erful. The former is not going to get
enhanced given that the latter exists.
Mark
On Sat, 21 May 2016 00:14 Justin Lemkul wrote:
>
>
> On 5/20/16 5:54 PM, Christopher Neale wrote:
> > Dear Users:
> >
> > I find that gmx make_ndx will create groups with names that have
&g
Dear Users:
I find that gmx make_ndx will create groups with names that have ampersands in
them and that this complicates piping the group name back into an analysis
tool. I have included an example below. There is an obvious solution with sed
to rename the group in the .ndx file after creation
Dear Users:
In an attempt to get around the '&' issue in index group names, I have tried
using the 'AND' keyword, which is noted in the gmx make_ndx -h output. Indeed,
the word "AND" replaces the ampersand in the index group in this case. However,
the selection seems broken to me. Details are b
Sent: 20 May 2016 13:37:01
To: Christopher Neale
Subject: Re: [gmx-users] OPLS problem
Thanks Christopher
I was using, as it is recommended, TIP4P. When I switched to TIP3P I no longer
get the error. So what do I do if I want to use TIP4P?
Steve
On Friday, May 20, 2016 11:06 AM, Christopher Nea
Did you select tip4p? It has 4 "atoms" per water molecule.
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
on behalf of Steve Seibold
Sent: 20 May 2016 11:38
To: gmx-us...@gromacs.org
Subject: [gmx-users] OPLS problem
HelloI have gromacs 4.5.4
Dear Szilárd:
I think that my ranks were set up similarly for GPU and non-GPU runs, though
you can see how I ran the jobs below. One thing that I also already checked,
but that I have not pasted here, is that all runs got the same DD and PME grid
reported from the log file (4x1x1 for each in al
t: 17 May 2016 17:12:52
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Pull code slows down mdrun -- is this expected?
Hi,
On Tue, May 17, 2016 at 10:41 PM Christopher Neale <
chris.ne...@alum.utoronto.ca> wrote:
> Dear Mark:
>
> GROMACS-2016-beta1 is not any faster for this test case wh
May 17, 2016 at 9:30 PM Christopher Neale <
chris.ne...@alum.utoronto.ca> wrote:
> These benchmarking numbers are from gromacs v5.1.2. Forgot to mention that
> in my initial post.
>
>
> From: gromacs.org_gmx-users-boun...@mailli
to do.
Cheers,
Mark
On Tue, May 17, 2016 at 9:30 PM Christopher Neale <
chris.ne...@alum.utoronto.ca> wrote:
> These benchmarking numbers are from gromacs v5.1.2. Forgot to mention that
> in my initial post.
>
>
> From:
In case anybody else finds the gmx distance input as confusing as I did... if
you want to get the distance between the center of mass of the peptide and the
center of mass of the SDS, you would first create Protein and SDS groups in an
index file (say they are groups 1 and 2), then send that to
These benchmarking numbers are from gromacs v5.1.2. Forgot to mention that in
my initial post.
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
on behalf of Christopher
Neale
Sent: 17 May 2016 15:27:37
To: gmx-us...@gromacs.org
Subject: [gmx
Dear Users:
I am writing to ask if it is expected that the pull code slows down gromacs in
such a way that a single pull group has fairly minor effect, but many groups
collectively really bring down the throughput. Based on Mark's response to my
previous post about the free energy code slowing
Maybe this:
http://scitation.aip.org/content/aip/journal/jcp/124/22/10.1063/1.2201698 ?
Can't claim to understand it though. If it were me, I'd pick another project or
pick another method.
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
on beha
ubject: Re: [gmx-users] mdrun -rerun does not reproduce itself
Hi,
Thanks (yet again) for your vigilance!
