bugzilla.
Thank you,
David Mobley
UCSF
http://www.dillgroup.ucsf.edu/~dmobley
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P
David and all,
> Sorry, my brain was on vacation (about the N). Anyway, having C2 as VS
> would mean the molecule remains perfectly linear as it should be, and
> you do not have to define angles of 180 degrees which gives you an
> ill-defined force.
Isn't there a robust implementation that wouldn
David,
On 10/16/07, David van der Spoel <[EMAIL PROTECTED]> wrote:
> David Mobley wrote:
> > All,
> >
> > I may be in a hole of my own digging, here, but I've been trying to
> > simulate a large set of small molecules in explicit solvent. I'm using
>
Alan Dodd's suggestion is nice, but there isn't always a lot of
experimental data available for a particular molecule we can compare
with -- or perhaps we want to begin with "good" parameters and then
see if our method can reproduce experiment. Anyway, for whatever
reason it isn't always possible t
All,
I may be in a hole of my own digging, here, but I've been trying to
simulate a large set of small molecules in explicit solvent. I'm using
the Amber GAFF parameters, converted over to GROMACS using our
amb2gmx.pl script.
The problem I'm running into is that for anything with a triple bond
(i
Dear Qin,
I believe the GROMACS manual recommends doing constant volume
equilibration prior to doing constant pressure equilibration. This is
what I always do. My understanding is that the Berendsen barostat
tends to be rather "picky" and crash (as you're seeing) when the
system is changing rapidl
Dechang,
>With the help of Yang Ye and Mark, I downloaded amb2gmx.pl to transform
> the topology from AMBER format to
> GROMACS. But the script requires an AMBER installation to work and I didn't
> have a AMBER package. How can I go on?
Mark pointed out one option -- rethink your choice of
> If it is fine, then how can I compare the result with ab inito's? Thanks.
Two things:
(1) Total and potential energies are only meaningful up to an additive
constant. So there is no reason in principle your potential energy (or
total energy) should be negative rather than positive. Just think
ab
Maybe this is naive, but:
(a) Are you using pressure regulation? (If so, with which barostat?)
(b) How do you know what you expect the pressure to be?
(c) By "fixed connections", do you mean fixed bond lengths? Are you
doing this using constraints?
David
On 8/13/07, Nicolas Schmidt <[EMAIL PROTEC
Hi,
> I just have a couple of things i want to clarify about the constrain
> distances i used. The distance I used to pull the ligand and receptor
> apart was a non-bonded distance between the amide nitrogen of the ligand
> and the oxygen carbonyl of the receptor (on both ends). looking at the
>
Hi,
> I have been reading your work about free energy calculations and it is
> impressive. I want to estimate binding free energy for a ligand/receptor
> complex and I would appreciate your valuable input on how to approach the
> system I am using. It is the first time I attempt free energy
> cal
around 2003 by Rodinger and Pomes,
and by David Kofke. Michael Shirts and John Chodera and I have another
review in press (Annual Reports in Computational Chemistry) and you
can find quite a few references in my latest paper:
http://dx.doi.org/10.1016/j.jmb.2007.06.002. There is also a recent
book e
Hi,
> I am trying to run some simulations in attempts to calculate binding free
> energy between ligands and a protein using the FEP method, but until now I
> did not have any success. I have been looking for bibliography over this
> subject, but, as you may know, there aren't many works about FEP
Hi,
I can't help with most of your e-mail, but I can comment on part of it.
After calculation of charges i am getting a small residual
charge of 3e-06 for my ligand. My ligand should be neutral.
Is this small residual going to impact my simulations?
You usually want to just round stuff so the
ECTED] on behalf of David Mobley
Sent: Tue 7/24/2007 5:00 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] FEP and soft-core potentials
Right. In fact, usually you would lose efficiency by using soft core
potentials for an electrostatic transformation over doing it without
soft core
Right. In fact, usually you would lose efficiency by using soft core
potentials for an electrostatic transformation over doing it without
soft core. The purpose of soft core is just to fix the problem with
disappearing/inserting atoms which have 1/r^12 repulsion.
David
On 7/24/07, Georgios Pata
You don't need virtual sites. That's for something else.
David
On 7/23/07, Wang Qin <[EMAIL PROTECTED]> wrote:
Hi everyone,
I am just thinking about if in FEP calculation, I have given the
position information for dummy atoms in the directory of [atoms], do I need
to give the directo
Berk,
Nearly anything can be done now in Gromacs :) (although sometimes not
easily).
