One thought from justins post in the past,
Look at the .trj in VMD with the unit cell box and see if something sticks out
at the end (ie comes up in the bootmn of the box from the top). It then does
what you show, however it may not be that. If it is, you'll have to increase
your box
I think the reality of biological systems is represented as such accurately.
Everyone always strives in biochemistry for a precise number, ie binding
affinity = 489.489 exactly. In real systems there are to many variables
(solvent, ions, particular position of moving amino acids at point A or
Dear All,
I have no clue what specifically you are trying, but I feal bad for all the
physicist and quantum chemist whom have provided the software and continued to
develop it.
Scanning in my free time, it seems a large amount of confusion on what people
are trying to do stems from
Dear Rankinib,
You can do it with a 5 line bash script as well, cat everything times x,y,z and
just cut and past them into a spread sheet, and save it with tabs or spaces.
Stephan Watkins
Original-Nachricht
Datum: Tue, 05 Jun 2012 09:05:09 -0400
Von: Justin A. Lemkul
Original-Nachricht
Datum: Tue, 05 Jun 2012 09:05:09 -0400
Von: Justin A. Lemkul jalem...@vt.edu
An: Discussion list for GROMACS users gmx-users@gromacs.org
Betreff: Re: [gmx-users] Trajectories
On 6/5/12 9:02 AM, rankinb wrote:
I am interested in pulling out the
Did you play with the time step? Just currious, but I woundered what happened
with 0.0008, 0.0005, 0.0002. I found if I had a good behaving protein, as soon
as I added a small (non-protein) molecule which rotated wildly while attached
to the protein, it would crash unless I reduced the time
Dear Vidhyh Sankar,
IndexError: list index out of range
When a program reads in lists or arrays, in the software there is usually a set
size, for lines or number of atoms, etc... If the array or list is longer than
the set value you get this error. Also, if a counter is off, ie stops one
I would wait for others to answere but,
a) you might try orienting your circular DNA in a visual program first and then
use say just pull nny or something just as it makes it easier to see output and
makes restraints nicer in output,
b) the pull k1 might be larger for an effect on
Thanks,
You should make sure your WHAM is good, or your DNA isnt moving out of the box,
as I watched a series of questions reply here before which showed that
irrelevant WHAM data might be produced when the molecule leaves the box edges,
ie you would be missing a piece or have a negative where
Dear Dmytro Kovalskyy,
The ARG CZ is at the end (tip of the ARG), what does the distances look like
over time? A floppy long amino acid? And your actual distance calculation?
Is it from a graphics/pdb file, or how is it measured?
Stephan
Original-Nachricht
Datum: Tue, 26
Dear Steven,
Where are you working?
From my experience the g_energy -fee only gives a free enrgy estimate for the
whole system, so one has to pull out all the energy terms based on your index
file of interest and sum them in a spread sheet. if the -fee can do the
energy estimates for a
-users@gromacs.org
Betreff: Re: [gmx-users] Free energy between residues
On 6/28/12 6:51 AM, Steven Neumann wrote:
On Thu, Jun 28, 2012 at 11:42 AM, Justin A. Lemkul jalem...@vt.edu
wrote:
On 6/28/12 6:33 AM, Steven Neumann wrote:
On Thu, Jun 28, 2012 at 11:20 AM, lloyd riggs
Dear Neeru Sharma,
I know off hand from years of work with Mg-GTP sites, they are realativly
rigid/staritforward. If the bonds arn't present with occupied GTP, or Mg at
the beggining, you should equilabrate your starting structures more. Unless
your looking at the GTP binding to Mg in which
Well,
Ill give that a shot from memory of a discussion some time ago, which you could
probably track down on the e-mails of past search engine. I think it has to do
with force field types, either they list the sigma values, or direct 6, 12 or
derived LJ parameters, so it would be related to
Dear All,
So I am using some scripts to parse through 100s of files using bash and awk.
In any case, I run into a problem as follows; I have Ubuntu at home on my PC
and I have a laptop at work with Ubuntu, same versions libraries, everything.
