Hello all,
I've been having a nightmare of a time trying to get order parameters for my
lipids. All pre-3.3 files I have can be processed quite happily with a version
of g_order from 3.2.1, but I can't seem to get 4.0 (or 3.3.1) to produce the
basic order.xvg. I've tried specifying all carbons
The topologies should not be identical, surely? Check out the section on
improper dihedrals in the manual, it's possible to specify an improper to keep
enantiomers in their intended handedness.
- Original Message
From: Anthony Costa <[EMAIL PROTECTED]>
To: gmx-users@gromacs.org
Sent
Please search the message archives for the thread entitled "Leaflet of Bilayer"
that discussed this precise task just a couple of weeks ago.
- Original Message
From: "[EMAIL PROTECTED]" <[EMAIL PROTECTED]>
To: "gmx-users@gromacs.org"
Sent: Saturday, October 4, 2008 11:00:22 PM
Subject
(Yes, what Chris Neale said). I had to do something similar myself, to make a
256-lipid square box from a 128 lipid box. I used genbox to make a new, larger
square box using my original lipid patch as the input file, and then tinkered
with the dimensions to get the lipids/leaflet as close to w
I'm having trouble with using make_ndx with a specific file. Whenever I try to
combine or use a specific group (group content at bottom) I get the error "One
of your groups is not ascending", and the group is not actually included in the
subsequent group produced. As far as I can see, the numb
I'm sure I have, in the past, found a way to use trjcat/trjconv to overwrite a
bad frame with a good one. From memory, I had to convert the area around the
bad frame to pdb/gro (for some reason that worked where normal tools didn't),
open up the files, rewrite several bad frames (just copied an
Yes, I never managed to get a later version of g_order to function properly. I
only ever get the -Sg and -Sk outputs, no matter WHAT I put in the index
files. I've just kept an old version of gromacs on the machine I use for
analysis. A copy of 3.2.1 should be quite easy to download, and will
Copy file, editconf to translate, then concatenate that with the original,
reorder and renumber everything; or genbox will also do something similar with
less tinkering.
- Original Message
From: "Wei, Xiupeng" <[EMAIL PROTECTED]>
To: "gmx-users@gromacs.org"
Sent: Wednesday, May 21, 200
How about you try the different options, see what they do, and then decide for
yourself how best to utilise them for whatever it is that you wish to do?
- Original Message
From: ANINDITA GAYEN <[EMAIL PROTECTED]>
To: gmx-users@gromacs.org
Sent: Monday, May 19, 2008 2:28:30 PM
Subject:
Yes, that's exactly what the first reply was telling you. The option is
"stride", I believe.
- Original Message
From: serdar durdagi <[EMAIL PROTECTED]>
To: Discussion list for GROMACS users
Sent: Tuesday, May 13, 2008 8:44:37 AM
Subject: Re: [gmx-users] cutting the trajectory in smal
You haven't edited your topology files correctly. If changing the number of
ions has not resulting in a change of charge, I'd suggest you haven't added the
ions in right; otherwise, I suspect it's something to do with the number of
waters. Particularly as the error in coordinates vs. topology
I suggest you search the archives too. This has been discussed several times.
- Original Message
From: pragya chohan <[EMAIL PROTECTED]>
To: gmx-users@gromacs.org
Sent: Wednesday, April 30, 2008 9:52:19 AM
Subject: [gmx-users] problem with g_order
Dear users
I am calculating order p
I've often found it necessary to do multiple trjconv steps to get the result I
want. So in this case, I'd probably make sure my protein is genuinely centered
in the box, then take that output .xtc and then make sure everything is whole
and approximately in the box (-pbc whole).
- Original
It sounds like you have it pretty clear already. A point to note, in GROMACS
the origin coordinate 0,0,0 is at a corner of the box, not the centre. This
could be what caused such a big (apparent) shift.
- Original Message
From: maria goranovic <[EMAIL PROTECTED]>
To: Discussion list
The end of the log files after the simulation finishes might help you
understand if there's anything odd that's taking more computation than normal.