Maybe I missed something, but according to me it should work.
Tabulated potentials work just like any other potential.
So they are soft-cored when the LJ-parameters or charge of one of
the two atoms in the pai
Berk,
Tabulated bonded potentials work fine with free-energy!
Or have you tried and they did not work?
Just to clarify -- it's not just an issue of free energy. We want to
do free energy calculations using the WCA separation and soft core
potentials.
Since tabulated nonbonded interactions wo
Hi,
I'm CCing the users list on this since it might be of general interest.
I
can't begin to tell you already how much help you've given me with your gromacs
user-list posts and free energy tutorial.
Glad I can help!
I was searching the Gromacs user list and came across a thread by you tit
Gerrit and David,
David wrote:
But wouldn't BAR work just fine?
And On 5/31/07, Gerrit Groenhof <[EMAIL PROTECTED]> wrote:
Hi Fiske,
From what I understand, you want to compute the free energy for
changing one or more atoms in the QM subsystem. I never considered doing
this because I do no
I think Erik is right, here. In a QM sense, what does it mean to have
an atom that is halfway in between, say, hydrogen and carbon?
You might want to look at what Wei Yang at Florida State has been
doing. If I remember correctly he has been making some efforts towards
QM/MM free energy calculatio
tests
with the free energy tutorial by David Mobley. I have matched his results
using a pure MM free energy run, and am now looking to move to the QM/MM
step.
I added the methane molecule as my quantum system and tried running the
first lambda. At the steep minimization step however I get a bus e
AIL PROTECTED]>
> Content-Type: text/plain; format=flowed
>
> I am trying to follow the free energy tutorial by David. Mobley, however my
> results are quite a bit off (after integration I get around -9.07) I have
> only used lambda's spaced at 0,0.1,0.2,... but surely I should
It seems the GROMACS web site has been hacked and perhaps loaded with
unpleasant things. May be advisable to stay away until the GROMACS
gurus let us know the coast is clear.
David
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code provides
serious advantages (parallelization? I see a lot of
warnings about this aspect, which with QM codes
belongs to the far past) over Amber code.
This is not endorsing any choice. I am still at the
window (without "s").
Cheers
francesco pietra
--- David Mobley <[EMAIL
David,
On 5/18/07, David van der Spoel <[EMAIL PROTECTED]> wrote:
Francesco Pietra wrote:
> Planning to use gromacs aided by antechamber/gaff for
> my recurrent need of new bonded parameters, and having
> noticed that antechamber's tutorial refers to Sybyl
> and Gaussian, my question:
>
> Is it
So what you really need to do, once you have worked out which forcfield
you are going to use, go back to the documentation / papers for that
particular forcefield, see how they generated the parameters, then use
that same procedure for the new parameters / molecules you want to
generated.
Strang
Jeroen,
However, in my opinion (assuming the total error should be calculated
from standard error propagation), the way g_analyze calculates the
total error is incorrect. It results in an overestimation of this
total error by at least a factor of sqrt((number of lambda points) -
1). This factor
http://www.alchemistry.org/FreeEnergyTools
On 5/15/07, [EMAIL PROTECTED] <[EMAIL PROTECTED]> wrote:
Hi David,
I checked the mailing list about conversion of Amber 8 or 9 topologies to
gromacs topology using in house amb2gmx code. I would be really greatful
if you can send me the code.
Thanks,
Justin,
I am interested in simulating some small molecules that involve oxygen in
aromatic rings (which thus bears a +1 charge). I tried to submit one of these
molecules to PRODRG, but got an error indicating that there were too many bonds
to O. I thought this issue might arise, due to the unu
All,
I'm trying to set up some storage-limited calculations. Two related questions:
(1) Is there a way to prevent dgdl.xvg from being written in free
energy calculations?
(2) Is there a way to prevent messages relating to COM removal from
being written to the log file? For example, I get stuff l
All,
I'm trying to write some wrappers to set up a project using standard
gromacs tools. Anyway, it looks to me like genbox is not handling its
path names correctly. In particular, here's what I did:
- Make temporary directory in which to run genbox
- Move to temporary directory, run genbox (rea
implemented the ability to write
out the potential energies for BAR into GROMACS, but I haven't heard
anything on this in a month or two.
