Dear Acoot:
You should be able to answer this one yourself. Moreover, you are
doing yourself a disservice by relying on the mailing list to do your
work for you because you will eventually need to learn how to find
answers to these things on your own.
Please remember the following:
1.
Dear Acoot:
The idea of convergence is this: start a large number of simulations
from different conformations, analyze some quantity over time in each
simulation, and when the deviation of the average value of that
quantity from each separate simulation is less than the time-variance
Dear Users:
I was previously able to compile template.c after I compiled gromacs
with autoconf. I was unable to compile templae.c, however, I used
cmake to compile gromacs. This is from gromacs-4.5.4.
I tried cmake . in the template directory with no success:
cmake .gpc-f102n084-$ cmake .
Dear Acoot:
I'll reply to general topics, not to the tutorial in particular.
If the opening is not large enough to allow the peptide to exit, then
the surrounding protein will need to change its conformation to permit
unbinding. This can happen, but you need (a) to have sufficiently long
It is not clear to me how one would do this with MD. The only thing
that I can think of doing in gromacs is to create a virtual particle
that is placed at the center of the protein and then apply forces
along the vector from this virtual atom to each of the Ca atoms. You
would need to
I didn't follow this whole thread, but I sometimes need to turn off
all constraints when doing minimization. In fact, for that reason I
entirely stopped ever using restraints during energy minimization. In
extreem cases, I have had success also by forcing the water to be
flexible with a
I disagree.
What one is generally trying to obtain with elevated temperatures is
enhanced sampling, not temperature-dependent properties. I believe
that even TIP4P-EW is not very good at getting the properties of water
correct at 600 K, temperatures that are commonly used during replica
You should absolutely publish this. it would be of great interest. You
can mitigate your chances of running into problems with the overview
by sending a version of the manuscript to the developers of each
software and asking them to provide a short paragraph, each of which
you could
Dear users:
can I use a .tpr file created with an intel icc compilation of grompp
and then do mdrun under a pathscale compilation of mdrun ? (same
version of gromacs)
I'm wondering if there would be some strange behaviour. It seems like it
should be ok, but I wanted to be sure.
I ask
= 3.467 ns/day
pgi 11.8 = 3.092 ns/day
pgi 11.8 with -tp istanbul -fast = 3.156 ns/day
Again, thank you,
Chris.
-- original message --
As far as compilation hanging...maybe hand-compile that .o with less
aggressive optimization flags, then try make again?
MZ
On Tue, Dec 6, 2011 at 2:20 PM, Chris
What you have done seems alright. I didn't look closely enough to be
sure though. One of the good things about this method is that you can
easily test it yourself. To do this, create two different .gro files,
one containing the atoms from one ff and the other containing the other
atoms. For
Dear Users:
I have 50 simulations that are all the same, except with different
random seeds for velocities. All were running fine for 24 hours. I
canceled the running jobs and resubmitted them as part of beta testing
a new cluster. All 50 started. I then canceled one of these jobs soon
I am using a new cluster of Xeons and, to get the most efficient
compilation, I have compiled gromacs-4.5.4 separately with the intel,
pathscale, and pgi compilers.
With the pgi compiler, I am most concerned about this floating point
overflow warning:
...
[ 19%] Building C object
Well, the positive way of looking at this is that it appears that
nobody has ever done it before. If somebody has done it (in charmm for
instance) then you might be able to convert the format of your .xtc
and use their tools to analyze it.
Good luck,
Chris.
-- original message --
Thank
Do you mean that you do constrained position simulations and want to
know how to process the force? If so, read about thermodynamic
integration (TI). I mostly work with US and position restraints, but
for absolute constraints I believe that you should take the average
force at each
It's more useful if you provide more information. What was the .pdb
file (can I download it from the pdb databank?) was there water? what
version of gromacs? was it compiled in double or single precision?
what were your mdp parameters?
-- original message --
There is something not quite
When people do this for lipid bilayers, they compute depth-dependent
diffusion profiles (often diffusion is computed separately for lateral
diffusion and diffusion along the bilayer normal). Sounds like you
might do something similar. I doubt that the standard gromacs tools
will do this
There is rounding because of angstroms vs nanometers and both files
maintain 3 decimal places (see below).