When I run the scripts at home they work fine,
Switzerland)
Original-Nachricht
Datum: Thu, 5 Jul 2012 22:25:06 +0200
Von: Elton Carvalho elto...@if.usp.br
An: Discussion list for GROMACS users gmx-users@gromacs.org
Betreff: Re: [gmx-users] Re:Shell scripts
On Thu, Jul 5, 2012 at 6:03 PM, lloyd riggs lloyd.ri...@gmx.ch wrote
, lloyd riggs wrote:
Dear All,
Thank you,
I finally got this to work on the other PC after four hours...
i=1
while [ $i -le 1322 ]
do
g_energy -f traj_x.edr -o ${i}.xvg EOF
${i}
EOF
i=$(($i+1))
done
Still can not figure out the difference, or why one works on one PC
Watkins
University of Bern-Inselspital
Original-Nachricht
Datum: Fri, 06 Jul 2012 09:11:22 +1000
Von: Mark Abraham mark.abra...@anu.edu.au
An: Discussion list for GROMACS users gmx-users@gromacs.org
Betreff: Re: [gmx-users] Re:Shell scripts
On 6/07/2012 7:25 AM, lloyd riggs wrote
and then parse the columns out of the .xvg file.
Cheers,
Tsjerk
On Fri, Jul 6, 2012 at 1:11 AM, Mark Abraham mark.abra...@anu.edu.au
wrote:
On 6/07/2012 7:25 AM, lloyd riggs wrote:
Dear All,
Thank you,
I finally got this to work on the other PC after four hours...
i=1
your pull force looks insanly high especially if your pulling a small piece of
residue? But for a whole protein of averidge 40 KDa, or 350 amino acids its
around 2000 to 3000 from liturature (only about 6 that I could find anyways).
I might thus be wrong, but wounder if you have a pull rate
A variabvle thermostat that increases from 180 K to 300 K over cycles of
100-1
Original-Nachricht
Datum: Tue, 17 Jul 2012 20:40:12 +0800
Von: Wu Chaofu xiaowu...@gmail.com
An: gmx-users@gromacs.org
Betreff: [gmx-users] How to speed up equilibrating the density of bulk
True, I found the lower bin numbers makes the error change (increase),
especially at ends of the run, howevere the mean values were the same. I also
checked with g_sham as comparision, and found again the means the same but
differences in error (max and min values if I include all data). So
Dear (sorry cant read chinese),
You can find some OPLS or 53a6 Parameters on the web by doing extensive
searches, mostly they are free, but hosted on varied individual lab web sites.
That, or it may be easier to define some sets of bonds (angles, dihedrials,
lengths charges, etc...from
Yeah,
I think based on some initial MDs I did with larger protein-protein interfaces
there is an oscilatory aspect to most, like large bodies tied together with
longerchains, where water moves in and out especially around edges, but
woundered if it was protein specific or a global phenomina.
Dear All,
Ill give this a shot. I guess it depends on your entire system (ie protein
+DNA or just DNA) and what it is you waant to observe.
and example of why answereing becomes complex. if A) I want to just look at
say the total delta G,S or H. I would only need to EQ several starting
Dear Dr.
I might be wrong, but I think you can use g_rms with two seperate trj files,
and it takes the rms from the starting structure of the first one. In which
case you would have to decide which is the reference, and then just do it three
times.
Theres also auxiliarry software which has
You can also just quickly visualize it in VMD and see if anything your looking
at is not centred properly. If it isnt you just have to centre it.
Stephan
Original-Nachricht
Datum: Mon, 24 Sep 2012 04:32:33 -0700
Von: naga sundar naga25sun...@gmail.com
An: Discussion list
Dear Dudu Tong
Theres a paper on using limited x y z restraints but I have forgotten it. In
any case theres a way to generate 1 2 or 3D positional restraints with just the
grompp , and you can cut and past. The output posre in the help command will
give you a file, and theres a selection for
Dear All,
Does anyone have a small script for converting Gromacs (GROMOS type) ff to
CHARMM format, or an amino acid top file in CHARMM format for such. I have
seen some scripts, but they work only with different topology types. Thought I
would ask, otherwise I sit here for three days
Dear All,
I spent two days converting a .top file from gromos53a6 to one readable by
VMD/NAMD.