Also, just one extra running process can slow down the entire simulation as all
processors will wait for the slowest. Check if it takes as long if
enzyme tutorial for Gromacs. But for membrane-bound case I
guess this tutorial is not enough to work.
Best Wishes,
Serdar
Alan Dodd <[EMAIL PROTECTED]> schrieb:
Firstly, a molecule of DPPC has less than 300 atoms.
Secondly, I'd suggest you look for stuff by Tieleman, White, or S
Firstly, a molecule of DPPC has less than 300 atoms.
Secondly, I'd suggest you look for stuff by Tieleman, White, or Sansom.
Googling/literature searching any of these names with "membrane" should give
you some rough pointers on how it's been done in the past.
There is no official membrane tutor
Editing mdout.mdp will not affect the parameters in your .tpr, and therefore
your simulation, I'm fairly sure. It's just a report of what you've specified,
with all the defaults.
Add the pbc=whatever line into your INPUT mdp to fix this.
- Original Message
From: Liu Shiyong <[EMAIL PR
== 250 ps
step 3 == 375 ps
Where is 125ps from ?
But
; RUN CONTROL PARAMETERS
integrator = steep
; Start time and timestep in ps
tinit= 0
dt = 0.002
On Wed, Mar 12, 2008 at 5:32 PM, Alan Dodd <[EMAIL PROTECTED]> wrote:
You asked for the frame at 1ps. The trajectory starts at 125ps, so
unsurprisingly the program does not give you an output.
- Original Message
From: Liu Shiyong <[EMAIL PROTECTED]>
To: Discussion list for GROMACS users
Sent: Wednesday, March 12, 2008 10:07:17 PM
Subject: [gmx-users] tr
f=ma?
- Original Message
From: avinash kumar <[EMAIL PROTECTED]>
To: gmx-users@gromacs.org
Sent: Tuesday, March 4, 2008 7:08:04 PM
Subject: [gmx-users] Relating acceleration to pressure
Hello all,
This is more of a theoretical question than relating to
the software. My ques
If you convert the tpr binary into a text file, it should have every parameter
in it I think?
- Original Message
From: LeeHui <[EMAIL PROTECTED]>
To: gmx-users@gromacs.org
Sent: Friday, February 15, 2008 4:57:13 PM
Subject: [gmx-users] How to ask pdb2gmx to print all parameters in the it
- Original Message
From: David van der Spoel <[EMAIL PROTECTED]>
To: Discussion list for GROMACS users
Sent: Thursday, February 7, 2008 6:35:55 PM
Subject: Re: [gmx-users] g_dist producing inconsistent values
[EMAIL PROTECTED] wrote:
>> I've since found the source of my problem - the pro
I've since found the source of my problem - the program was measuring the
(marginally shorter) distance across the PBC boundary, rather than the distance
within the box. Unfortunately there doesn't seem to be a way to turn PBC
images off (correct me if I'm wrong?), so I guess I'm going to do so
I've been using g_dist to plot distances along the normal to my bilayer between
groups. Namely in this case, between the phosphates of opposing leaflets, and
the peptide.
I would expect the sum of the distances between the peptide and each leaflet's
phosphates to equal the distance between the
You'd have thought the MD papers you have would also compare values against
experimental data?
These papers do exist, I'm sure, I came across the all the time while looking
for DOPC data - though I didn't make a note of them. Plus the people who
initially parameterised the POPC topology (Tielem
see what I mean? i.e. that the error due to not accounting
for constraints is constant.
Alan.
- Original Message
From: David van der Spoel <[EMAIL PROTECTED]>
To: Discussion list for GROMACS users
Sent: Tuesday, January 29, 2008 9:45:01 PM
Subject: Re: [gmx-users] Temperature without
Gromacs users,
I want to look at the temperature difference between groups, to check whether
temperature coupling is working ok (specifically if the lipid is at the same
temperature as the water).