The intention of pdb2gmx is not to get a .gro , but to get a .top or
.itp file.
I see your point, but I don't think it matters. If you really need
that precision, then I'd think
1. why repeat the calculations? If you're talking about simulations
then there is no need to repeat them due to this. You will get
different answers with the same starting coordinates if you simply
change the initial velocities. If you're talking about instantaneous
energy calculations
You could create an atomistic charged wall by placing atoms in a plane
or grid and using position restraints or freeze groups to keep them in
place. You could them use the pull code to restrain part of the
protein relative to an atom(s) in this atomistic wall. You could
obtain your desired
Dear Vijay:
Can you please provide evidence for your claim that the harmonic
potential is not applied properly, since you may decide to use
pull=umbrella once you have set that up correctly. Importantly,
movement out of the unit-cell is not a problem, as discussed a lot on
this list.
If you add position restraints to your DPPC molecules, then you are
changing your effective order parameter. The PMF for the solute along
the normal to a restrained bilayer will have a different shape than a
PMF for the solute along the normal to an urestrained bilayer. Whether
or not this is
Thank you Tom!
Aqvist_A12 = sqrt(gromacs_C12*10^12/4.184)
Aqvist_A6 = sqrt(gromacs_C6*10^6/4.184)
(equation verified based on the SPC water oxygen parameters, also
listed in Aqvist).
This reference (Aqvist, J (1990) J. Phys. Chem., 94 (21), pp
8021?8024) should probably be noted somewhere
Dear users:
does anybody know where the OPLS magnesium parameters are from? As far
as I can tell, they are not in Jorgensen 1996 or Kaminski 2001, In
spite of the fact that many simulation studies reference these papers
for their magnesium opls parameters.
In fact, I do not think that
The criteria are the same for any type of simulation. Generally, you
must show that, as far as you can tell, the values that you derive are
not going to change if you run the simulation a lot longer. Different
quantities converge at different rates, so ideally you should check
them all
Dear James:
Next time, please specify exactly what you did in enough detail for
somebody else to reproduce it, much as in a manuscript. e.g. there is
no dmpc.gro in that website. I can guess what you did, but that is
not ideal.
I took a look at the files that I suppose you used and the
You need to evaluate convergence yourself for any simulation. I
suggest doing the whole thing twice (or more) with different starting
conformations. Also, look at the PMF from block averaging (generate
one PMF from the 0-2 ns data, another from the 2-4 ns data, and so on)
and see if there
Speaking of which, I think that all programs should by default list
-hidden when they are run with -h so that users are aware that there
are hidden options and know how to access them. The -h output could
clearly indicate that such options are not fully tested, etc.
Chris.
Justin A.
Dear Shilpi:
Can you use something like this?
pull = umbrella
pull_geometry= position
pull_dim = N N Y
pull_vec1= 0 0 0
pull_start = no
pull_ngroups = 1
pull_group0 = PRO-1
pull_pbcatom0
, i haven't outputted
md.log file for each window.
Kind Regards,
Chetan.
From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On
Behalf Of Chris Neale [chris.ne...@utoronto.ca]
Sent: 19 September 2011 17:59
To: gmx-users@gromacs.org
I have used tpbconv -until to extend a US simulation without error, and I
assume that tpbconv -extend is also fine for US simulations.
1. Are you using the same version of gromacs mdrun as you used to produce your
.cpt file initially?
2. what happens when you run gmxcheck on the .cpt file?
You still haven't provided all of the relevant information. For
example: what ff are you using? But please don't just sent that
information now... better for you to read about how to develop a good
post and next time be suer to include enough information that we could
reproduce the problem
the errors in free energy differences
on DOPC were rather small, the errors on octanol were strangely high.
We have prepared smaller slabs (as Chris Neale suggested) of octanol with
comparable size of box and we have also tried to analyze the position of
centres either via pullx.xvg provided by pull
Zhijun:
This is a question for the gmx-users list, so I will address it there.
Please keep this type of question on the users list.
1.Are hydrogen ion H+ probably bind to POPC's phosphate O atom when
I randomly assign it?