Best wishes,
David Mobley
UCSF
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Hi,
I wish to simulate a ligand-protein system..I have used
the prodrg server to create the .itp file for my ligand. I
have done gaussian charge calculation for my ligand using
the chelpg method. how should i incorporate the gaussian
charges into my .itp file. should i copy the charges for
hea
Patrick,
My first
observation was that 1 ns seemed to be a minimum for certain lambda values
(e.g. lambda=0.70). I sometimes read in literature that some authors
used a few hundreds of ps, which seemed (to me) not sufficient for
proper convergence.
My experience is that the range of lambda=0.7
Erik and all,
I think this is a great idea. I've been working on (and plans to work
more on) a bit of a free energy wiki/tutorial page beyond what's
already available; depending on how this develops I can
transfer/combine with what's already on the wiki.
As you probably know there are lots of th
Chris,
>Right. I remember looking into this at one point, and I don't think
>the manual is correct; it looks to me like dihres.c handles
>periodicity properly. In particular, there is the followign comment in
>dihres.c:
It's good to see that this is actually a comment in the source code, I didn
Chris,
I have included my .top file. The relevant section is in [ dihedral_restraints ]
This file is a template that I use like this:
sed 's/PHI/${phi_value}/' template.top | sed 's/PSI/${psi_value}/' >
phi${phi_value}_psi${psi_value}.top
Just out of curiousity, which GROMACS version are you
Chris,
I'll have to assume you know what you're doing with using impropers to
calculate PMFs. I've done this using the dihedral restraints code.
Have you double-checked that? That's the first place I would look.
Otherwise, I don't have a great test system for you.
David
On 4/25/07, Chris Neal
This usually means the sections in your topology file are not iin the
correct order. In particular it is not happy with the order of
something in FE.itp, probably the position restraints section.
On 4/24/07, S O N A L I <[EMAIL PROTECTED]> wrote:
hi everybody,
i am working on melenin binding co
e meantime I can fix errors in the existing one or clarify.
David
Greetings,
Jeroen
> Date: Fri, 13 Apr 2007 09:18:21 -0700
> From: "David Mobley" <[EMAIL PROTECTED]>
> Subject: Re: [gmx-users] soft-core potential in combination with PME
> (sorry, agai
Berk and all,
I don't understand what David Mobley meant exactly.
There is no Coulomb singularity with soft-core.
Maybe one could have an unfortunate situation where the LJ
is already very soft, but the Coulomb not very soft,
which could lead to instabilities.
But I have never encountered
Another possibility is to use a force field which has already been
developed for small molecules that makes it easier to parameterize.
One example is the Generalized Amber Force Field for small molecules,
which can be used with the AMBER protein force fields (which, I might
add, have been ported t
st for GROMACS users
Subject: Re: [gmx-users] modify C6 directly in FF using sigma and
epsilon
David Mobley wrote:
> David,
>
> I'm using 3.3/3.3.1.
>
> Is there an easy tweak to the source code that would allow something
> like this? i.e. could I somehow easily tweak
David,
It seems that your best bet is to write that little Perl script to
convert the whole force field to C6/C12.
It's a little worse than that, since I still need to use the same
combination rules. I'll have to create a new "force field" where I
define all possible pairs of nonbonded interac
David,
I'm using 3.3/3.3.1.
Is there an easy tweak to the source code that would allow something
like this? i.e. could I somehow easily tweak the bit where it reads
the nonbond_params section so I can use an alternate combination rule
there by specifying, say, a different nonbonded parameter typ
Gromacs users,
I'm using a force field (the port of AMBER to GROMACS) which uses
combination rules (combination rule 2), etc. in terms of sigma and
epsilon. However, I need to be able to modify C6 directly (in
particular, I want to be able to set it to zero). Can anyone give me
any pointers on a
All,
I'm using the CVS version of 3.3.1 from last week, and am trying to
get the new pairs types Berk Hess has implemented to work for doing
decoupling. There's an old e-mail here on the subject, which is all
I've got to go by:
http://www.gromacs.org/pipermail/gmx-developers/2006-March/001530.htm
Alan,
Thanks. That's very helpful. I'm actually not using OPLS at all myself
-- I just stumbled across this really odd looking set of F- parameters
when troubleshooting for someone else. Anyway, your comments are very
helpful. I appreciate it.
David
On 3/31/07, Alan Chen <[EMAIL PROTECTED]> wro
Erik and all,
No, I don't think so, or at least it's not our typo :-)
It is quite common that ions end up with strange radii when you
parametrize for free energy of solvation, and in addition those
parameters are somewhat old (1984). Here's the extract from Bill
Jorgensens file that we translat
All,
I'm looking at the epsilon value in ffoplsaanb.itp (i.e. from CVS of
3.3.1) for opls_400, F-. It's lilsted as 3.01248e00. This is roughly a
factor of 10 larger than many of the other anions (i.e. Cl) and also
roughly a factor of 10 larger than the AMBER96 value (in the same
units) for F-: 2.
told that the ability is no
longer in GROMACS.