Unfortunately, I've rather foolishly deleted all my trrs due to a lack of
space, thinking xtc/edr w
If the runs all finish successfully, then incorporating run continuations into
your script is simple, but I believe the issue may be more the tendency of
tpbconv to fail unpredictably - should the .edr file be even one frame shorter
than the .trr file due to a crash, for instance, then tpbconv w
Check the bugzilla server, is it the same problem as #126?
- Original Message
From: Arnau Cordomi <[EMAIL PROTECTED]>
To: gmx-users@gromacs.org
Sent: Monday, January 21, 2008 2:12:17 PM
Subject: [gmx-users] Specified frame doesn't exist or file not seekable
Dear all,
I'm getting the fo
nd do normal g_msd for the P
atoms only. (no mol flags etc.)
>
> Thanks again.
>
> -Justin
>
>
> Quoting Alan Dodd <[EMAIL PROTECTED]>:
>
>> What happens if you visualise the trajectory? Two orders of magnitude in
>> scale of lipid movement sh
What happens if you visualise the trajectory? Two orders of magnitude in scale
of lipid movement should stick out like a sore thumb.
- Original Message
From: Justin A. Lemkul <[EMAIL PROTECTED]>
To: gmx-users@gromacs.org
Sent: Wednesday, January 16, 2008 12:27:45 AM
Subject: [gmx-users]
ly typing box size at the bottom of
.gro file)
On Jan 15, 2008 10:13 AM, Alan Dodd <[EMAIL PROTECTED]> wrote:
I'd suggest this is an issue with VMD rather than gromacs. You have to be
quite careful which .gro you use to provide the original structure, make sure
it is actuall
I'd suggest this is an issue with VMD rather than gromacs. You have to be
quite careful which .gro you use to provide the original structure, make sure
it is actually the starting frame and not anything else - this is something
I've seen cause this sort of problem before.
Normally, of course, P
Atoms.
- Original Message
From: Antonia Vyrkou <[EMAIL PROTECTED]>
To: gmx-users@gromacs.org
Sent: Tuesday, January 8, 2008 4:05:26 PM
Subject: [gmx-users] g_density
Dear all,
When using the g_density tool am I calculating the density of a group of
molecules in respect to the atoms
I'm going to assume you've read
http://wiki.gromacs.org/index.php/Doing_Restarts.
I suggest you also look more closely at the manual page for trjconv.
- Original Message
From: pragya chohan <[EMAIL PROTECTED]>
To: Discussion list for GROMACS users
Sent: Monday, December 31, 2007 1:56:41
What's the difference between the two runs? Isolate which of the differences
makes your simulation run slow, and then the answer might present itself.
- Original Message
From: sudheer <[EMAIL PROTECTED]>
To: gmx-users@gromacs.org
Sent: Monday, December 31, 2007 12:20:48 PM
Subject: [gm
Does the water move through the bilayer, or is this a PBC thing? It sounds
like your bilayer is translating upwards?
- Original Message
From: pragya chohan <[EMAIL PROTECTED]>
To: gmx-users@gromacs.org
Sent: Sunday, December 30, 2007 3:25:51 PM
Subject: [gmx-users] problem in bilayer s
Have you tried running trjconv with -centre (selecting SOL, obviously), and
then running trjconv -pbc on the result? I have a vague memory of finding
seperating the commands gives a different result, as if the two options were
interfering with each other. What does the output look like when yo
Of course it's unnatural, it's a membrane made of gas instead of lipid ;) I'd
recommend that you equilibrate the "membrane" first, and check it actually
behaves in a manner close enough to one for what you want - and then insert a
protein into it. You might want to look into the make_hole suit
What topology are you using? If you're using one based on the Kartunnen's
group POPG (the only publicly available one I know of), then be aware that I
think they saw gel phase too.
Oh, and read the email you replied to, particularly the bit about 18 angstroms.
- Original Message
From:
(only
coordinates).
I have edr file also.
I found the following to make the restart file (gro file).
tpbconv -s eq5.tpr -f eq5.trr -e eq5.edr -o eq6.tpr -time 6870.000
Since I have velocity only in the trr file, I can't apply this.
Any idea?
