box of simulation
On 15/08/2012 10:27 PM, mohammad agha wrote
Dear Gromacs Users,
I have one problem about the way of computation in the Gromacs with frame and
time. (I work with MARTINI CG)
I have one md.mdp file that the parameters of output control in it is as
follows:
nsteps = 3000
dt = 0.030
; Output control
nstxout = 2000
nstvout = 2000
n
? or does
Gromacs perform the computations untill end of simulation (90 ps) and only
doesn't printe in the command line?
Best Reagrds
Sara
- Original Message -
From: Justin Lemkul
To: mohammad agha ; Discussion list for GROMACS users
Cc:
Sent: Monday, August 20, 2012 10:
Dear Mark,
Thank you very much from your help.
Best Regards
Sara
- Original Message -
From: Mark Abraham
To: Discussion list for GROMACS users
Cc:
Sent: Tuesday, August 21, 2012 9:45 AM
Subject: Re: [gmx-users] parameters for output control
On 21/08/2012 2:55 PM, mohammad agha
Dear Gromacs Users,
I have doubt about temperature bath coupling (v-rescale). I use this method
(v-rescale) for my system, and my system is NPT ensemble.
Has it problem? is v-rescale just used for NVT ensemble or it doesn't have
restriction?
Please help me.
Thank you in advance
Best Regards
Sar
Desr Gromacs Users,
I have several systems consist of: surfactants, solvent, and additives
molecules in several concentrations. I want obtain extent of movement each of
materials in the mixture in different concentrations. Is the self-diffusion
coefficient good foe this? I have doubt about this
Dear Gromacs users
I have one big problem with g_clustsize!
I see 9 micelles in my system after running. When I use g_clustsize for number
of clusters and average cluster size, they don't emphasize each other, and I
see 9 micelles from 36 ps to 120 ps in my box, but results of
nclust.x
Dear GROMACS Users,
I asked this question before but I don't understand it!
I placed several materials in my box of simulation for example box with
6nm*6nm*6nm and my materials are not placed in the smaller box but when I
equilibrate my system, the box became smaller and temperature and pressu
istake and it is natural?
Best Regards
Sara
- Forwarded Message -
From: Justin Lemkul
To: mohammad agha ; Discussion list for GROMACS users
Cc:
Sent: Thursday, October 4, 2012 5:52 PM
Subject: Re: [gmx-users] equilibrium for box of simulation
On 10/4/12 10:06 AM, mohammad agha wro
48 PM
Subject: Re: [gmx-users] equilibrium for box of simulation
On 5/10/2012 12:06 AM, mohammad agha wrote:
> Dear GROMACS Users,
>
> I asked this question before but I don't understand it!
>
>
> I placed several materials in my box of simulation for example box with
> 6
Message -
From: Justin Lemkul
To: mohammad agha ; Discussion list for GROMACS users
Cc:
Sent: Thursday, October 4, 2012 7:01 PM
Subject: Re: equilibrium for box of simulation
Please keep the discussion on the gmx-users list.
On 10/4/12 11:28 AM, mohammad agha wrote:
> Dear Justin,
>
&
didn't see the report of decreasing of box dimensions!
May I know your idea about it, Please?
Best Regards
Sara
- Original Message -
From: Justin Lemkul
To: mohammad agha ; Discussion list for GROMACS users
Cc:
Sent: Thursday, October 4, 2012 7:57 PM
Subject: Re: [gmx-users]
34 AM
Subject: Re: [gmx-users] equilibrium for box of simulation
On 5/10/2012 3:55 PM, mohammad agha wrote:
> Dear Justin,
>
> Thank you very much.
> So, decreasing of box dimensions is not bad, if all thing process natural,
> yes?
> The cause of my doubt was because of in the most o
Thank you very much from your time.