That sounds a lot like something that you can test. Na+ ions do
I think it's reasonable for you to post this on-list. It's not your
method and you got help here and somebody else might want the same
help in the future.
Chris.
-- original message --
ABEL Stephane 175950 Stephane.ABEL at cea.fr
Thu Sep 1 22:22:27 CEST 2011
* Previous message:
I am glad that the pressure coupling intervals have been identified as
a source of instability for poorly equilibrated systems as I was
unaware of that. Still, the fact that the SD integrator also solves
the problem also suggests that this is simply a poorly equilibrated
system. I am not
6.30e+01 = 63
-- original message --
My system had a no zero total charge:
System has non-zero total charge: 6.30e+01
I used genion to neutralize the system by adding 6 CL ions.
After updating the topology file, the system still seems to have the
same problem.
It still has a
That all makes sense Tsjerk.
I wonder if mdrun terminations based on LINCS warnings should come
with an additional message to explain that one may try running for a
while with nstpcouple=1.
Also, I'm still a little curious about a question that Itamar asked a
few posts ago:
If this is
Dear Stephane:
We discussed this in April:
http://lists.gromacs.org/pipermail/gmx-users/2011-April/060839.html
At that time I also provided a method for you to verify your files
(and the method in general).
It is possible for you to answer your gen-pairs question by looking
into the
In addition to Justin's comment about g_order being incorrect for
unsaturated carbons, you won't ever get numerical agreement with
g_order, even for saturated carbons, because g_order does not use your
explicit hydrogens. g_order uses the positions of the carbons to
rebuild the hydrogen
It's a typo, but it's in the discussion and not in the do this part
of the method so I decided not to mention it. I don't see another
question in this post, so I hope that you have figured things out.
Note that I have never tested the exact implementation that I
suggested in that April
That seems possible Mark. I had actually assumed that Itamar extracted
a .gro from the 4.0.7 simulations and created a new .tpr with 4.5.4
grompp. If that was the case, then I would still be surprised that it
had instability problems. One sees a lot of charmm papers where people
do slow
Dear Ramya:
Are you simulating all-atom lipids (with explicit hydrogen atoms on
the acyl chain)? If not, then you missed a step in your description of
what you have done (g_order, for example, ignores explicit hydrogen
atoms so that it can act on united atom lipids).
Not sure why PBC
Itamar:
We really are trying to help. I think that perhaps you don't grasp how
difficult it is to help without being able to access the simulation
directly. Therefore we have ideas and we ask you to do specific things
that are going to move us toward a solution, either by finding answers
Please provide very much more information. Unless somebody has run
into the exact thing that you are describing it is currently
impossible for us to help you.
One thing I can suggest now is to construct histograms of the sampling
from the coord.xvg files yourself with some scripting and
Try running for longer and look at the convergence of the temperatures
over time. I suspect that what you are reporting is actually just
statistical noise.
I am not sure about using the sd integrator and defining multiple
temperature coupling groups... If you define the same temperature
Your density seems to be about 70% of what I would expect. Are you
sure that this is not just a normal case of a poorly equilibrated
system crashing? That matches with what you say about the density
growing (although perhaps it has more to do with poor equilibration
than with mixing, as
g_density is not compatible with constant pressure simulations. You
must modify it to construct the bins outward from the bilayer center
when doing NPT:
http://lists.gromacs.org/pipermail/gmx-users/2010-November/055651.html
Further, trjconv -center is misleading. I actually lost a lot of
That's 9 times in the last 20 days that a single user has hit the list
with an auto-reply that seems a lot like an advertisement. Can
somebody please ban this user?
The most recent example:
http://lists.gromacs.org/pipermail/gmx-users/2011-August/063991.html
--
gmx-users mailing list
Slightly off-topic, but for all but the smallest systems, I get a
further 10% efficiency by running a 16-process mpi job on an 8-core
machine. I suspect that the story is the same with threads. Thus, on a
16-core node, you could try starting 32 threads. Note that this will
report a 2x
You'll need to provide a much better report than this if you want to
receive any useful help.
Copy and paste the exact commands of what you did
Copy and paste the exact log file and error messages
Do this for 4.0.7 and 4.5.4, for which I trust that you have been
using exactly identical test
run an EM with flexible water. I often find that this is the only way
to get a stable system. 500 steps of steep with define=-DFLEXIBLE (or
different depending on your water model I think) should be enough.