On Nov 29, 2007 11:17 AM, Ala
http://wiki.gromacs.org/index.php/Doing_Restarts
You can make a gro with what you have. You *may* be able to continue your run
properly. Read the above link.
- Original Message
From: Myunggi Yi <[EMAIL PROTECTED]>
To: gmx-users@gromacs.org
Sent: Thursday, November 29, 2007 4:06:06 PM
- Original Message
From: maite lopez cabezas <[EMAIL PROTECTED]>
To: Discussion list for GROMACS users
Sent: Sunday, November 25, 2007 10:48:31 AM
Subject: Re: [gmx-users] area by lipid
Well I know that the x/y directions are scaled isotropically and the z
direction is scaled independien
0 0 0
14 6.3696 6.3998 6.54126 0 0 0
15 6.3696 6.3998 6.53768 0 0 0
On Nov 24, 2007 6:00 PM, Alan Dodd <[EMAIL PROTECTED]> wrote:
> I didn't think g_energy was useful for that - I've always used g_traj -o
I didn't think g_energy was useful for that - I've always used g_traj -ob to
get box dimensions. If noone has a better answer, you should probably just try
that and see if you get the same effect.
- Original Message
From: maite lopez cabezas <[EMAIL PROTECTED]>
To: Discussion list for
The length of your simulation is irrelevant, the frequency of frame output is.
If you don't output frames at least 5x per picosecond, asking for the frames in
a 0.1ps gap is not going to produce an output - because there probably won't be
any. Check your mdp.
- Original Message
From:
The quick answer would be to look at the ffgmx forcefield, and the ffgmx/Berger
hybrid that can be obtained (either from Tieleman or the Gromacs website, I
forget) and work out how the former was incorporated into the latter. Then
replicate that for ffG43a2.
Not necessarily simple or even valid
You can play with mdrun_hole (search the site) which is designed to create a
protein-shaped hole in a lipid simulation (also making a hole in the water).
I'd probably just delete the offending waters, and reequilibrate, myself.
- Original Message
From: N-J.M. Macaluso <[EMAIL PROTECTED]>
Did you perhaps use semiisotropic pressure coupling? I'd expect the X-Y values
to be the same for that.
- Original Message
From: Sona Aramyan <[EMAIL PROTECTED]>
To: Discussion list for GROMACS users
Sent: Thursday, November 1, 2007 1:18:07 PM
Subject: [gmx-users] Regarding Box-X Box-Y
g_bundle does give the angle between helix pairs...? Not directly, admittedly,
but it gives you the tilt from the main axes, which you can use with some basic
math to work out the angle between helices.
- Original Message
From: Anupam Nath Jha <[EMAIL PROTECTED]>
To: Discussion list fo
Use the topologies/forcefields in a simulation/energy minimisation, and check
that any predictions made by the simulation match up with any available
experimental evidence. Hopefully, you'll see that predictions are confirmed by
existing experiments, and will suggest new experiments to be done.
Have you simulated the system without the annealing, to see if it does the same
thing? Bilayers are very sensitive to minor changes in setup, using someone
else's equilibrated bilayer coordinates doesn't mean it's equilibrated for your
system.
- Original Message
From: Q733 <[EMAIL PR
You can apply external forces to subsets of atoms, in such a way as to cause
your box to shrink by itself.
- Original Message
From: WU Yanbin <[EMAIL PROTECTED]>
To: gmx-users@gromacs.org
Sent: Tuesday, October 9, 2007 11:40:21 PM
Subject: [gmx-users] How to change the box size during s
am a little busy today, sorry for replying so late...
On 10/8/07, Alan Dodd <[EMAIL PROTECTED]> wrote:
Check the MPICH manuals for how to specify the nodes to run on. From memory,
the option -machinefile lets you do this.
- Original Message
From: liu xin < [EMAIL PROTECTED]&g
Check the MPICH manuals for how to specify the nodes to run on. From memory,
the option -machinefile lets you do this.