Best Regards
Sara
- Original Message -
From: Mark Abraham
To: Discussion list for GROMACS users
Cc:
Sent: Friday, October 5, 2012 9:48 AM
Subject: Re: [gmx-users] equilibrium for box of simulation
On 5/10/2012 4:12 PM, mohammad agha wrote
Dear Gromacs Users,
I have one system consists of: surfactant, solvent and additives. I made one
box with only solvent and one box with only additives and equilibrated them
little separable for better placing into the box, and then made one box with
surfactant and then placed box of solvent and
Dear Gromacs Users,
I have one system consists of: surfactant, solvent and additives. I made one
box with only solvent and one box with only additives and equilibrated them
little separable for better placing into the box, and then made one box with
surfactant and then placed box of solvent
Dear Gromacs Users,
I have one system consists of: surfactant, solvent and additives. I made one
box with only solvent and one box with only additives and equilibrated them
little separable for better placing into the box, and then made one box with
surfactant and then placed box of solvent
Dear Gromacs Users,
I have one system consists of: surfactant, solvent and additives. I made one
box with only solvent and one box with only additives and equilibrated them
little separable for better placing into the box, and then made one box with
surfactant and then placed box of solvent
after that equilibrate totally, there
are not previous problems and I wanted to know that this method is correct?
Best Regards
Sara
From: Justin Lemkul
To: mohammad agha ; Discussion list for GROMACS users
Sent: Monday, October 15, 2012 5:21 PM
Subject: Re:
licating, we
can't help at the moment. See previous comment about relevant
information :-)
Mark
>
> Best Regards
> Sara
>
>
>
> - Original Message -
> From: Mark Abraham
> To: Discussion list for GROMACS users
> Cc:
> Sent: Friday, October 5, 20
Dear Justin,
Thank you very much from your time.
Best Regards
Sara
- Original Message -
From: Justin Lemkul
To: mohammad agha ; Discussion list for GROMACS users
Cc:
Sent: Monday, October 15, 2012 9:54 PM
Subject: Re: [gmx-users] about equilibrium
I didn't see any
Dear Gromacs Specialists,
I ran one system (to create of micelles) tow times. Time of creation of
micelles was different in each run and for example if it has been created 5
micelles (in the end of simulation) in both of them but the number of molecules
presence in micelles (aggregation number)
is opposite of experimental results.
Can you help me about this problem, Please?
Best Regards
Sara
- Original Message -
From: Justin Lemkul
To: mohammad agha ; Discussion list for GROMACS users
Cc:
Sent: Wednesday, December 5, 2012 12:31 AM
Subject: Re: [gmx-users] results of md
--
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Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-u
Dear Gromacs Users,
>
>
>
>I want to simulate 150 surfactant molecules in the water by MARTINI
>Coarse-Grained force field, and I have several questions please:
>1- I defined 2 groups in index.ndx file named "surfactants"
and "w_ion_ wf" that second group is consist of water,
a
Dear Gromacs Users,
>
>
>
>I want to simulate 150 surfactant molecules in the water by MARTINI
>Coarse-Grained force field, and I have several questions please:
>1- I defined 2 groups in index.ndx file named "surfactants"
and "w_ion_ wf" that second group is consist of water,
a
Dear Gromacs Users,
>
>
>
>I want to simulate 150 surfactant molecules in the water by MARTINI
>Coarse-Grained force field, and I have several questions please:
>1- I defined 2 groups in index.ndx file named "surfactants"
and "w_ion_ wf" that second group is consist of water,
a
Dear all,
I doubt about "gro" file of antifreeze water (in martini coarse-grained) that I
use for adding to my system.
May I ask you send for me a correct "gro" file of antifreeze water, Please?
Best Regards,
SARA--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mail
Dear Prof.
I have problems about density. I equilibrated my system consist 500 surfactants
and 6 water molecules in martini coarse-grained for 120 ns and my results
of g_energy next pr.mdp for density are:
average = 907.701
err.est = 0.61
rmsd = 2.54989
tot-drift = -3.4173
I don't know a
from : N= 4 π ρ∫ 0 00 r2 g(r) dr. , but I don't know how to find
N and what is the computation carefully?
Please help me.
Best Regards
Sara
From:Dallas Warren
To: mohammad agha ; Discussion list for GROMACS users
Sent: Monday, November 21, 2011 2:
Dear Prof.
I have some problems about g_clustsize program and I didn't find my answer in
mailing list. Please help me.
I don't know what is the base of selection for -cut option?
In my system after doing g_clustsize, when I see nclust.xvg file, it looks like
all the atoms in the system were used
On 2011-11-26 18:55, mohammad agha wrote:
> Dear Prof.