On Tue, Apr 26, 2016 at 7:44 PM Christopher Neale <
chris.ne...@alum.utoronto.ca> wrote:
> Dear Users:
>
> I find that running gromacs 5.1.2 mdrun -rerun many times gives diff
Dear Users:
I find that running gromacs 5.1.2 mdrun -rerun many times gives different
energies for some components. On GPUs I find that its the SR interactions (both
LJ and q) that are inconsistent. On CPU only, I find that its the Coul. recip.
that is inconsistent. On CPU only with NPME=1 I fi
There are many published approaches. Here is the one that I use:
http://origami.phys.rpi.edu/racc/rate_of_acceptance.php
Another example is here: http://folding.bmc.uu.se/remd/
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
on behalf of YanhuaOu
one that I admit is easy to test.
Thank you,
Chris.
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
on behalf of Mark Abraham
Sent: 18 April 2016 06:59
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Dihedral convention
Hi,
On Thu, 14 Apr 2016 21:10
Then don't use settle for your minimization?
(mdp option define = -DFLEXIBLE for most water models)
You can always turn it on again and run another EM after whatever problematic
configurational feature has relaxed.
From: gromacs.org_gmx-users-boun...@mail
acs charmm port?
On 4/15/16 1:29 AM, Christopher Neale wrote:
>
> Dear Users:
>
> When I look at charmm36-jun2015.ff/merged.rtp downloaded from
> http://mackerell.umaryland.edu/charmm_ff.shtml , it has a cholesterol
> molecule named CHL1. However, I do not find such a molec
Dear Users:
When I look at charmm36-jun2015.ff/merged.rtp downloaded from
http://mackerell.umaryland.edu/charmm_ff.shtml , it has a cholesterol molecule
named CHL1. However, I do not find such a molecule in the charmm-specific
toppar_c36_feb16.tgz downloaded from the same site. In the later ta
s...@gromacs.org
Subject: Re: [gmx-users] Dihedral convention
Hi,
Also, the details of angle conventions are all covered in the reference
manual.
Mark
On Thu, 14 Apr 2016 20:37 Christopher Neale
wrote:
> Make a box with a single molecule of n-butane, no pressure coupling o
Make a box with a single molecule of n-butane, no pressure coupling or pme, use
the sd integrator, test it out?
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
on behalf of Parvez Mh
Sent: 14 April 2016 12:47
To: gmx-us...@gromacs.org
Subject:
This is not enough detail for us to know what the problem is. Did you set
things up correctly so that posre_cpn.itp is actually used? You can check by
gmx energy and see if you have restraint energies there. To use these
restraints your .top file needs to #include "posre_cpn.itp" , which you can
sys.kth.se
on behalf of Szilárd Páll
Sent: 08 April 2016 06:42
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] desired usage of verlet-buffer-tolerance with charmm
ff?
On Thu, Apr 7, 2016 at 9:55 PM, Christopher Neale
wrote:
> Dear users:
>
> Charmm mdp options
Dear users:
Charmm mdp options are listed here:
http://www.gromacs.org/Documentation/Terminology/Force_Fields/CHARMM with the
following values:
constraints = h-bonds
cutoff-scheme = Verlet
vdwtype = cutoff
vdw-modifier = force-switch
rlist = 1.2
rvdw = 1.2
rvdw-switch = 1.0
coulombtype = PME
rc
zegrp = Protein-H, YB and
freezedim = Y Y Y Y Y Y?
Best,
Irem
> On Apr 4, 2016, at 5:21 PM, Christopher Neale
> wrote:
>
> I've never understood it, but when your system gets more complicated it is
> often necessary to use flexible water during minimization. define =
> -DFLEXI
where near the protein). However, the MD simulation seems to be running,
after doing the minimization with just position restraints. Is this expected
behavior?
Best,
Irem
> On Apr 4, 2016, at 4:23 PM, Christopher Neale
> wrote:
>
> Check the manu
als cut-off
pbc = xyz ; Periodic Boundary Conditions (yes/no)
Best,
Irem
> On Apr 4, 2016, at 1:36 PM, Christopher Neale
> wrote:
>
> What did you set for refcoord-scaling ? How are you treating volume/pressure?
