all-bonds and none work, so I assume, as alternating between these settings speeds up the EM. However, I always see the protein move around in the box after centering, so just re-center after reaching pressure and temp stability before the extended pre-run equilibration with set restraints (which
I dont know how well v-rescale works with pulling. It could be after removing some restraints it still had not reached a good equilibrium (ie let it run a while/nanosecound or 5, before pulling it), or maybe generating velocities on start causes more caos than the proteins or system can handle,
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gmx-developers...
Sorry I was trying to post this to the Feature suggestion/request site on
I ran into this, you basically should determine your time frame, and install 4.5.4 if its a problem local (only 1-2 hours), to finish the work, otherwise you need to start from scratch. But I did this with older versions, so do not know about higher versions (such as if theprogrammerseliminated
This is my own experience, someone may have better suggestions. First, you can look on the internet for .py .c++ or java matix manupulation tools/small programs run in bash shells. These allow the output from the g:sham or other (2d or 3d) to be turned into mtricies. These can then be fed into
There isnt one it depends on your experiment, and what factors you take into account such as resources, time available or what you wish to observe. All atom is more realistic, but if time retraints or computer resources are limiting, you may wish a partial atom or hybrid atom system. In addition,
it more accuratly represents reality (my opinion), but is not feasable with high energy affinities such as protein-protein or DNA-protein interactions with short (under u or m seconds) and is used as such (I assume) in many things, or you cant pull them apart. A comparison however, would probably
will get the PMF profile for my
ligand binding or ligand and two ions binding?
It would be the ligand and two ions unless the ions also at some point discossiate from the ligand once in solvent. Could add positional restraint for them, but dont know how that effects the calculation?
in this group included.
On Wed, Jul 31, 2013 at 11:01 AM, lloyd riggs lloyd.ri...@gmx.ch wrote:
will get the PMF profile for my
ligand binding or ligand and two ions binding?
It would be the ligand and two ions unless the ions also at some point
discossiate from the ligand once in solvent. Could add
Your pulling it in all 3 directions at one time. Also, you should check the COM you want to be pulling from, but I do not know your experimental design. I would say look at Justins tutorial and example .mdp files.
Stephan Watkins
Gesendet:Montag, 29. Juli 2013 um 20:42 Uhr
Von:kim2811
Just read your other responses, didnt know it would overide with vector set, but if it doesnt work try the _dim
Stephan
Gesendet:Montag, 29. Juli 2013 um 20:42 Uhr
Von:kim2811 kmani...@iastate.edu
An:gmx-users@gromacs.org
Betreff:[gmx-users] constant force pulling
Hi,
I am trying to
Play with the domain decomposition, lincs itr/order, -ntomp and -ntmpi, etc... I was able to get a 4 day simulation which often gave that error to speed up to 12 hours on 24 CPU/3 nodes/144 cores but it took 2 days of submitting, checking speed, and killing jobs to try another grid routine. My
Dear Amin,
I did such things in the past, and had similar issues. First of, somone may have beter suggestions. The coupling time will bring it down a bit in the .mdp file (0.2 Vs 2 picoseconds. However, I have found that you will still see large fluctuations around a mean once equilibrated
You still might be able to with a static group, such that you pick 5 random ones, then the rest as a block (all lipids). Your only problem may be if you define say 5 of 100 independent, then you would have to sum A-B plus A-all others, so more complicated, but its just a suggestion.
Stephan
I thought about this reguaring solvation energy. If you use a good water model, and make a secoundary index for solvent (ie Solvent2 atoms x-xn), the normal Gromacs energy extraction would allow you to just extract all energy between protein and solvent2. I assume you could do some extreemly
You can also look them up (angles bond distances) in the CRC handbook or online and just put the angle(distances direct into the .itp file for your ligand, as well as impropers...it works for all the force fields, unless you use hybrids (CH3=1 representation)...it comes out wierd as the different
Whats the energy of each waters hydrogen bonding strength respective of each one...as they vary by a couple kcal/mol according to the new IUPAC standard deffinition of hydrogen bonds (2011)? And the energy of the internal structural hydrogen bonds that were disrupted? Assuming no acidic
There vectors. Theres some good older papers explaining the whole thing from Van Gunstern, Berendsen, and some other good ones from de Groot that explain them well and includes combining them with other data analysis types, but I dont remeber the actual publications. A few are in the mid 1990s,
From running a bunch of these your pullf.xvg should look like a curve and taper off at the end (go down) or you didnt reach the maximum...with the force I had to play around and started with published work for similar proteins, but had to increase the force from 1000 (published) to 2000, so a
I had this some time ago and cant remember everything, other than its a format problem. My end solution that worked was to simply cut and past in columns the entire pullf into one .xvg, say in gnumeric retaining an origional header, than read it into xmgrace, and then just write it out from
I should add, one is an automated submit system, the others manual quing where you set parmeters (the ones that work), and the system is large around 90 120 90 angstrom box with around 170-180,000 atoms. Still, the que output from the manual submission simply sets -nt 6, and the rest of the input
I have a bizzar problem. I did 21 simulation for 4 ns each. These were equd for 4ns prior, then taken from an assembly run over 4ns so between 300 pico and 4ns additional each. A reviewer wants a couple extnded ends added,say like 4 extra ns, which I can only do 1-4 at most due to time limits
I appologise with the below, I got entropy and enthalpy confused for a mement. Funny.