>
> I have some problems about g_clustsize program and I didn't find my
> answer in mailing list. Please help me.
> I don't know what is the base of selection for -cut option?
> In my system after doing g_clustsize,
Dear Prof.
I have a system consists of 500 surfactants + 61000 water beads + 500 ion in
martini force field into cubic box with 20.3*20.3*20.3 dimensions, May I know
the best quantity for -d option in editconf program to prevent from artificial
forces, please?
Best Regards
Sara
--
gmx-users m
Dear Prof.
I have a question about g_rdf.
I have a box consists of 500 surfactants that make 10 micelle. I want to
compute rdf for surfactant relative to the center of mass of micelle.
When I do g_rdf, the program ask me 2 groups that the first one is COM, but it
is COM of molecules that I defin
Spoel
To: Discussion list for GROMACS users
Sent: Sunday, November 27, 2011 3:08 PM
Subject: Re: [gmx-users] g_rdf -com
On 2011-11-27 12:27, mohammad agha wrote:
> Dear Prof.
>
> I have a question about g_rdf.
> I have a box consists of 500 surfactants that make 10 micelle. I want
Dear Prof.
I have a system consists of 10 micelle after production simulation. How can I
select a micelle with 92 monomer?
I know that I should use from g_select, but I don't know which argument is
proper for me. I also checked -select help in g_select program.
Please help me.
Best Regards
--
Thanks for your reply.
Best Regards
From: Justin A. Lemkul
To: Discussion list for GROMACS users
Sent: Wednesday, November 30, 2011 11:27 PM
Subject: Re: [gmx-users] g_select
mohammad agha wrote:
> Thanks for your reply, but how can I define resi
Dear Prof.
May I know the best quantity for -d option in editconf program? for example for
a cubic box consists of 7 water molecules and 500 surfactant molecules with
22 , 022 , 22 box dimensions in x , y and z?
Best Regards
Sara
--
gmx-users mailing listgmx-users@gromacs.org
http://li
- Forwarded Message -
From: mohammad agha
To: "gmx-users@gromacs.org"
Sent: Thursday, December 1, 2011 10:48 PM
Subject: editconf -d
Dear Prof.
May I know the best quantity for -d option in editconf program? for example for
a cubic box consists of 7 water molecul
Dear Prof.
I want to obtain the coordinate number from the first shell around my cluster,
I want to use from integration of the 4*pi*(number density)*area(g(r)r2dr)
until the first minimum of the RDF, but I have some questions: Please help me
1- How do I obtain the number density for special rd
every problem begins to resemble a nail.
From:gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On
Behalf Of mohammad agha
Sent: Sunday, 11 December 2011 11:15 PM
To: gmx-users@gromacs.org
Subject: [gmx-users] coordinate number aroud the first shell
Dear Prof.
I want to o
Dear Prof.
I have a doubt about my way to add antifreeze water to my system, also I think
my question looks silly but please help me for more certainty.
I changed "W" to "WF" in water.gro file of water that I downloaded from MARTINI
site and named that antifreezewater.gro , and with below comm
but the original placement of the WF might be silly.
Do not separate the two groups in the mdp file for the temperature control.
Leave them together.
On Dec 13, 2011, at 4:09 PM, mohammad agha wrote:
Dear Prof.
>
>
>Thanks for your reply.
>
>
>Yes, for example if I need 1
Dear Prof.
May I ask you two questions, Please?
1- I work with MARTINI force field. I have a surfactant molecule consists of 5
beads. After I placed 151 surfactants into my simulation box (cubic) with
length of 10 nm, Gromacs reported:
Volume = 1000 nm3
Density = 15.8111 gr/l
My volume is right
OMACS users
Sent: Thursday, December 15, 2011 11:19 AM
Subject: Re: [gmx-users] calculation of density for martini coarse-grained
On 15/12/2011 5:59 PM, mohammad agha wrote:
Dear Prof.
>May I ask you two questions, Please?
>1- I work with MARTINI force field. I have a surfactant molecule
thanks for your reply.
Best Regards
Sara
From: Mark Abraham
To: Discussion list for GROMACS users
Sent: Thursday, December 15, 2011 6:31 PM
Subject: Re: [gmx-users] calculation of density for martini coarse-grained
On 16/12/2011 1:36 AM, mohammad agha
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