- Original Message
From: liu xin <[EMAIL PROTECTED]>
To: Discussion list for GROMACS users
Sent: Monday, October 8, 2007 1:51:12 PM
Subject: [gmx-users] only one cpu
I believe I got as far as determining that the frame coordinates were stored in
the rvec fr.x after being read, and passed to do_fit. That rvec structure
would be the key to achieving what you want, I guess. When I got to about that
point, I decided I could handle a little bobbing about when w
Yes, I know what you mean - I keep meaning to make a modified trjconv where
'-fit trans' only affects the xy coordinates, for my bilayers, but it never
quite seems important enough. If your droplet moves at a constant rate,
trjconv -shift will, I think, move the coordinates by an amount proport
http://moose.bio.ucalgary.ca/index.php?page=Structures_and_Topologies should
have roughly what you want. Failing that, google is your friend.
- Original Message
From: Rina Ghosh <[EMAIL PROTECTED]>
To: gmx-users@gromacs.org
Sent: Monday, September 17, 2007 1:12:05 PM
Subject: [gmx-users
Subject: RE: [gmx-users] make_ndx and residue name length
>From: Alan Dodd <[EMAIL PROTECTED]>
>Reply-To: Discussion list for GROMACS users
>To: gmx-users@gromacs.org
>Subject: [gmx-users] make_ndx and residue name length
>Date: Tue, 4 Sep 2007 10:55:07 -0700 (PDT)
>
&g
The maximum permissible residue name length is at least 5 characters long for a
tpr or gro, but the length of residue name permitted by make_ndx is only 4
characters. And of course, pdb should have only 3 characters. While I can
change the names in a gro or a pdb quite quickly and easily, is t
Capping peptides is non-trivial, so the error may have been introduced there -
certainly the approach you stated is not what I or others have used
successfully. There have been a number of posts discussing how to do this,
check the archives.
- Original Message
From: OZGE ENGIN <[EMAIL
The end structure is the same as the start because gromacs cannot find a lower
energy structure than the initial one. This indicates something severely
wrong, either with the topology or starting structure. You could get a better
idea of what's going on by telling gromacs to output structures
There's probably a problem either with your structure or your topology. Spend
some time looking at what you've done. I'd start by investigating atom 483.
It should be pretty obvious what's wrong, with a force like that.
- Original Message
From: Q733 <[EMAIL PROTECTED]>
To: gmx-users@
I've always used HDDs for the main backup/working copies, and DVDs for
longer-term backup. You can get hold of 100x spindles of DVDs quite cheaply
these days... I wouldn't call it convenient, though.
- Original Message
From: Monika Sharma <[EMAIL PROTECTED]>
To: Discussion list for GR
tpbconv -extend ???
- Original Message
From: gurpreet singh <[EMAIL PROTECTED]>
To: Discussion list for GROMACS users
Sent: Wednesday, July 25, 2007 6:21:06 PM
Subject: [gmx-users] problem regarding total time elapsed
Hello users
I am using gromacs 3.3 with 43a1 force field.
My ques
I noticed the time provided was:
tpbconv -s protein.tpr -f protein.trr -o protein2.tpr -time -1300
I'd have thought Gromacs would have provided an error if this were the case,
but it may be that it's taken the frame closest to the (negative) time
requested, and consequently just removing the minu
Fair enough, but I'll just repeat that g_bundle does *exactly* what you want in
your example - provide it with an index file with two groups with the COMs
defining the ends of the axes (in your case, one C in one group and one O in
the other) and the option -z, and it'll dump out a file of the a
For some reason this didn't send to the mailing list...
I use C-terminal amidated peptides, which sounds similar to what you're trying
to achieve. Still, more info about what you've done would have made this reply
rather shorter. Is the residue still there after pdb2gmx, for instance? I've
n
Check out the file template.c, in gromacs/share/template. I'm being rather
rude, and assuming you haven't read the FAQ, of course.