My question: Is the 3.3 manual in error when it says that g_rdf can do
this? If not, how do I use g_rdf in this manner?
Thanks,
David Mobley
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All,
I'm trying to figure out how to use tabulated nonbonded interactions
in GROMACS in conjunction with free energy calculations. While the
documentation addresses both separately, I am somewhat confused about
what would happen if I try to use both simultaneously. In particular,
I'm looking at t
Hi,
I am not an expert about heavy water -- but it does seem strange to me
to think that you could get "heavy water" just by changing the mass of
the hydrogens in a conventional water model. The *only* thing this
will affect is the kinetic energy and mass of water. Presumably
changing hydrogen to
pends on what you mean by correct. Formally,
the sum works out OK. And since the charge is uniform, it won't affect
the dynamics/thermodynamics. Of course, in real life there is no such
thing as a uniform background charge, and neutralization comes from
counterions. So in that sense it's incorre
d of boolean, and initialize it to -1.
Then cell getenv() (which can be slow) outside the init part, but
only if bDumpOnError==-1, and set it to 0 or 1. Finally edit the
conditionals for bDumpOnError to check if it is 1 instead.
Cheers,
Erik
On Mar 22, 2007, at 5:30 PM, David Mobley wrot
.
David
Cheers,
Erik
On Mar 22, 2007, at 12:59 AM, David Mobley wrote:
> Berk,
>
> What value does this need to be set to for it to work?
>
> Thanks,
> David
>
>
> On 3/20/07, Berk Hess <[EMAIL PROTECTED]> wrote:
>>
>> There seems to be an environ
Berk,
What value does this need to be set to for it to work?
Thanks,
David
On 3/20/07, Berk Hess <[EMAIL PROTECTED]> wrote:
There seems to be an environment variable NO_SHAKE_ERROR
Berk.
>From: "David Mobley" <[EMAIL PROTECTED]>
>Reply-To: Discussion
What version of GROMACS are you using? Also, your force constants seem
sort of small. Have you tried larger values?
David
On 3/20/07, Jonathan Khao <[EMAIL PROTECTED]> wrote:
Hello
My goal is to make dihedral restraints on the backbone of a bent
alpha
helix to obtain i
All,
Under some circumstances, mdrun writes out pdb files with previous and
current coordinates. Is there some way I can turn this off?
For reasons I'd rather not explain, I'm reprocessing a single
precision trajectory using the double precision version of mdrun, and
this results in pdb files be
David,
> I ask this, because I read on severel places (e.g. the online mdp
> options manual and in one of the tutorials) that you could use the -
> DFLEXIBLE definition to "allow steepest descent to minimize further".
> So I've used it for most of my minimizations up til now, assuming
> that was
th L-BFGS or other
minimizers aside from steepest descents, you're probably deforming
your water molecules, as well.
David
Thanks,
David
On 3/16/07, David Mobley <[EMAIL PROTECTED]> wrote:
> Bob,
>
> > Maybe this is a stupid suggestions butdid you check if your two
&g
S don't respect constraints. I think I'll try again with only
a steepest descents minimization (I think steep works OK with
constraints, if I remember correctly) and see if this helps.
Thanks,
David
On 3/16/07, David Mobley <[EMAIL PROTECTED]> wrote:
Bob,
> Maybe this is a stupid s
rt -- I just can't figure out why freeze groups isn't
working. (Incidentally, if I look at a movie of the trajectories run
with freeze groups, it does look like they stay frozen -- just not at
the positions I've specified).
Thanks,
David
On 3/16/07, David Mobley <[EMAIL PROTECTED]&
All,
I'm trying to be ultimately able to fix the position of several
arbitrary atoms (think of them just as spheres) in a simulation. One
would think this should be straightforward, but I'm having big
problems.
In particular, right now I'm just using two atoms, which I initially
have at a separa
If you're not planning on running parallel jobs I would go for the
higher clock speed. If you're running parallel, well, I am not sure.
On 3/13/07, Andrei Neamtu <[EMAIL PROTECTED]> wrote:
Hello,
We are in the process of building a cluster on which GROMACS will be
the main computational engine
All,
Just in case there are those on here who don't know, Chimera is a nice
viewing program for molecular structures, trajectories, etc. It also
has a lot of bells and whistles relating to preparing structures for
simulation (i.e. building in missing residues/loops, etc).