Now I am about to begin the ffbonded/nonbonded to a readable format for the
same and would like to know beforehand if anyone has already done this so I can
just use the library? Most are
you have to play with the ratio usually of domain decompositions Vs. Grid size,
I had that error some time ago though, if you look at the generated .mdp from
the one you show (-o xxx.mdp), then look at the set FFT or xyz grid spacing and
play with it. It dosent like odd numbers or non-whole
Could you explain to me how this would effect your domain decomposition?
Original-Nachricht
Datum: Fri, 05 Oct 2012 23:05:33 -0400
Von: Justin Lemkul jalem...@vt.edu
An: Discussion list for GROMACS users gmx-users@gromacs.org
Betreff: Re: [gmx-users] Re: Error There is no
Quick question,
I went and calculated the Ka/Kd with the g_hbond -- -g_analyze and just
wondered, if all my simulations are pulled, does it in the end make any sense,
or is there ways to compensate for this. I assume the h_bond life would be
meaningless, as under a normal situation, 2
jalem...@vt.edu
An: Discussion list for GROMACS users gmx-users@gromacs.org
Betreff: Re: [gmx-users] Re:Ka/Kd
On 11/5/12 9:59 AM, lloyd riggs wrote:
Quick question,
I went and calculated the Ka/Kd with the g_hbond -- -g_analyze and just
wondered, if all my simulations are pulled, does
it into a
histogram, but not in 2D grids. This I am sure is somewhere (a script or
software), but have no clue whom/where to ask.
Sincerely,
Stephan Watkins
Original-Nachricht
Datum: Tue, 06 Nov 2012 13:18:48 +0100
Von: lloyd riggs lloyd.ri...@gmx.ch
An: Discussion list for GROMACS
, 08 Nov 2012 11:46:32 +0100
Von: lloyd riggs lloyd.ri...@gmx.ch
An: Discussion list for GROMACS users gmx-users@gromacs.org
Betreff: Re: [gmx-users] Re:Ka/Kd
Dear All,
So I went over the below Ka/Kd...Seems doesnt fit for anything, the DelG I
found doesnt change for components, and just fit
: Justin Lemkul jalem...@vt.edu
An: Discussion list for GROMACS users gmx-users@gromacs.org
Betreff: Re: [gmx-users] Re:Ka/Kd
On 11/9/12 1:02 PM, lloyd riggs wrote:
Dear All,
Reguarding a question I asked below. Does anyone know what the
formulei, etc...are for g_sham taking in 2 columns
Dear All,
I remember a post in the last couple months but cant find it. In any case, by
searching through van der groot et alls. papers, the -xmin, -xmax, -dim and
-ngrid options third point, example: -xmin 3 3 3 -xmax 3 3 3 is for reading in
the output 3d (projections on V1, V2, V3 or first
Dear Stephane Abel,
Theres a link I on the gromacs web site to ATB, or you can google it. If it is
not in Gromacs format you can just write a couple 6 liner scripts to re-format
it by parsing into the gromacs format,
Stephan Watkins
Original-Nachricht
Datum: Wed, 13 Feb
Dear All,
I read a paper by Van der Groot and realized some tool regarding simple
paersons r values, or correlation co-efficient by different names would be a
great analytical asset for macromolecular biology. Looking over the code,
g:sham seems to have begun implicating such things but it
Dear All,
I had a quick 2 questions, 1) does anyone know (as a long whiles back I looked
over CUDA code not the CUDA Gromacs) if there is more than just obtaining the
specs for an ATI GPU within Gromacs (explanation:For CUDA alone it appeared all
you needed was an elaborate definition in the
I can imagine why you would go past the first few, but does it print the zero's
or just negate them from the equation, as there 0?