Chris.
Hi Chris and Justin,
On 18/08/2011, at 9:36 AM, Justin A. Lemkul wrote:
OK, here's my last few ideas:
1. Please try to repeat this with gen_vel set to the same value as
your temperature coupling
2. Can you reproduce this in serial?
3. Can you reproduce this with the sd integrator?
4. Can you reproduce this with a simpler system? protein in vacuum or
just
Currently, gromacs4.5.4 gives a segfault if one runs mpirun -np 8
mdrun_mpi -npme 120 with no warning of the source of the problem.
Obviously npmennodes is a bad setup, but a check would be nice.
Thank you,
Chris.
--
gmx-users mailing listgmx-users@gromacs.org
Dear Krapnik:
1. please make the test cases identical, that means doing a simulation
that you may not really be interested in so that the solutes are the
same for both lipid and octane. It also means setting the
displacements to similar values in my opinion (because perhaps the
problem
This is fixed, just posting for posterity.
If one wants to run pdb2gmx with -vsites hydrogens on gromacs 4.5.4 or
4.0.7 while using the oplss ff, there is the error message:
Fatal error:
Can't find dummy mass for type opls_242 bonded to type opls_238 in the
virtual site database (.vsd
I agree that Justin is probably correct, although constraints should
technically work just fine with a highly dynamic reference group. Any
problems should show up as the system blowing up, but not in correctly
setting the position. I think that the problems can arise, however,
when you
I think that you have a misconception about what g_spatial does. For a
system with many type A and many type B, you need to average over all
of one type as the central solute to compute an rdf, and perhaps that
is what you want for your sdf. g_spatial, however, does not do any
fitting.
Here's the totally wasteful way for you to get what you want:
1. for each molecule in type A: trjorder everything around that
molecule and output only the closest N atoms of type A and the closest
M atoms of type B. Ensure that the coordinate order is: your central
molecule of type A is
I've never actually reweighted with F-values. These are the values by
which the component PMFs are shifted during WHAM after debiasing the
umbrella potentials.
Look at equations 6 and 7 in The multicanonical weighted histogram
analysis method for the free-energy landscape along structural
format your data for 2D-WHAM with 1D being the distance and the 2nd-D
being your other coordinate of interest. Specify a value of zero for
the force constants for your 2nd-D. Run 2D-WHAM. Boltzmann project the
2D PMF onto your 2nd-D.
I think you can also do essentially the same thing by
I don't see why the box-type makes any difference whatsoever. It is
possible that if you use a rhombic dodecahedron, you may reduce the
system size, thus simulate more ns/day, thus converge faster, but that
should be the only effect. I would be interested to hear more from
Justin about how
I see now what you mean. As it happens, I doubt that this would have
caused the problem since no force was applied on X and Y dimensions,
so it would require that there was a PBC-based distance degeneracy
along Z, although this is of course possible and hopefully Rebecca
will answer this
600 GB of memory? I highly doubt that you have that much memory
available. Are you sure that this is not a typo? Can you please post
evidence that you have =600 GB of memory available? It is common for
clusters to disallow an individual process from using 10% of the
total memory on a
Thank you Rossen and Roland.
I was able to obtain the source but not compile it. It would be
appreciated if you can offer any suggestions.
I obtained gromacs via:
git clone git://git.gromacs.org/gromacs.git
git checkout release-2-0-01
But I can not compile it. When I cd src and run make or
In the middle of my last post, it should have stated:
I moved the **include** directory into src/ and that solved the error
messages that I was obtaining, but now make errors with:
Sorry for the confusion,
Chris.
Quoting chris.ne...@utoronto.ca:
Thank you Rossen and Roland.
