- Original Message -
From: vinothkumar mohanakrishnan
Date: Wednesday, October 6, 2010 17:18
Subject: Re: [gmx-users] Reg: Energy minimisation of hexane
To: Discussion list for GROMACS users
> Hi Mark
>
> I saw both the .gro file of hexane before and after EM in VMD as well checked
>
Hi Mark
I saw both the .gro file of hexane before and after EM in VMD as well
checked their coordinates. I am not able to make anything out of it. it will
better if one knows how to find the steric clash between two molecules?.
Regards
Vinoth
On Wed, Oct 6, 2010 at 11:08 AM, Mark Abraham wrote:
- Original Message -
From: vinothkumar mohanakrishnan
Date: Wednesday, October 6, 2010 15:20
Subject: [gmx-users] Reg: Energy minimisation of hexane
To: Discussion list for GROMACS users
> Hi all
>
> I am trying to simulate 150 molecules of hexane in a triclinic box
> (8.319*3.01*3.0
I recommend to use Linux inside a Virtualbox (http://www.virtualbox.org/)
over Cygwin. Cygwin is rather slow.
We should have a Virtual Appliance with GROMACS installed ...
On Tue, Oct 5, 2010 at 11:42 PM, Justin A. Lemkul wrote:
>
>
> #ZHAO LINA# wrote:
>
>> sudo apt-get install grace
>>
>
> Fo
Hi all
I am trying to simulate 150 molecules of hexane in a triclinic box
(8.319*3.01*3.01 nm^3) using OPLSAA force field.I got the .gro file from
PRODRG and generated the topology using X2top command. when i run energy
minimisation for hexane my potential energy is positve. is this right?. what
i
#ZHAO LINA# wrote:
sudo apt-get install grace
For Linux sure, but I think the Cygwin equivalent is something like cyg-get
(which is probably not standard) and there may or may not be a "grace" package
available.
-Justin
From: gmx-users-boun...@g
sudo apt-get install grace
From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf
of Justin A. Lemkul [jalem...@vt.edu]
Sent: Wednesday, October 06, 2010 11:29 AM
To: Gromacs Users' List
Subject: Re: [gmx-users] Re : installation of
bharat gupta wrote:
thanks for ur help.. I have figured out the problem and not installation
is going on .. I want to know one more thing that xmgrace which is
required for plotting the data .. how can we install it as I have
searched on google .. but I am not able to get the correct link
thanks for ur help.. I have figured out the problem and not installation is
going on .. I want to know one more thing that xmgrace which is required for
plotting the data .. how can we install it as I have searched on google ..
but I am not able to get the correct link
--
Bharat
Ph.D. Candidate
bharat gupta wrote:
build type ?? ... actually I am new to cygwin so I don't know .. what
exactly do I have to do for this one ??
If you installed FFTW, then its configure script must have properly detected
your build type. Check the config.log from that process to see what it used.
It i
build type ?? ... actually I am new to cygwin so I don't know .. what
exactly do I have to do for this one ??
--
Bharat
Ph.D. Candidate
Room No. : 7202A, 2nd Floor
Biomolecular Engineering Laboratory
Division of Chemical Engineering and Polymer Science
Pusan National University
Busan -609735
South
bharat gupta wrote:
Hi all
I am trying installing gromacs 4.5.1 in windows using cygwin .. I have
fftw3 package also without any error.. but the moment I use ./configure
command given in the installation instruction I am getting the following
error :-
se...@selva-pc /fftw-3.2.2/gromacs-4
Hi all
I am trying installing gromacs 4.5.1 in windows using cygwin .. I have fftw3
package also without any error.. but the moment I use ./configure command
given in the installation instruction I am getting the following error :-
se...@selva-pc /fftw-3.2.2/gromacs-4.5.1
$ ./configure
checking
Szilárd wrote:
The beta versions are all outdated, could you please use the latest
source distribution (4.5.1) instead (or git from the
release-4-5-patches branch)?
The result is the same for both the distribution 4.5.1 and git from the
release-4-5-patches. See the output bellow.
Hello,
Can g_densmap produce 2D plots that one axis is the position in box, and
the other is time? In other words, evolution of box content density with
time on either axes of the box?
Regards,
Paymon
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/
On Tue, 5 Oct 2010 20:03:41 +0530 (IST)
ras...@chem.iitb.ac.in wrote:
> Hi All,
>
> I want to install Gromacs 4.5.1 version on a cluster system (high
> performance computing facility) in our institute. I don't have access
> to root and thus, I have to install gromacs in my home directory.
>
> Th
Hi,
We had issues with 4.1 series compilers, but we are not longer sure if there
really
are issues in 4.1.2 and 4.1.3. I would surely avoid 4.1.0 and 4.1.1.
But we found that one or two issues in Gromacs only showed up with 4.1.2 and
4.1.3,
but there were problems in Gromacs, not gcc.
So we are
Hi All,
I want to install Gromacs 4.5.1 version on a cluster system (high
performance computing facility) in our institute. I don't have access to
root and thus, I have to install gromacs in my home directory.
The problem is that, the cluster has CentOS 5.4 as the operating system
and the gcc ver
Hi all,
can someone tell which compressibility should be used for
DMSO at 300K?
Thanks a lot
Sebastian
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before
Hi,
Units are listed in the large table in the topology section of the pdf manual.
(hint: the energy unit everywhere in Gromacs is always kJ/mol and length always
nm)
Berk
> Date: Tue, 5 Oct 2010 15:14:18 +0200
> From: apanczakiew...@gmail.com
> To: gmx-users@gromacs.org
> Subject: [gmx-users
As one of the early chapters in the GROMACS manual points out, GROMACS always
uses energy and distance quantities in particular units. The use of kb depends
on those conventions, so you should look up the relevant formulae for AMBER and
GROMACS and see how the conversion should work (hint: there
I think you don't want to use the gmx2 force field.