> Please post a full .mdp file. If you want,
What did you set for refcoord-scaling ? How are you treating volume/pressure?
Please post a full .mdp file. If you want, you can simply fix the positions and
not let them move at all with freezegrps etc.
From: gromacs.org_gmx-users-boun...@maillist.sys.kt
Possibilities that come to mind:
(1) absolute position restraints
(2) pull code distance restraints of each arm separately to the bottom of the U
(3) put 2x U-shaped proteins in the same box. It takes longer to simulate, but
you get twice the sampling
(4) go back to the drawing board (this is lik
of atoms
See: https://groups.google.com/forum/#!topic/plumed-users/eJ0xpnHPb_s and
https://github.com/GiovanniBussi/plumed2/tree/v2.2-hrex
Nicolas
2016-04-02 12:09 GMT+02:00 Mark Abraham :
> Hi,
>
> On Fri, Apr 1, 2016 at 11:39 PM Christopher Neale <
> chris.ne...@alum.uto
ermediates. Changing the way the code is structured would again
require some significant changes and time.
On Thu, Mar 31, 2016 at 10:49 AM, Christopher Neale
wrote:
> Dear Szilárd, Mark, and Michael:
>
> Thank you for your suggestions.
>
> 1. I did use the icc compiler
> 2. I teste
Dear Mark:
The value of f listed under eq. 4.11 is wrong in the gmx 5.1.2 manual. The
correct value is reported on the bottom of page 7 at the start of section 2.2
on "MD Units". I verified this using the values in src/gromac/math/units.h.
--
Gromacs Users mailing list
* Please search the arch
macs.org
Subject: Re: [gmx-users] Suggestion to update online .mdp options for pull
code
Hi,
On Thu, 31 Mar 2016 19:23 Christopher Neale
wrote:
> Dear developers:
>
> The online manual lists pull-code options here:
> http://manual.gromacs.org/current/online/mdp_opt.html#pull
No,
Dear developers:
The online manual lists pull-code options here:
http://manual.gromacs.org/current/online/mdp_opt.html#pull
that seem to have not been updated since:
http://manual.gromacs.org/documentation/5.1/ReleaseNotes/new-features.html#changed-the-way-pull-directions-are-selected
It took m
> unable to find a function called "gmx_waste_time_here()" and beyond that
> I
> > was out of my depth.
> >
> > But it's much more the fact that the non-free energy nonbondeds are
> > SUPER optimized.
> >
> > I don't see a particularly
It depends on what you want to do. If you simply want to minimize the system so
that the dynamics will be stable in MD, then I have never needed more than 500
steps of minimization (though in some cases I find it necessary to use flexible
waters and solutes via the mdp options define=-DFLEXIBLE
, Mar 30, 2016 at 7:42 PM Christopher Neale <
chris.ne...@alum.utoronto.ca> wrote:
> Dear Users:
>
> I find release notes for gromacs 5.1 here:
> http://manual.gromacs.org/documentation/5.1/ReleaseNotes/index.html . The
> text on that site ( "These release notes document
Need it for what? To solvate a solute with genbox or for some other sytem setup
needs? Common protocol would be to simply use tip4p.gro and then to equilibrate
it with the new tip4p/ice parameters. tip4p.gro is in share/gromacs/top/
Chris.
From: gromacs.
Dear Users:
I find release notes for gromacs 5.1 here:
http://manual.gromacs.org/documentation/5.1/ReleaseNotes/index.html . The text
on that site ( "These release notes document the functionality changes that
have taken place in GROMACS since version 5.0." ) is kind of vague and I am not
sure
Dear Users:
I am trying to do some Hamiltonian replica exchange (H-REMD) in gromacs 5.1.2
and am running up against really large slowdowns when decoupling a large number
of atoms. I am decoupling 5360 atoms out of the 15520 atoms in my system. The
goal is not to get a PMF, but to enhance sampl
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] REMD and distance restraints problem in gmx 4.6.7
Hi,
On Fri, Sep 18, 2015 at 6:27 AM Christopher Neale <
chris.ne...@alum.utoronto.ca> wrote:
> Dear Users:
>
> I have a system with many distance restraints, designed to maintain
>
Dear Users:
I have a system with many distance restraints, designed to maintain helical
character, e.g.:
[ distance_restraints ]
90 33 1 1 2 2.745541e-01 3.122595e-01 999 1.0
97 57 1 2 2 2.876300e-01 2.892921e-01 999 1.0
114 73 1 3 2 2.704403e-01 2.929642e-01 999 1.0
...