I was able to
Dear Adam:
I have a number of questions listed below. But first, I think it would
be useful if you explain exactly what you want to accomplish and how
you tried to do this with non-modified code and what problem you ran
into that caused you to modify the code. After you outline that,
Actually, this depends on what you are trying to achieve. If you
simply want to obtain the standard binding free energy, and somehow
you know that the bound state is represented by your umbrella at
dist=0 (via a crystal structure, for example), then using additional
restraints is common,
Dear Users:
Has anybody else looked at simulation speed (ns/day) over the segments
of long runs? I always benchmark and optimize my systems carefully,
but it was only recently that I realized how much variability I am
obtaining over long runs. Perhaps this is specific to my cluster,
Dear Lishan:
First, it would be great to see some evidence that you have tried to
do this yourself before posting. Your I think makes it a possible
waste of time for us to suggest a resolution to a problem that may or
may not exist.
Second, if indeed it is a problem, perhaps you could
Try Loopy. You can get it to build termini in addition to loops.
http://wiki.c2b2.columbia.edu/honiglab_public/index.php/Software:Loopy
Nevertheless, I'd suggest simply omitting that part of the protein and
capping your new terminus to remove the charge. You will have more
difficulties
Thank you Mark, I really appreciate it.
-- original message --
On 20/06/2011 1:23 AM, chris.neale at utoronto.ca wrote:
Dear Mark:
Now I am confused. Your first post indicated that P-LINCS did the
angle constraints. But here you indicate that the v-site algorithm
does it.
No... my
Dear Mark:
Now I am confused. Your first post indicated that P-LINCS did the
angle constraints. But here you indicate that the v-site algorithm
does it. This is probably because my first post was incomplete about
the method that I used.
Can you please confirm my current understanding?
Dear Users:
If I create the topology of a peptide like this:
pdb2gmx -f protein.gro -vsite hydrogens
And then simulate it in vacuum, is lincs used at all? I believe that
it is, as if I use a timestep that is too large then I get LINCS
warnings about angles rotating more than 30 degrees,
Thank you Roland.
I did use:
constraints = all-bonds
lincs-iter = 1
lincs-order = 6
constraint_algorithm = lincs
From looking at the manual, I figured that angle and bond constraints
would all be done by LINCS if I had done (A):
pdb2gmx -vsite none
constraints = h-angles
(a combination
For the quick fix:
1. run genion on your topology that does work. Look at this to see the
format of the ion atom and residue names
2. Pick a few waters in the structure containing the ligand and
replace the OW by the ion and remove the hydrogens, then fix the
number of atoms on the
Dear Nilesh:
You don't seem to have made any progress since Mark gave you some
reading hints. Your best chance to get a useful response follows the
general form:
1. I want to do A.
2. I tried method B, here are the exact commands that I used (copy and paste)
3. With that method, I obtain C
Dear Hsin-Lin:
The first thing that comes to mind is using very high temperatures with NVT.
Obtaining the desired denatured state is a complex challenge, but you
might try this paper:
Phys. Rev. Lett. 93, 238105 (2004)
Reversible Temperature and Pressure Denaturation of a Protein
Fragment:
Dear Hsin-Lin:
I am no expert in this area. I am just saying that if you get
densities that are way too low in NPT, then you might alleviate this
problem with NVT.
In fact, I would personally do this in vacuum without pbc and use the
sd integrator. Then you can sample extended
From g_hbond -h
OH and NH groups are regarded as donors, O is an acceptor always, N
is an acceptor by default, but this can be switched using -nitacc.
Dummy hydrogen atoms are assumed to be connected to the first
preceding non-hydrogen atom.
The two groups are to find hbonds between
Dear users:
I am trying to process a trajectory so that a group of molecules has
their center of mass at a constant position in Cartesian space. I have
not been able to figure out how to do this.
The reason that I would like this is that I have conducted umbrella
sampling of a solute
I solved it. It was my own error to assume that trjconv -center
centers the COM. Actually, it centers the value of (min+max)/2 in each
dimension.
I can modify trjconv locally to do what I want.