David
On 2/27/07, Eri
You might want to start with an introductory simulation book like the
one by Andrew Leach.
David
On 3/1/07, Mark Abraham <[EMAIL PROTECTED]> wrote:
Shulin Zhuang wrote:
> Great thanks. Would you like to give me several papers on this field.
No, I don't have any, and that's your job :-)
Mark
Michael,
2) i get the same results when using md+NH thermostate
with two thermostates, or langevin dynamics (sd), the
error bars are somewhat larger with sd though.
Well, that's fine -- but it doesn't mean that everything is OK. NH has
known problems. There is also a bugzilla relating to this
Arneh,
How does one build a topology using a different force field (say for
instance, oplsaa)? Is there a simple way to do it,
I think OpenEye (or someone else, I forget whom) has some sort of
automatic parameterization tool for OPLS that automatically generates
parameters. Of course, this is
Michael,
I calculated the free energy of solvation of water
(basically its chemical potential). The literature value for TIP3P
water, which I used, is about -6.3 kcal/mol -
I get something like +2.5 (!) ...
I suggest doing the charging component separately. I *think* this is
more efficient tha
Chris,
Does anybody have any experience with DispCorr=EnerPres and a
heterogeneous system (e.g. aggregation of detergents to form micelles)?
What about membranes? Even if it is not a perfect method, is an
imperfect assumption of homogeneous LJ density beyond the cutoff better
than entirely ignor
Michael,
Yes, the units are kJ/mol/nm^2. I think the default values in
posre.itp are designed for something like equilibrating your water
with the protein held rigid or something, so they are pretty big.
(This is not insanely large, though -- keep in mind it's only 10
kJ/mol*A^2).
David
On 1/3
All,
I'm having a perplexing problem(?) with a double-precision version of
GROMACS 3.3 I just compiled. I'm using it to reprocess a single frame
of a trr file using mdrun -rerun and a particular mdp file, topology,
and gro, and looking at the resulting energies. For some reason, my
coulomb-14 and
Paolo,
can anybody tell me what happens to lennard jones parameters and coulomb
charges varying the lambda parameter?
I know from the manual how the interaction is rescaled but what i'm
concerned in is now how C6 C12 and charge vary with lambda.
What happens then to the interaction between two
Hi,
You are probably starting your runs from a non equilibrated structure.
I don't think this is necessarily true: For example, you could be
seeing the crash you describe on the first step of equilibration...
However, you might want to make usre you have thoroughly *minimized*
at each lambda v
I agree that this would be a good idea. We would need to think
carefully about how to validate it though.
On 1/30/07, Jay Mashl <[EMAIL PROTECTED]> wrote:
On Tue, 30 Jan 2007, David van der Spoel wrote:
>
> Mark Abraham wrote:
>> Florian Haberl wrote:
>>
>> > > 1) how can i explaine "pH" int
Hi,
The test I ran was just rotating a side chain of an amino acid residue
over one of its dihedral angle 360 degrees with dihre_fc = 8000.
OK. I was doing a val sidechain.
I originally thought fc = 8000kJ/mol unit^2 would give fluctuation of
about the half the unit size since I use fc = 800
Chris,
On 1/23/07, Chris Neale <[EMAIL PROTECTED]> wrote:
Quoting manual-3.3 page 58
"Note that in the input in topology files, angles are given in degrees
and force constants in kJ/mol/rad2."
I assume here that force constants refers to dihre_fc. However, although the
test
PMF's that I have g
Ignacio,
OK, I do basically the same, but instead of starting the second
equilibration from the same structure for each lambda, I start from the
final structure of the previous lambda (still, I equilibrate before
production for each lambda). I don't see why this strategy should be
worse the one
Stéphane,
I'm willing to do some FEP using the slow groth approach available in
gromacs (as of 3.3.1). While retrieving articles and the mailing list, i
found out there where arguments against sequential runs (particularly
for avoiding the hysteresis problem), and other against parallel runs.
Anirban and all,
I am putting this on list since I don't want to make a full-time job
out of answering free energy questions (although stay tuned for a more
extensive tutorial) and hopefully I can avoid answering the same
question more than once.
I have seen your posts on gromacs mailing list r
ith a finite difference scheme (f(l+dl)-f(l))/dl or some such), but
there's no reason to do that, since the derivative approach is
simpler.
Isn't this clear from the manual? As much as I think the manual is
unclear sometimes, this isn't one of those times...