Stephan
Original-Nachricht
Datum: Sun, 10 Mar 2013 14:34:52 -0500
Von: Hyuntae Na h...@hotmail.com
An: gmx-users@gromacs.org
I had problems having not used gromacs in years a couple years ago. Try
running it through with the output as a pdb from pdb2gmx, cut off all headers,
and you can then just compare the two files in gedit emacs or word and see
differences. That might help. I routinely just keep everything in
If you back the origional papers alot of the conversions can be found. I dont know the papers off the top of my head,
so you should just ask your PI, collegues or the board. They are a pain, one paper will have 2 and be missing one definition you want, etc...
Stephan Watkins
Sorry, meant to post this on the bb.
Gesendet:Dienstag, 02. April 2013 um 11:50 Uhr
Von:lloyd riggs lloyd.ri...@gmx.ch
An:vvcha...@gmail.com
Betreff:Aw: Re: [gmx-users] Re: density profile
How would you set up a gas/gas interface, say modeled after a large gas planet or upper
So last week I read a post about liquid/gas layers in a box and it has me thinking (ie I cant shut it off). As it would sim wise (and I asume there is already something somewhere that does it) for a large body of fileds such as astrophysics, liquid dynamics, gas/gas interface I woundered if
Funny, I thought of a large Ribosome system. You can in vacuo already with an i7 or AMD equivalent EM a 600 amino acid system with a 12-15A solvent shell in an hour to three using the CPU alone. Thats from test of Gromacs and a non-eqd system. so about 1 work day to get through NPT. Thus, I doubt
Sorry, I tried posting this once but it was spammed or something. In any case, are there any suggestions for mostly MD based journals (publication wise as content), a favorites or something if somone wanted to turn it into that,
Stephan Watkins
--
gmx-users mailing list
You can also embed your protein-bound small molecule, protein unbound small molecule a good distance away in solvent of choice, then eq it at the proper temp/pressure. Then take several samples along an equed space, let them just run unrestrained, and you can calculate the energy change
Dear All,
Doing a water/temp energy minimization just for a figure with a large molecule that has several connected parts, I ran into a bizzar question.
So I found its possible by accident to define improper dihedrails forwards and backwards without gromacs complaining, such as atom 1 2 3 4
I appologise, I meant defined at the same time without complaining, not just either direction.
Gesendet:Montag, 29. April 2013 um 22:23 Uhr
Von:lloyd riggs lloyd.ri...@gmx.ch
An:S. Watkins gmx-users@gromacs.org
Betreff:Aw: [gmx-users] Re: how is the pulling force measured
Dear All,
Doing a
You probably have to do a hand job. Look at the .itp/top files and then the force field parmeters, theres not many atoms, so it would take only a couple hours.
Stephan Watkins
Gesendet:Freitag, 03. Mai 2013 um 12:36 Uhr
Von:micheal j twin michealj.t...@gmail.com
An:gmx-users@gromacs.org
That works, wish you could choose more force fields in the anti-chamber as a plugin. Theres some auxillary scripts also for martini and gromos force fields to .psf but they were mostly for the ff19, so partial atom. They antichamber is probably easier, and if you get something in ff19 (or better
You should make a good index file and read the options in g_covar and g_anaeig in the manual and just the command line help. I found the new builds of Gromacs allows indexing after a long trajectory, but did not know this before hand. I had tried it with older versions, a couple years back, but it
I was under the impression a vacumn, or even gas/liquid interface becomes uniform molecule wise in such simulations due to scale. Thus, the applied pressure and other corrections necessary to set up the interface on a small scale, such as caclulated force at an imaginary interface for given
Or just do it by hand and replace the lines in the .top with each protein chains .itp file.