- Original Message
From: Mark Abraham <[EMAIL PROTECTED]>
To: Discussion list for GROMACS users
Sent: Thursday, June 21, 2007 2:16:05 PM
Subject: Re: [gmx-
I've used g_bundle a lot for just this sort of thing. You need to define the
top and bottom of the helix as seperate groups, and define them *very*
carefully - it does make a difference how you do it, presumably because
g_bundle just plots the axis between the COM of both groups? I usually def
rs
Sent: Sunday, June 10, 2007 4:15:29 PM
Subject: Re: [gmx-users] tpbconv restart crashing on 3.3.1
Alan Dodd wrote:
> Hello all,
> A recent simulation has been running on a cluster for a couple of weeks.
> 5.something-ns in it crashed due to a hardware glitch. All perfectly
&g
Small errors like that are usually down to things like running genion and not
changing the .top. I think I made a problem for myself once with
non-consecutive atom numbering, too.
- Original Message
From: Mark Abraham <[EMAIL PROTECTED]>
To: Discussion list for GROMACS users
Sent: Fri
like a bug. Any suggestions as to why LINCS errors
could suddenly now prevent the simulation from running *any* of the steps that
it previously ran just fine? I just want a hint as to what we could have
missed, really.
Alan Dod
Check the manual for 'genbox'. Once you work out how to use it, remember to
check your output for waters within the bilayer - I'm not sure how big the
cavities are, but I wouldn't be surprised if you could fit a water molecule or
two in.
- Original Message
From: naga raju <[EMAIL PROT
Read the manual. There's a section on available analysis programs towards the
back, all of which start with g_
If I were you, I'd narrow my search to something along the lines of: g_dist,
g_angle, and g_dihedral.
That might be uncannily helpful.
- Original Message
From: Mark Abraham <
Don't use -timestep. Just -skip will do for what you want.
- Original Message
From: "[EMAIL PROTECTED]" <[EMAIL PROTECTED]>
To: gmx-users@gromacs.org
Sent: Tuesday, May 8, 2007 7:20:39 PM
Subject: [gmx-users] Trjconv: reducing frames and Time issue
Hello All,
I have a xtc file and I u
Short answer? RMSD is a lousy measure of convergence :)
- Original Message
From: Caterina Arcangeli <[EMAIL PROTECTED]>
To: Discussion list for GROMACS users <[EMAIL PROTECTED]>
Sent: Friday, April 13, 2007 10:58:54 AM
Subject: [gmx-users] ED analysis: help on cosine content and overlap o
>From memory, deshuffling, followed by using editconf to change confout.gro to
>a pdb and back again, results in the molecule types all being in the same
>order again (in my case, protein, lipid, solvent, ions instead of protein,
>lipid, ions, water, lipid, ions, water, lipid, ions, water, prote
I've noticed something similar... it's worth noting that you appear to be
getting duplicates around the join mark. I suspect, for me at least, it's
because my .edr output interval doesn't quite tally with the total runtime - so
I not only get a output at every required step, but also a final ou
Have you tried running for a short period without PR, then putting the output
from that into PR again? If the initial run is short enough, it shouldn't
affect things too much, but may still randomise out whatever's causing the
problem.
- Original Message
From: andrea spitaleri <[EMAIL
Incidentally, if PME has been specified correctly, am I right in assuming there
should be an energy term available within g_energy for long range forces?
Which one is it? For some reason, I haven't been able to find it yet.
- Original Message
From: Richard Vadnais <[EMAIL PROTECTED]>
st for GROMACS users
Sent: Wednesday, January 17, 2007 8:10:22 PM
Subject: Re: [gmx-users] inconsistent XTC/Magic number error in g_density
Alan Dodd wrote:
> g_density produces an error every time I try to run it on two of my
> trajectories at frame 0 - magic number for one, and a ridiculo
ROTECTED]>
To: Discussion list for GROMACS users
Sent: Wednesday, January 17, 2007 8:10:22 PM
Subject: Re: [gmx-users] inconsistent XTC/Magic number error in g_density
Alan Dodd wrote:
> g_density produces an error every time I try to run it on two of my
> trajectories at frame 0 - magic
g_density produces an error every time I try to run it on two of my
trajectories at frame 0 - magic number for one, and a ridiculous number of
atoms for the other. Oddly, every other program I've used (trjcat, trjconv,
g_covar, g_dist, etc etc) is perfectly happy with the files, and gmxcheck al
Original Message
From: Mohamed Osman <[EMAIL PROTECTED]>
To: gmx-users@gromacs.org
Sent: Thursday, January 11, 2007 10:49:29 PM
Subject: [gmx-users] box size for simulation of membrane protein
My questions:
1. Protein is closer to one edge than the other. Does this make any
difference
I don't know of anything publicly available, but have a look around for voronoi
cell analysis. People have used it before for lipid area calculation, and may
be willing to let you use their code. Alternatively, read up on the theory and
try it yourself.
