Thank you very much from your answer.
Best Regards
Sara
From: Justin Lemkul
To: mohammad agha ; Discussion list for GROMACS users
Sent: Wednesday, September 25, 2013 3:07 PM
Subject: Re: [gmx-users] force field for Titanium
On 9/25/13 4:54 AM
Dear Gromacs Specialists,
I am searched force field for Titanium (Ti) element. Parameters consist of
sigma and epsilon. Can you help me, Please?
Best Regards
Sara
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Dear Justin,
Thank you very much from your response.
Best Regards
Sara
From: Justin Lemkul
To: mohammad agha ; Discussion list for GROMACS users
Sent: Saturday, July 20, 2013 3:47 PM
Subject: Re: [gmx-users] old and new versions of gromacs
On 7/20
Dear Gromacs Specialists
I already worked with Gromacs-4.5.4. In the Gromacs site has been released new
several versions. Has the old version (4.5.4) defects? Or are the new versions
more complete? I want to continiue my simulations with 4.5.4, are there
problems for it?
I compared the manual o
Dear Gromacs Specialists
I already worked with Gromacs-4.5.4. In the Gromacs site has been released new
several versions. Has the old version (4.5.4) defects? Or are the new versions
more complete? I want to continiue my simulations with 4.5.4, are there
problems for it?
I compared the manual o
- 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 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
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 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 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@
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,
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
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,
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 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 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 = (
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 GROMACS Users,
I work with NPT ensemble. Is the total energy equal to Gibbs free energy?
Thanks in advance.
Sara
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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
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
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
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)
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
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
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:
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
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
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
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
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]
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,
>
&
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
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
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
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
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 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
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
? 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 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
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 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,
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,
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
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
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
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
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
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
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,
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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* Only plain text messages a
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 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 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 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 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
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 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
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
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
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
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
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 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
-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)"
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
- 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
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
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 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 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 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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http://lists.gromacs.org
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
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
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
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
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(
- 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,
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
Hi Tsjerk,
Thank you very much from your help.
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,
> # Extr
ce again your
workflow. I hope work this time.
I thank you very very much again.
Best Regards
Sara
From: Tsjerk Wassenaar
To: mohammad agha ; Discussion list for GROMACS users
Sent: Saturday, December 31, 2011 2:18 PM
Subject: Re: Fw: [gmx-users] trjconv in mart
Hi Tsjerk,
Thanks for your reply, yes, I did this, too! but my problem wasn't solved!
Best RegardsSara
From: Tsjerk Wassenaar
To: mohammad agha ; Discussion list for GROMACS users
Sent: Saturday, December 31, 2011 11:42 AM
Subject: Re: Fw: [gmx-
Hi Tsjerk,
Thanks for your reply, yas, I did this too!
Best Regards
Sara
From: Tsjerk Wassenaar
To: mohammad agha ; Discussion list for GROMACS users
Sent: Saturday, December 31, 2011 11:42 AM
Subject: Re: Fw: [gmx-users] trjconv in martini
Hi Sara
Hi Tsjerk,
Thank you for your reply, yes it is #!/usr/bin/env python
May I ask you to help me?
Best Regards
Sara
From: Tsjerk Wassenaar
To: mohammad agha ; Discussion list for GROMACS users
Sent: Friday, December 30, 2011 8:06 PM
Subject: Re: Fw: [gmx
- Forwarded Message -
From: mohammad agha
To: Tsjerk Wassenaar
Sent: Friday, December 30, 2011 3:16 PM
Subject: Re: [gmx-users] trjconv in martini
Hi Tsjerk,
Thank you very much from your reply, I have a problem about ./xtcrev.py 1a.xtc
> 1a-rev.xtcI did ./xtcrev.py 1a.xtc &
Dear gromacs users,
At the first I thank from Tsjerk and Mark because of their answers to me but
unfortunately I don't understand that where is my mistake, still?
I work with MARTINI coarse-grained and I have a problem after -pbc nojump! My
simulation lasts 600 ns and 2 micelles are created fro
Thank you very much from your reply.
Best Regards
Sara
From: Tsjerk Wassenaar
To: mohammad agha ; Discussion list for GROMACS users
Sent: Thursday, December 29, 2011 1:56 AM
Subject: Re: [gmx-users] -pbc nojump
Hi Sara,
Please keep discussions on the
Dear GROMACS users,
I have a problem
about trjconv -pbc nojump, I have 2 micelles in the end of my simulation.
For analysis I should do three steps for micelle clustering at
http://www.gromacs.org/Documentation/How-tos/Micelle_Clustering?highlight=micelle+clustering
Steps 1 and 2 work good and
- Forwarded Message -
From: mohammad agha
To: Discussion list for GROMACS users
Sent: Tuesday, December 27, 2011 8:59 PM
Subject: Re: [gmx-users] trjconv and g_clustsize
Thank you very much from your reply.
I found out that my problem is at step "c" (-pbc nojump)
and g_clustsize
On 12/26/2011 7:53 PM, mohammad agha wrote:
Dear Prof.
>
>
>I have several questions about trjconv, please help me.
>
>
>In my simulation is created 2 micelles.
>1- When I do 3 steps of micelle clustering as follows:
>
>
> a- trjconv -f md.xtc -o a_cl
Dear Prof.
I have several questions about trjconv, please help me.
In my simulation is created 2 micelles.
1- When I do 3 steps of micelle clustering as follows:
a- trjconv -f md.xtc -o a_cluster.gro-e 60 -pbc cluster
b- grompp -f md.mdp -c a_cluster.gro -o a_cluster.tpr
c- trjconv -f md
Thank you very much.
Best Regards
Sara
From: Mark Abraham
To: Discussion list for GROMACS users
Sent: Saturday, December 24, 2011 1:48 PM
Subject: Re: [gmx-users] micelle clustering
On 12/24/2011 8:01 PM, mohammad agha wrote:
Dear GROMACS users
>
&
Dear GROMACS users
I want to analysis of 2 micelles that are created in one simulation, when I
view output of trajectory by vmd or ngmx:
ngmx -f md.trr -s md.tpr
has been created 2 micelles, then I try to micelle clustering by:
1. trjconv -f md.xtc -o a_cluster.gro -e 0.001 -pbc cluster
Dear GROMACS users
I doubt about calculate the concentration of my system. I know that
concentration is calculated from the number of molecules / Avogadro’s number
and divided by volume of box, but I think I calculate wrong, for example in one
of articles had been written:
7579 water molecules
From: Mark Abraham
To: Discussion list for GROMACS users
Sent: Saturday, December 17, 2011 10:22 AM
Subject: Re: [gmx-users] pressure coupling
On 17/12/2011 5:40 PM, mohammad agha wrote:
Thank you very much.
>Excuse me, I did another thing, may I know is it ri
: Saturday, December 17, 2011 9:31 AM
Subject: Re: [gmx-users] pressure coupling
On 17/12/2011 4:58 PM, mohammad agha wrote:
Dear GROMACS Users
>
>
>I have a warning after doing pr.mdp as followed, I read errors in GROMACS site
>and checked mailing list, but my warning is only step1 an
Dear GROMACS Users
I have a warning after doing pr.mdp as followed, I read errors in GROMACS site
and checked mailing list, but my warning is only step1 and after that
equilibration is run normally till end.
500 steps, 15.0 ps.
step 0
Step 1 Warning: pressure scaling more than 1%,
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