Thank you,
Chris.
static void center_x(int ecenter,rvec x[],matrix box,int n,int
nc,atom_id
Dear Matthias:
Did you run trjconv -center -pbc mol at some point before running
g_density? With pbc, there are multiple ways to put the center of a
system at the center of the box. This can lead to having the water
slab in the center of the unit cell and the bilayer on the top and
Unfortunately, I don't think that there is any way to use this data
(and only this data) to derive the PMF along z. The way that you did
your US, the PMF along z is convoluted with xy motion. You can get the
PMF along the reaction coordinate that you actually used (XYZ) using
standard WHAM
Dear Aditi:
you can do this by scripting gromacs to run in short segments,
modifying the force constant for each run. e.g.:
#!/bin/bash
for((i=1;i=100; i++)); do
let j=i-1
grompp -f ${i}.mdp -p ${i}.top -f ${j}.gro -o ${i}.tpr
mdrun -deffnm ${i}
done
You only need to use some more
Dear users:
Does anybody have the source code for gromacs version 2.1? I would
like to check the original source of g_order, but only versions 3.0
and above are available on the gromacs website.
Thank you,
Chris.
--
gmx-users mailing listgmx-users@gromacs.org
I have patched g_order version 4.5.4 to compute the order parameters
in a different way. Despite trying, I don't understand the original
g_order implementation. In the version that I am providing, the
hydrogens are explicitly built and the coordinates of these hydrogens
are output to
Dear Thomas:
I agree with your conclusions about g_order.
My usage of the Berger POPC lipids in combination with the g_order
command (as per the instructions in
http://www.gromacs.org/Documentation/Gromacs_Utilities/g_order )
yields order parameters of 0.193 and 0.051 for the first and
Dear Dimitar:
to me, your posts have indeed appeared very aggressive. So much so
that there are probably many people who can help who have decided not
to bother due to what they perceive your tone to be.
On to the problem at hand: I agree with the previous suggestion that
you may have
1. you're not doing energy minimization as your title suggests, please
use a better title:
integrator = md
2. generally, when you have a problem it is useful to try to simplify
the system (e.g. get rid of those tables) and try to reproduce the
problem with the simplest system possible
1. Determine some mathematical calculation that you want to apply to
some atoms.
2. make a .ndx group that includes all of those atoms
3. Run g_traj -ox to output the coordinates of those atoms
4. Apply your mathematical calculation using awk.
-- original message --
Can anyone tell how to
Dear users:
with assistance from Berk on the developers list, I am posting a
work-around to this issue.
the nonbonded interactions calculate the nonbonded distance, r, using
the gmx_invsqrt function. Thus, the optimized kernel from 4.5.4 and
4.0.7 both give nan when two charges occupy
If I read between the lines correctly, you know how to do this in
gromacs, but you wish that you got a big speedup from freezing most of
the atoms in your system. If that is the case, then I think that
gromacs can not help you in its current form. Therefore, I suggest
that you try the
Regarding gen-vel=no as discussed here:
http://lists.gromacs.org/pipermail/gmx-users/2011-May/061151.html
I would caution against the general use of gen-vel=no and then
coupling to a temperature of 300 K with the Berendsen thermostat. One
problem that can arise is concerted unfolding.
Dear Users:
Using gromacs 4.0.5, I find that there are at least some cases where
some type of disk error can get propagated through both my.tpr and
my_prev.tpr, complicating restarts. This used to be a bigger problem in
gromacs 3, and I don't recall ever seeing it in gromacs 4 so I thought I
Apologies: my.tpr and my_prev.tpr should have read my.cpt and my_prev.cpt.
On 11-05-05 12:36 PM, Chris Neale wrote:
Dear Users:
Using gromacs 4.0.5, I find that there are at least some cases where
some type of disk error can get propagated through both my.tpr and
my_prev.tpr, complicating
generally, look at mdout.mdp from grompp
-- original message --
In my input file if I don't specify constraints then
What is default
constraints=none
constraints=all bonds
NIlesh
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Your windows are restrained. The PMF that you get out of WHAM is a
representation of the relative sampling after removing the umbrella
biases. Sounds like you are saying that you look at the still-biased
trajectories and you see different a different distribution of states
than you do in
yes it will, and so will it affect the profile if water molecules or
ions go in when both chains are absent.
You'll need to determine what question you are trying to answer and
also think pretty hard about what your PMF really means in the context
of this system.
Chris.
-- original
Dear Gavin:
I'm not seeing a lot of effort on your part to answer these questions.
I suspect that you can answer some of this. Good luck!
Chris.
-- original message --
The current simulations are currently in vacuum. Does the following mdp
file seem ok. Note that this is a production run
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