It does say "DEPRECATED" without reason.
Berk
Date: Tue, 5 Oct 2010 21:13:46 +0800
From: kecy...@sina.com
To: gmx-users@gromacs.org
Subject: [gmx-users] Use the TIP4P water model in the gmx2 force field
Hello, I want to use the tip4p water m
Hello, I want to use the tip4p water model in the gmx2 force field, but
it seems that it doesn't have the nobond parameter of the OWT4 in the gmx2
force field ,does it need add by myself?
look forward to your respond. --
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.o
Dear All,
Do you know what is the unit of kb in ffamber94bon.itp file? I need to
add some missing parameters for my system however I have them in
kcal/mol and it seems that ffamber94 uses another units. For example:
b0 kb
C O2 10.12500 548940.
Dear gmx-users,
I have the following problem with g_h2order tool (4.0.7 and 4.5.1 versions). It
works perfectly fine when I apply it to a box of SPC/E water, but I have
something really strange if I try to apply it to SW or SWM4-NDP water models
(both are 5 sited models). In my index file I ha
Dear Zhongjin:
1. You have indeed provided more data, but please try to make some
progress on your own. E.g. you tell me the order of selections into
g_dist, but you should try reversing the order.
2. Your figures are difficult to interpret -- I only opened Snap5, but
I don't know what pa
Yeah... A equilibration can be complish within the ps n we have to make
ensure that the there should not be more fluctuation in the potential energy
in other words it should be stabilize.
On 5 October 2010 17:47, Justin A. Lemkul wrote:
>
>
> Anil Mhashal wrote:
>
>> Just plot a graph of the pot
- Original Message -
From: Anil Mhashal
Date: Tuesday, October 5, 2010 23:11
Subject: Re: [gmx-users] Reg:Equilibration
To: Discussion list for GROMACS users
> Just plot a graph of the potential energy with respect to the time and check
> the energy fluctuation, it should be less than
Anil Mhashal wrote:
Just plot a graph of the potential energy with respect to the time and
check the energy fluctuation, it should be less than 10% of the average
potential energy then u can say that ur protein is equilibrated.
I would think that, for most systems, a fluctuation of 10% is
Just plot a graph of the potential energy with respect to the time and check
the energy fluctuation, it should be less than 10% of the average potential
energy then u can say that ur protein is equilibrated.
On 5 October 2010 17:16, vinothkumar mohanakrishnan wrote:
> hi anil
>
> i get the pote
hi anil
i get the potential energy at the end of the mdrun. if i want to calulate
the deviation with what i should compare and calculate the deviation.can you
be more specific.
Regards
Vinoth
On Tue, Oct 5, 2010 at 4:51 PM, Anil Mhashal wrote:
> To check ur equilibration, just look at the pote
You can use the m2p file to tune the size of the datapoint in the x-
and/or y-dimension.
Erik
Carla Jamous skrev 2010-10-05 13.21:
Thank you Justin,
I used an .m2p file to change the properties of my .xpm.
I got an .eps file that I opened with Gimp. In order to visualize this
.eps file, I
Thank you Justin,
I used an .m2p file to change the properties of my .xpm.
I got an .eps file that I opened with Gimp. In order to visualize this .eps
file, I have to put 200% in Gimp.
But my problem is that my graph is too large, so I can't seem to print it
out.
I really to print the .eps file,
To check ur equilibration, just look at the potential energy and find out
the deviation in the energy if the deviation in the energy is within 10%
then ur equilibration is successful...
On 5 October 2010 14:56, vinothkumar mohanakrishnan wrote:
> Hi all
>
> Suppose say i have a box of decane mol
vinothkumar mohanakrishnan wrote:
Hi all
Suppose say i have a box of decane molecules and i want to equilibrate.
say i have all the necessary files to run mdrun. on what basis i say
whether my equilibration is successful r not after the mdrun. what
properties i should measure to know whethe
Hi all
Suppose say i have a box of decane molecules and i want to equilibrate. say
i have all the necessary files to run mdrun. on what basis i say whether my
equilibration is successful r not after the mdrun. what properties i should
measure to know whether my equilibration was successful.
Regar
- Original Message -
From: Trang
Date: Tuesday, October 5, 2010 19:12
Subject: Re: [gmx-users] Water molecule starting at atom x can not be settled
- minimization step
To: Discussion list for GROMACS users
> I checked the initial coordinate file for overlapping atoms, but nothing
>
Hi,
The beta versions are all outdated, could you please use the latest
source distribution (4.5.1) instead (or git from the
release-4-5-patches branch)?
The instructions are here:
http://www.gromacs.org/gpu#Compiling_and_custom_installation_of_GROMACS-GPU
>> The requested platform "CUDA" could n
I think this mail belongs to the user's list, CC-d will continue the
discussion there.
--
Szilárd
2010/10/5 Igor Leontyev :
> Dear gmx-developers,
> My first attempt to start GPU-version of gromacs has no success. The reason
> is that grompp turns off setting of electrostatics overriding them b
I checked the initial coordinate file for overlapping atoms, but nothing
found.
I checked the step*.pdb file written after each crash but did not really
understand those coordinates, for the problematic molecules have MORE THAN 1
positions in those files. what does that mean?
I tried to reproduce
- Original Message -
From: ahmet yıldırım
Date: Tuesday, October 5, 2010 17:41
Subject: Re: [gmx-users] resolved pdm2gmx
To: Discussion list for GROMACS users
> Dear Dr. Abraham,
>
> I have been trying to install gromacs-4.5.1 for a week but I could not it. I
> review the installati
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