Stephan
Gesendet:Freitag, 17. Mai 2013 um 16:17 Uhr
Von:Mark Abraham mark.j.abra...@gmail.com
An:Discussion list for GROMACS users gmx-users@gromacs.org
Betreff:Re: [gmx-users] Expanding a .top file
Dear All,
Hope this is not tooo stupid a question. I recenttly reduced my file sizes by
increasing the time between writing. However, if I do an Umbrella run I get
the following to my logfile output, which makes my log file in the end larger
than my trajectory;
Dispersion correction
Message: 3
Date: Tue, 06 Dec 2011 18:58:50 +0100
From: Javier Cerezo j...@um.es
Subject: Re: [gmx-users] RE: logfile size
To: Discussion list for GROMACS users gmx-users@gromacs.org
Message-ID: 4ede57da.80...@um.es
Content-Type: text/plain; charset=UTF-8; format=flowed
Not the main problem, but
mark.abra...@anu.edu.au
Subject: Re: [gmx-users] RE: logfile size
To: Discussion list for GROMACS users gmx-users@gromacs.org
Message-ID: 4edf2ea5.5020...@anu.edu.au
Content-Type: text/plain; charset=UTF-8; format=flowed
On 7/12/2011 7:41 PM, lloyd riggs wrote:
Message: 3
Date: Tue, 06 Dec
Message: 6
Date: Wed, 7 Dec 2011 11:38:58 -0500
From: Jose Borreguero borregu...@gmail.com
Subject: Re: [gmx-users] Newbie: How to modify the topology file after
addingions?
To: jalem...@vt.edu, Discussion list for GROMACS users
gmx-users@gromacs.org
Message-ID:
So,
This is slightly aside from the installation of the openMM (cuda), but is CUDA
related.
Does anyone know the state of the CUDA to OpenCL porting the AMD (CUDA teams
said they were going to do this) and then further all CUDA work as OpenCL, as
no one has mentioned anything on this since
Dear All,
Does anyone know the equation used to calculate the dH and dH/dl in free energy
calculations via gromacs (other than looking at code that looks like
3*pi/(pi-.). That or the actual reference for it. I found a couple
references for the gromacs use of the free energy but none
Dear Alexey Zeifman,
From my experience it is just the nodes have to break down into some sort of
even multiple by dividing the domain decomposition size or vise versi. I
think somone elses answere was just to try it with a couple sizes for the
decomposition, as multiples of the number of
Hello,
I was following your argument but then doesnt pull_dim=Y Y Y mean it pulls in
all directions at once? I use pull_dim=N N Y , or just 1 pull direction and it
works. I might be wrong, but would be interesting if you got it to work like
that for a small molecule.
Stephan Watkins
A quick answer to this is, there's two sets of tables based on equations I know
of off hand for LJ's and calculating the other such LJ parameters from these.
In one it uses the epsilon/ sigma and the other a table of either the 9-6 or
the 6-12. The later two you can look up either on the
Dear Rama,
Since the latest version, I have to use -noappend and then just concantenate
them when they are finished. I gave up as no mater how many paths to files,
listening to the error messages, I supplied to the mdrun it still complained.
Dont know if this is a personalized bug or more
Dear All,
I went through and did some initial things with WHAM, and found the following.
if I use pullf the calculated free energy change, and change over time makes a
nice perfect hemi parabolic graph that fits all the data in our and other labs.
if I use the pullx I get a graph of a zero
Dear All,
Is there a way to either supress the interactive portion of g_energy and print
out everything listed, or pass it to something more automated? MY problem, I
spent an hour or three trying to just write an automated four line shell or
python script to extract all the terms listed
Dear All,
I was going to use g_enemat to make my life easier than splitting things up
into individual files for a break down of multiple components in a trajectory
(multiple protein domains and atooms, etc...I indexed before the run rather
complex or long depending on your point of view).
-Does anyone off hand know the code (or line numbers ) for the actual energy
calculations in either g_energy or g_enemat?
Basically, it says it does not implement this yes (the error) or just does not
print something out. Basically, I wanted to look at the code but didnt want to
sit there
You guys should hit up UniZurich, the have a series of 1024 CPUs in combination
with several hundred GPU's in a cluster system. You could then test out some
things, including scalability etc...