Distance restraints are
São José dos Campos - SP
> Página: sites.google.com/site/fileti/
>
>
>> --
>>
>> Message: 2
>> Date: Sun, 26 Jul 2015 02:45:50 +
>> From: Christopher Neale
>> To: "gmx-us...@gromacs.org"
>> Subje
>
> Message: 2
> Date: Sun, 26 Jul 2015 02:45:50 +
> From: Christopher Neale
> To: "gmx-us...@gromacs.org"
> Subject: Re: [gmx-users] PMF using umbrella sampling and Gromacs 5.0
> (Eudes Fileti)
> Message-ID:
> <
> blu
_
Eudes Eterno Fileti
Instituto de Ciência e Tecnologia da UNIFESP
Rua Talim, 330, São José dos Campos - SP
Página: sites.google.com/site/fileti/
>
> --
>
> Message: 4
> Date: Wed, 22 Jul 2015 14:56:50 +
> From: Christopher Neale
> To: "
Dear Users:
I believe that gromacs 5 pdb2gmx does not faithfully reproduce the
AMBER99sb-ILDN force field. I wanted to make a notice here so that people who
are using that combination can compare the topologies they get out of gromacs 5
pdb2gmx to gromacs 4 pdb2gmx.
Details are here: http://re
Dear Eudes:
There are two issues: The first issue is the fact that you've got a sampling
problem near the bilayer center. The second issue is the periodic bumps that
you see in your PMFs. I'll take the second part first.
The source of the periodic bumps in PMFs from umbrella sampling is, to me,
: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
on behalf of Justin Lemkul
Sent: 05 July 2015 13:12
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Why is there a difference between an angle of 0 or 180
deg. for a type 9 proper dihedral with multiplicity of 2?
On 7/5/15 9:10 AM, Christopher Neale
r a type 9 proper dihedral with multiplicity of 2?
On 7/5/15 12:56 AM, Christopher Neale wrote:
> Dear Justin:
>
> Thank you for your help. I am glad to see that I was not way out to lunch in
> my interpretation of multiplicity and proper dihedral angles.
>
> First, the out-of-plane motions
Verified same behaviour in gromacs 4.6.7 and 5.0.5 for the Phe-Phe system.
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
on behalf of Christopher
Neale
Sent: 05 July 2015 00:56
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Why is there a
on behalf of Justin Lemkul
Sent: 04 July 2015 09:41
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Why is there a difference between an angle of 0 or 180
deg. for a type 9 proper dihedral with multiplicity of 2?
On 7/4/15 3:32 AM, Christopher Neale wrote:
> Dear Gromacs users:
>
&g
Dear Gromacs users:
I have been working on creating a topology for an exotic molecule. It contains
aromatic rings and my parameters always seemed to allow the rings to buckle and
become non-planer, much like a glucose ring would (though a little less
extensively). However, I have managed to sol
If you just want to make a new, larger water box, try editconf to make the box
larger and then genbox to add water. Any help beyond than that requires us to
guess at at least four questions:
What is an "unloading simulation"
How did you "pull a protein"
What exactly do you mean by "both ends of
what about "editconf -f orig.pdb -o new.gro" followed by figuring out the new
residue numbers and running make_ndx on new.gro ?
I don't think you'll need the "-resnr 1" editconf flag, but if you run into
other problems then you might try that.
Chris.