Stephan
Gesendet:Dienstag, 11. Juni 2013 um 23:54 Uhr
Von:lloyd riggs lloyd.ri...@gmx.ch
An:Discussion list for GROMACS users gmx-users@gromacs.org
Betreff:Aw: [gmx-users] Enthalpy Confusion
If you
If you only want the total for the system or a delta for an entire run, indexed group there of, covarience (covar/aneig) does a good job. I found neither actually fit, but the covarience does, or if you do it by hand using only LJ parmeters for the indexed sets, however I was using proteins, so
Dear All or anyone,
A stupid question. Is there an script anyone knows of to convert a 53a6ff from .top redirects to the gromacs/top directory to something like a ligand .itp? This is usefull at the moment. Example:
[bond]
6 7 2 gb_5
to
[bonds]
; ai aj fu c0, c1, ...
6 7 2
Thanks, thats exact what I was looking for.
Stephan
Gesendet:Dienstag, 04. Juni 2013 um 22:28 Uhr
Von:Justin Lemkul jalem...@vt.edu
An:Discussion list for GROMACS users gmx-users@gromacs.org
Betreff:Re: [gmx-users] GPU problem
On 6/4/13 3:52 PM, lloyd riggs wrote:
Dear All or anyone
Off subject, I thought a good pop up for the end of file processing etc...would be
___
Government spies are everywhere, theyre in your home, theyre in your hair
theyre down the street and hiding in walls
Theyre waiting to take you away Fabulous flying
Dear Jiom,
Look at justines tutorial, theres example pull .mdp.
Stephan Watkins
Gesendet:Donnerstag, 30. Mai 2013 um 14:44 Uhr
Von:gromacs query gromacsqu...@gmail.com
An:Discussion list for GROMACS users gmx-users@gromacs.org
Betreff:[gmx-users] umbrella sampling for two polymer
Ive had 2 problems like this. 1 was solved by doing all eq to a good degree first in one thread, then the domain decomposition worked in 8 or 16...the secound I had to break down the charge groups in the .itp (cg) into smaller charge groups and it worked,
there might be better suggestions though.
frequency Intel CPUs (6+ cores 2.2
GHz), otherwise you may not see as much benefit as you would expect
based on the insane price tag (especially if you compare to an i7
3939K or its IVB successor).
Cheers,
--
Szilrd
On Sat, May 25, 2013 at 1:02 PM, lloyd riggs lloyd.ri...@gmx.ch wrote:
More RAM
station ?
James
2013/5/25 lloyd riggs lloyd.ri...@gmx.ch
Theres also these, but 1 chip runs 6K US, they can get performance up to
2.3 teraflops per chip though double percission...but have no clue about
integration with GPUs...Intell also sells their chips on PCIe cards...but
get only about 350
each with 2
quad-core xeon processors I get 30-40ns/day.
I think that to achieve reasonable performance the system has to be
balanced between CPUs and GPUs probably getting 2 high end GPUs and a
top end xeon E5 or core i7 would be a good choice.
Richard
From: lloyd riggs lloyd.ri
between CPUs and GPUs probably getting 2 high end GPUs and a
top end xeon E5 or core i7 would be a good choice.
Richard
From: lloyd riggs lloyd.ri...@gmx.chmailto:lloyd.ri...@gmx.ch
Reply-To: Discussion users gmx-users@gromacs.orgmailto:
gmx-users@gromacs.org
Date: Saturday, 25 May 2013 12:02
Dear Dr. Starlight,
Dont know the answere to all, but funny I was looking at performance on varied others web sites. I use a core i7 970, but it seems their newest chip is almost the same as the i7 in performance (thier newer chips dont scale past 12 cores for some internal chip based design,
The hydrogen bonding energy would have/is usefull to myself. An example, I use the .ndx as you did below for protein-protein interactions only. I get around 25 and 28 for two different states. The interesting part is the 25 is about 7 times the delG, however the hydrogen bonds move much less,
Theres also these, but 1 chip runs 6K US, they can get performance up to 2.3 teraflops per chip though double percission...but have no clue about integration with GPUs...Intell also sells their chips on PCIe cards...but get only about 350 Gflops, and run 1K US.
Dear Andrish Reddy,
Dont know if it works but I have for small molecules just put all the parmeters within the .top file right below the defaults, instead of user defined tables, and removed the forcefieldX/SPC.itp or equivalent section so it doesnt loop, but dont know if it works in your
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
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
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
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 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
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
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
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
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
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
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
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
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
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
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
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 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 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
: 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
, 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
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
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
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
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
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
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
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 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
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 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
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
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 (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
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
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
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
, 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
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
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 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
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 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
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
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
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
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 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
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
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
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
: : 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,
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
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
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