Sincerely,
Stephan Lloyd Watkins
Original-Nachricht
Datum: Thu, 15 Mar 2012
From liturature it ranges around 1K for unravling proteins, and
protein-protein dissociations range around 2-3k (kj/mol that is). For small
molecules I have no clue. Id like to know if somone finds out ranges for any
of these though
Stephan Watkins
Original-Nachricht
Quick question to anyone,
can you extract energies and forces with g_traj and g_energy and feed them to
WHAM for molecule by molecule or atom by atom PMF determination. If so, how do
I get WHAM to read the extracted enrgies as they are written out. I did read
something about a .pdo file if
Another WHAM question,
If I use the pullx (position) Vs the pullf(force) i get differ4ent graphs but
the same overall delG (or PMF).
in the positional one it is a juttery line then at the break point (when the
protein finally lets go enough) it jumps up to almost its maximum. When I use
the
From my limited experience,
...Also, VMD makes this easier. I learned the hard way to center on a molecule
when making the initial box in editconf. Otherwise varied combinations of the
-mol, -pbc , -nojump -center options usually work, but never consitent at least
for me. Still, if its 4
Hello all,
Does anyone know where to look to do a slice of my unit cell along sections
(energies, forces etc...) or to just give a list of all atoms in the slice.
Something like an h,k,l or x,y,z slice through a section.
Stephan Watkins
--
NEU: FreePhone 3-fach-Flat mit kostenlosem
Merci,
Thats what I was afraid off. Small script might be able to do it with x1Nx2,
xyz coordinates and just ripping atoms from the index with those criteria?
Thanks,
Stephan
Original-Nachricht
Datum: Sat, 31 Mar 2012 13:35:06 -0400
Von: Dr. Vitaly V. Chaban
Dear All,
Is there a way to extract the pull force (and not the total force or energy)
for a specified group (indexed) or center of mass, rather than just the total
pullf over a run? I wanted to break up the pullf into varied sub
contributions, however as it is applied to the center of mass
Dear all,
Im using wham on series of runs and have run into the following proble.
The command line
g_wham_d -if pullf.dat -it tpr.dat -temp 300 -o whamf.xvg -hist outf.hist
-unit kCal
will work in one run, but not the next one as I go through I found a couple
that give the error
Fatal
If I just make a sub directory and move every fill (.tpr, pullf.xvg, etc... it
works, so must not be gromacs realted I appologise)
Stephan Watkins
Original-Nachricht
Datum: Mon, 16 Apr 2012 15:35:17 +0200
Von: lloyd riggs lloyd.ri...@gmx.ch
An: Discussion list for GROMACS
Original-Nachricht
Datum: Tue, 17 Apr 2012 07:49:06 -0400
Von: Justin A. Lemkul jalem...@vt.edu
An: lloyd riggs lloyd.ri...@gmx.ch, Discussion list for GROMACS users
gmx-users@gromacs.org
Betreff: Re: Questions
lloyd riggs wrote:
Dear Justin,
So I get
I dont know. All I know is if I have it print one of the other deminsions, I
get the other curves mentioned.
When accusing the code of doing something wrong, I don't know isn't a very
good justification ;) The contents of pullx.xvg are the COM coordinates of the
reference group on the
I solved the problem on a Linux machine, with about all the text editors, I was
stuck for days on a PC, which even the script editors couldn't spot a
difference in files. all i used was ms txteditor to cut and paste.
I dont know. All I know is if I have it print one of the other deminsions,
Original-Nachricht
Datum: Wed, 18 Apr 2012 03:13:09 +1000
Von: Mark Abraham mark.abra...@anu.edu.au
An: Discussion list for GROMACS users gmx-users@gromacs.org
Betreff: Re: [gmx-users] Re: Questions
On 18/04/2012 12:10 AM, lloyd riggs wrote:
Included below (although Im
Original-Nachricht
Datum: Wed, 18 Apr 2012 08:18:27 -0400
Von: Justin A. Lemkul jalem...@vt.edu
An: Discussion list for GROMACS users gmx-users@gromacs.org
Betreff: Re: [gmx-users] Re: Questions WHAM
lloyd riggs wrote:
Original-Nachricht
Datum
When accusing the code of doing something wrong, I don't know isn't a very
good justification ;) The contents of pullx.xvg are the COM Acoordinates of
the reference group on the axis or axes along which the restraint was
applied, followed by the distance between the reference and pulled group,
Original-Nachricht
Datum: Wed, 18 Apr 2012 10:49:00 -0400
Von: Justin A. Lemkul jalem...@vt.edu
An: Discussion list for GROMACS users gmx-users@gromacs.org
Betreff: Re: [gmx-users] Re:WHAM question
lloyd riggs wrote:
When accusing the code of doing something wrong
Dear All,
Another error here with Gromacs
The append from continuing runs does not work. It complains that several files
are missing. When I try to give it the files in the working DIR or direct
paths, it still gives the same complaint.