Not gromacs specific, but I thought it was worth posting here. Basically, if
you use putty, check the "about" button and make sure that you don't see the
text "unidentified build".
http://blogs.cisco.com/security/trojanized-putty-software
--
Gromacs Users mailing list
* Please search the arch
Sounds like you are asking for packed nodes on a cluster that allows jobs to
take only a single core of a full node. You should do some benchmarking to see
what performance you get when you allow your mpi job to use distributed cores
(rather than packed nodes). You'll need to run a few repeats o
Dear Carlos:
Are you using a .top file from gromacs 5 with your gromacs 4 runs? If so, try
regenerating your topology (and .itp files) using gromacs 4 (with GMXLIB set
correctly). Not sure if that would even cause a problem, but it seems like it
probably would and is the only thing that comes t
and dirty install
steps suggest:
http://www.gromacs.org/Documentation/Installation_Instructions_5.0#quick-and-dirty-installation
--
Szilárd
On Thu, May 21, 2015 at 5:11 PM, Christopher Neale
wrote:
> Dear Users:
>
> This is just a note about compiling gromacs 5 so that the solution can be
> found by
Dear Users:
This is just a note about compiling gromacs 5 so that the solution can be found
by others if they need it.
I used to compile gromacs like this:
download and unpack tarball
cd gromacs-5.0.5
mkdir source
mv * source
mkdir exec
cd exec
** run my build script from here, using CMAKE_INST
Dear Cheng:
You can define protonation states like this:
echo "0 1 2" | pdb2gmx -ff amber99sb-ildn -water tip3p -his
That will give you, in order for three HIS residues:
0. H on ND1 only (HID)
1. H on NE2 only (HIE)
2. H on ND1 and NE2 (HIP)
You can also use -inter, but you'll need to do a dry-
Dear Users:
I have a system with an 8-mer peptide in a box of water. After a 2-ns npt
equilibration, I run 100 ns of nvt at various temperatures (300-800 K) in
preparation for a REMD simulation. I am using velocity langevin for temperature
control.
Everything is fine for <=600 K. Above that,
-users] mdp options for charmm27 force field in gromacs
version 4.6.7
Hi
On Tue, May 19, 2015 at 5:35 AM Christopher Neale <
chris.ne...@alum.utoronto.ca> wrote:
> Dear Justin:
>
> Thank you for the suggestion. I don't use gromacs 5 because of things like
> this: http://red
mx-us...@gromacs.org
Subject: Re: [gmx-users] mdp options for charmm27 force field in gromacs
version 4.6.7
On 5/18/15 2:21 PM, Christopher Neale wrote:
> Dear Users:
>
> I would like to use the charmm27 force field in gromacs version 4.6.7 and I
> would like to know if it is possible
Dear Users:
I would like to use the charmm27 force field in gromacs version 4.6.7 and I
would like to know if it is possible to get the proper treatment of vdw
interactions.
Information for gromacs 5 is here:
http://www.gromacs.org/Documentation/Terminology/Force_Fields/CHARMM
However, Gromacs
I don't think it is a bug per se, more like something the developers didn't
consider. The HREX fork of the plumed code (which only works right now for v. 4
of gromacs) does what you want (and it does it a lot faster if your heated
group is large since the gromacs free energy code is inexplicable
If your sysadmin has a hard rule against multiple aprun instances then that is
something that we obviously can't fix ;) However, I will note that (with
mpirun) on some clusters multiple sequential instances will work and on other
clusters it simply does not. The issue on some of these clusters i
Gromacs only notified you about turning off the GPU code, that was not an
error. The error was the AVX vs. SSE4.1 problem. Not sure why you are getting
that since I thought cmake would get these things straight.
Chris.
From: gromacs.org_gmx-users-boun..
nm. Which means by pulling from
11nm to 6 nm I am passing from organic layer and reached the water bulk.
In mdp file:
A is one water molecule
B is the bulk water
Maybe I should play with pulling rate and force constant?
On Wed, May 6, 2015 at 2:34 PM, Christopher Neale <
chris.ne...@alum.
more figures to check the statistics which are bsProfs and
bsResult.