David
Best regards,
Maik,
I'm trying to do a simple FEP within a simple protein, which seems to
make things simple...but as you may expect...it is anything else than that.
What I'm trying to do is morphing a Tyrosine into a Phenylalanine in OPLSAA.
Therefore the CZ is changed from the type of TYR to the type of
y the code.
> > >
> > > I am not sure if that's helpful at all, as I'm not entirely sure
> what
> > > problem you're having. After all, whenever you do TI calculations
> in
> > > GROMACS, the code gives you back dG/dl (or dH/dl, or dA/dl) for
ound in rtp database in residue TRP (Joern Lenz)
> 5. Re: Fw: gmx-3.3.1_cpmd-3.11.1 with mpirun (Pradip K Biswas)
> 6. Re: (dH/dl) calculation (David Mobley)
>7. Molecular volume (Mohan Boggara)
>8. Re: Molecular volume (David Mobley)
>
>
>
---
I think in 3.3, there was a new option added to g_sas that allows you
to calculate the solvent accessible volume, which may be what you
want. Try searching the list.
David
On 11/6/06, Mohan Boggara <[EMAIL PROTECTED]> wrote:
Dear users,
Is there a way to calculate molecular volume of small sol
ered that above), or are you trying
to figure out how to use it? If you're confused about how to use it,
try to ask a question that relates to the specific issue you're
confused about.
Best wishes,
David Mobley
UCSF
On 11/5/06, Mauricio Sica <[EMAIL PROTECTED]> wrote:
Dear ex
Komath,
2. What is the common practice to deal with breaks in the protein chains? Is
it good to terminate each fragment with acetyl groups?
If you are referring to missing residues, these are, of course,
typically present in the protein itself, but just not resolved in some
crystal structures.
Narcis,
You might try doing a literature search, or be more specific with your
question (i.e., what would you like to know about? What do you hope to
learn by doing such study? (Are you trying to calculate/estimate
binding free energies, or just study binding modes? Do you already
have co-crystal
Soren,
I don't have much (any?) experience with the pull code. But I've done
some computing of PMF's that is somewhat similar to this using just
orientational (angle and dihedral) and distance restraints,
appropriately defined. That might be an option.
David
On 10/19/06, Soren Enemark <[EMAIL
Paolo,
As for the LJ decoupling,I cannot obtain a smooth curve and dG/dlambda
has large deviations even if I use sc_alpha = 0.5 and sc_power = 1 as
suggested by Shirts.
This doesn't typically give a smooth curve in the sense of
featureless, like the electrostatics curve. However, the particula
Hi,
Dear gromacs users,
I am trying to use FEP method for the calculation of relative binding free
energy of peptide-protein complex. I am using gmx-3.3.1.
As per previous discussions on the mailing list, i learnt that i need to
do two different sets of simulations for my case. first set will
This may be naive, but have you defined POSRES_WATER, i.e. in your top
or mdp file? If not, the position restraints will be unused.
On 9/28/06, [EMAIL PROTECTED] <[EMAIL PROTECTED]> wrote:
Hi all,
I am facing a problem in constraining the crystallographic water molecules
during invacuo simulat
Ignacio,
Thanks for your reply. I had actually search the archives but didn't
find any clear answer (maybe the search was not so good)... You mention
this is a problem with PME, would plain Ewald or even Reaction-Field be
less problematic in this case? And how large do you estimate the cutoff
sh
Ignacio,
Is there some precaution or additional term I should take into account
when calculating the free energy of solvation for a charged molecule?
I plan to make the molecule "disappear" whith lambda moving from 0 to 1
and then perform a thermodynamical integration, this seems to work
reaso
Kanin,
On 9/11/06, kanin wichapong <[EMAIL PROTECTED]> wrote:
Hi All,
I would like to know how to make a distance constraint between the
ligand and the protein. If I just merge two chain together by pdb2gmx, it
can done if the two chain are both protein. However, if it is a ligand and
protei
Allow me to take this opportunity to reiterate that the ability to
only apply distance/angle/dihedral restraints between atoms in the
same "molecule" (in the topology sense) is really lame. It would be
really nice if GROMACS could handle absolute atom numbering for
restraints (i.e. using the numbe
Manohar,
I don't have a tutorial, but have done a bit of this. I think GROMACS
has some built in tools for WHAM, but I have never used these. I just
apply harmonic restraints to pull a ligand out of the binding site and
then use my own WHAM code to analyze the data.
In terms of picking the numbe
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