I woundered if such a thing could also be a
: : Extending run append
On 20/04/2012 1:45 AM, lloyd riggs wrote:
Dear All,
Another error here with Gromacs
The append from continuing runs does not work. It complains that
several files are missing. When I try to give it the files in the working
DIR or
direct paths, it still gives
Dear All,
A question about data analysis. When Generating raw .xvg files of energies I
have found say 3-4 points out of 2000 (per run 11 total) is erroneous.
something like
20.43534
21.7657
22.212
-34.88
23.680
Something like that.
Now is there a routine in handling these? I
list for GROMACS users gmx-users@gromacs.org
Betreff: Re: [gmx-users] Re: Data Analysis
lloyd riggs wrote:
Dear All,
A question about data analysis. When Generating raw .xvg files of
energies I
have found say 3-4 points out of 2000 (per run 11 total) is erroneous.
something
This sounds to me like a periodicity issue. Were these runs conducted
with
pull_geometry = distance? If so, were the COM distances always less
than half
of the box vector along the restrained dimension(s)? Are you running with
NPT?
If the answer to any or all of these is yes,
Dear Folks,
I am new to posting here. In any case, I wanted to set initial trajectories
for two large macromolecules. Basically I am using gromacs for several things,
on would be simple energy calculations. For this I wanted to take to proteins,
or protein and larger ligands and set an
Dear All,
I recentlly started using Gromacs again. I was just woundering if anyone had
some .rtp libraries available to add on to the software, or for VMD.
I am particularly interested in lipid .rtp libraries hopefully for something
that has all-atom force fields, as I personally believe
Dear All,
This is a follow up on a post last week. I was trying to find pre-made .rtp
libraries to add on for membrane lipids (other than DOPC, etc...). My critique
was the complexity of membrane lipids means for most real processes we need to
have a synthetic membrane (s) that reflect real
Thank you for the advice Dr. Warren,
I often find the same problem with charges and parameters, and have pulled some
from the web in some instances. I have an old CRC book with tables when in
doubt,
But I wounder if anyone is interested in just making a tabulation, or wiki site
to deposite
I also found this usefull, but have a question on what one would consider the
standard. from eyeballing mostly the charges I get for .itp files from PRODRG
server fall into mullikin charges, but usually 3-4 dont or have no charge, but
I woundered if the ESP or AIM charges would be beter. From
Message: 1
Date: Sun, 11 Sep 2011 13:01:28 +0200
From: gal.fra...@live.biu.ac.il
Subject: [gmx-users] g_lie
To: gmx-users@gromacs.org
Message-ID: blu160-w601d2ab913084c46676afee9...@phx.gbl
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Greetings to all!
I have a question for the g_lie
Message: 2
Date: Mon, 12 Sep 2011 18:38:57 +0300
From: ? ?? glapid...@gmail.com
Subject: [gmx-users] g_lie (again..)
To: gmx-users@gromacs.org
Message-ID:
CAB7OWN9sbMP+4XSaYF-ZNLZTy1Ve2e8cJ4pEb-RPdxc9P=y...@mail.gmail.com
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Hi all,
Could
Dear All,
I woundered if anyone has scripts/tools or suggestions for analyzing energy
changes from extracted run data. Mostly I end up with 20 spread sheet columns
for a large system with 2x2 domain proteins, a peptide of 10-20 amino acids and
soome small molecules. I've been playing with
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