There is also histogram image.
On Tue, May 5, 2015 at 5:40 PM, Christopher Neale <
chris.ne...@alum.utoronto.ca> wrote:
> post the images elsewhere and the post a link on this list. I did not get
> the attachment.
>
This is actually kind of unfortunate. I'm not sure where these gromacs VDW
radii come from, but they're nowhere near what I presume to be the standards
(either Bondi et al. or something similar). Note that even the recent updates
to the Bondi values are very minor in comparison to the difference
I didn't read the whole thread, just chiming in based on the title.
I can see up to 3x differences in performance when using clusters that don't
pack nodes. If you're using a cluster that is set up this way, then it can make
a huge difference how may cores you get on each node and how many switc
d by bulk
phase. However I can not capture this maxima on free energy if I do not
restraint my organic molecules.
Here you can find my density profile for water and organic layer.
On Tue, May 5, 2015 at 2:32 PM, Christopher Neale <
chris.ne...@alum.utoronto.ca> wrote:
> Dear Gozde:
>
ving
physically realistically and ii) if not then why not (i.e., adjust the
parameters).
Chris.
____
From: gozde ergin
Sent: 05 May 2015 07:16
To: Christopher Neale
Subject: Fwd: About 2011 paper
-- Forwarded message --
From: gozde ergin mailto:go
I see your confusion now.
The PMF is actually defined as dG(x) + C, where C is some unknown constant.
Therefore, in the left figure, you have "dG_a(x) + C_a" and on the right you
have "dG_b(x) + C_b", so if the profiles have the same shape then the PMFs can
be identical if C_a is different from
t;
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a
> mail to gmx-users-requ...@gromacs.org.
>
>
> --
>
&
Better yet, repeat something that is already out there in the literature. PMFs
for water, lipids, and some amino acid side chains across the bilayer have been
tested extensively.
Chris.
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
on behalf
Take a look at profiles in the literature for arginine across a bilayer. It has
a maximum at the center. Probably true for any molecule with a large
charge/molecular weight ratio. For more help you'd likely have to reveal your
system and provide an image of the PMF. However, there is no reason t
correctness. (there may be chances that I may have understood the
parameters wrongly), and from this simulation I want to do the umbrella
sampling for free energy calculation.
with regards
Mahender Singh
> Hi
> Christopher Neale and Justin
>
> I used now following pull code (wha
romacs.org_gmx-users-boun...@maillist.sys.kth.se
on behalf of Justin Lemkul
Sent: 22 April 2015 08:12
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Steered MD simulation of drug molecules across the
plasma membrane in gromacs 5.0.4
On 4/21/15 6:54 AM, Christopher Neale wrote:
> Dear Ma
Dear Mahender:
It's a real pity that the pull_geometry = position has been removed. So now
it's impossible to do umbrella sampling of a solute across a lipid bilayer
properly? Anyway, I see a note about this removal here (
http://redmine.gromacs.org/issues/1346 ), though no reason is given. I'd
How about temperature replica exchange with de novo folding, then convert the
probabilities of the folded and unfolded states into a free energy difference?
You'll obviously need to be really careful about cutting off a sufficient
amount of initial simulation time as equilibration, but you might
You can get the coordinates of all P and N atoms with g_traj and then write an
awk script to process the output (determine the angles and make the histogram).
But if g_angle in gromacs 5 can do it, then why not just use that? Many
analysis programs will take a .gro file for the -s option, and if
Dear Bahare:
this is not necessarily a problem. If what you are saying is that in two
separate runs of the same system from the same coordinates you got different
trajectories then this is expected under most conditions:
http://www.gromacs.org/Documentation/Terminology/Reproducibility
However,
Dear Bahare:
what data does not match what other thing? What type of crash did you
encounter? What version of gromacs? etc... Please provide as much detail as you
can. As your question stands, we could as easily answer the question "how deep
is water?"
Chris.