- Original Message
From: linfu
Hello,
(background)
I recently compiled a new version of the 3.2.1 mdrun to make use of the lam
7.1.2 that's just been installed. For some reason, I can't get a run to work
with it - it goes fine until:
Back Off! I just backed up enerG.edr to ./#enerG.edr.1#
starting mdrun '?'
143 steps,
tem by looping over lipids
> and ask whether that atom type
> > has a z-coordinate within some amount around the
> input value. From this you
> > know the membership of the leaflets. A more
> automatic way would be to have the
> > program first discern the distribution and t
Wouldn't shuffle/sort undo all the good work? I did
wonder if I should have labelled the lipids in
different leaflets as different molecule types, or
different chains, but it's a bit late now...
--- Jay Mashl <[EMAIL PROTECTED]> wrote:
> On Wed, 8 Nov 2006, Alan Dodd wr
them -
they do the opposite of what they say. From the
gromacs 3.3.1 source download I did on April of this
year.
Alan Dodd
University of Bristol
__
Do You Yahoo!?
Tired of spam? Yahoo! Mail has the best spam prote
x27;m not intending to do a pure
bilayer, just dope the existing one with a few
negative charges. And a high concentration of ions
near the membrane is not entirely unrealistic, I
believe. So does anyone know of any gromacs stuff
using negative lipids, or alternatively a reason why
this hasn'
Configuring the .itp files etc initially is a bit
tricksy without knowing what you're doing, the short
not-very-helpful answer is "read the manual". There's
a whole chapter (5?) on forcefield files and their
formats.
It's entirely possible to set it all up so that
pdb2gmx does in fact work, but to
>
> > I'm also aware of the make_hole tool. My question
> here is: Does
> > make_hole create a hole of specified dimensions
> and orientation,
> > according to the solute coordinates? And can you
> specify exactly
> > where in the membrane you want the whole?
>
> Make_hole doesn't actua
Interestingly, merging the peptide chains to one
results in PR working fine. Smells like a bug to
me... but I guess that's the price of using an old
version.
--- Steffen Wolf <[EMAIL PROTECTED]> wrote:
> Yes, so it looks that minimization ended at a
> metastable point, which
> was surmounted by
my carefully-placed peptide.
Interestingly, I've had similar problems before, but
only when I use multiple peptides. Might try merging
the chains and see what that does.
I used CG with steep every 50 steps... sounds weird I
know, but it's proved pretty reliable.
--- Steffen Wolf <[EMAI
e system.
> Sounds more like your
> system is still not well minimized. Using the
> freezegroup option is not
> such a good way, because it will not work well
> together with the
> pressure coupling. Did you use the restraints during
> minimization as well?
> Bye
> St
Hello,
I'm trying to run position restraints on multiple
peptides in a protein/bilayer/water system. MD
*without* position restraints runs absolutely fine,
but as soon as I stick that "define = -DPOSRES" in,
some of the molecules explode within a matter of fs.
Any idea why this might be? Is MD w
I use the option -merge with my SS-linked peptides,
and pdb2gmx always asks me if I want to join my
cysteines with a bond. If they're internal to the
protein, perhaps it's either that they're too far
apart, or you need -ignh as otherwise they've got
hydrogens on and potentially can't bond.
--- Ce
I find getting a system minimised is often quite
tricky. There's a variety of things that can be
fiddled with, using cg with various intervals between
steps of steepest descent, running a few steps of md
(say, 10 to 100) after minimisation and then
minimising again, randomly perturbing the coordin
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