_
Dear membrane simulators:
If you use g_density from gromacs versions 5 to 5.0.4, please be aware that the
-center option may be wrong:
http://redmine.gromacs.org/issues/1698
(g_density is also wrong for NPT simulations in previous versions, but for
other reasons)
This is in addition to the fac
Dear Users:
I have sorted out the issue and filed a redmine:
http://redmine.gromacs.org/issues/1688
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
on behalf of Christopher
Neale
Sent: 12 February 2015 22:53
To: gromacs.org_gmx-users
Not sure about the differences, but focusing on what is similar: you're not
getting anything close to the desired temperature (in one case half and in one
case 3 times after only 10 integration steps). I suspect that there is
something else going wrong. I've never combined the sd integrator with
Thanks guys, this is very useful.
Chris.
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
on behalf of Justin Lemkul
Sent: 13 February 2015 16:53
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Semiisotropic pressure coupling
On 2/13/15 4:00
Dear Justin:
If you have time, can you please provide a link / reference for your comment
that potential switching leads to errors in the charmm lipid force field? I
tried a google search, but couldn't come up with anything specific. You
mentioned noticeable artifacts, so I'm hoping that you ca
(A) modify your .mdp to increase nsteps and then make a new .tpr, then run
mdrun -cpi my.cpt files and use the new .tpr file.
(B) use tpbconv to modify your original .tpr file and then rerun using mdrun
-cpi
(C) simply run as before (though you need -cpi option to mdrun since it is a
restart) an
Make a group of the "or" selections first, then run an "and" on group 4 and
your new group.
I don't exactly remember, but maybe you can do it in one step by simply putting
the "& 4" at the end instead of the beginning.
Chris.
From: gromacs.org_gmx-users
aryam
On Fri, Feb 13, 2015 at 8:42 AM, Christopher Neale <
chris.ne...@alum.utoronto.ca> wrote:
> Dear Maryam:
>
> I don't know. If g_dipoles doesn't give you what you want (and I have no
> idea if it will), then g_traj -ox will give you positions that you can then
>
the angle between the dipole moment
vector of a molecule and a special vector (for a very simple assumption X
axis for example). I found two options g_angle and g_sgangle but I think
non of them can help. Are there any other commands to use?
thank you!
On Fri, Feb 13, 2015 at 8:18 AM, Christo
Dear Daniel:
It is perfectly fine to use different force constants for different umbrellas.
This is commonly done, for example, when you have a very sharp maximum in your
PMF and you need to place a few umbrellas at and near this maximum with very
strong force constants in order to get good sam
How does one compute the angle between a vector and a molecule? I think you
need to define your goal more completely.
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
on behalf of Maryam Kowsar
Sent: 12 February 2015 23:45
To: gromacs.org_gmx-us
Dear Users:
I have run g_cluster from gromacs 4.6.5 as follows:
g_cluster -s my.tpr -f tmp.xtc -method gromos -nofit -o rmsd-clust_nofit.xpm -g
cluster_nofit.log -sz clust-size_nofit.xvg -cl clusters_nofit.pdb -n index.ndx
-cutoff 0.275 -wcl 10 -cl finally.xtc
The top of cluster_nofit.log look
] tabulated non-bonded potentials with replica exchange
(potentials that change with temperature)
On Mon, Jan 19, 2015 at 12:39 AM, Christopher Neale <
chris.ne...@alum.utoronto.ca> wrote:
> Dear Users:
>
> I presume that I can use tabulated non-bonded potentials with replica
> excha
Dear Mark:
my mistake. I was using "-multidir 2" when really I should have been using
"-multidir 0 1", which is why gromacs complained that I only had one replica.
Works as expected now.
Thank you again,
Chris.
________
From: Christopher Ne
Dear Users:
I presume that I can use tabulated non-bonded potentials with replica exchange
in gromacs 4.6.7. However, my question is whether it is possible to supply
different tables for each of the different temperatures?
My actual use involves the plumed plugin to do hamiltonian replica excha
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