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
bottom
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 conformatio
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 gro
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 second
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, but
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 t
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 second
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?
Th
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 conve
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, ac
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,
which
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 u
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,
plea
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 o
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 head
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 pa
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 re-
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
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. g_sd
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 fir
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 have
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 is
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 files
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 npme>nnodes is a bad setup, but a check would be nice.
Thank you,
Chris.
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/ma
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:
c
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 wate
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 large
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 tim
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 listgmx-
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 you
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 for
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 plo
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 woul
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
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 su
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 non-zer
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 manua
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 pos
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 em
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 hea
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: [gmx-us
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 not
sly, while 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 provid
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
I believe the first mention of a twin-range cutoff was:
H. J. C. Berendsen in J. Hermans (Ed.): Molecular Dynamics and Protein
Structure, Polycrystal Book Service, Western Springs, IL, USA 1985. 18
There is also a nice discussion of it here:
W.F. van Gunsteren and H.J.C. Berendsen. Agnew. Ch
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?
3.
, 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@gromac
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
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. Lemkul
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 i
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
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 inde
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
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 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. Neve
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 a
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
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 constrai
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 ri
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 for
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 that
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 then
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 yo
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 src/gmxlib/
Dear users:
My compilation with the pathscale compiler hangs for over an hour on the
gmx_rms.c.o file (or perhaps the one that comes next).
[ 83%] Building C object src/tools/CMakeFiles/gmxana.dir/gmx_principal.c.o
[ 84%] Building C object src/tools/CMakeFiles/gmxana.dir/gmx_polystat.c.o
[ 84%
Dear Szilárd:
Thank you for the advice. I made a mistake when I said that I was
using new Xeons. The new cluster is actually composed of AMD Opteron
Magny-cours 6172 (12-cores at 2.1 or 2.2 GHz grouped as 24-cores per
node). It was because of the AMD architecture that I was trying with
th
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
af
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 eac
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 beca
.12.1 = 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
You are experiencing problems because popc is not a protein and
pdb2gmx is currently only set up for proteins. More importantly, you
already have popc.itp so you don't need to run pdb2gmx on it.
I suggest that you read the manual more closely about setting up a
simulation and clarify your
If I understand correctly, the rebuilt residues do not connect to each
side of the gap correctly? You state about gaps: "actually it
shouldn't appear after minimisation.", but it is not necessarily true
that EM is capable of bringing the residues properly close together. I
think you mean th
Please keep this on the mailing list.
I use OPLS + tip4p for protein in water, then I use the Berger lipids
downloaded from Peter Tieleman's website using some special
considerations for scaling of the 1-4 interactions. You can find some of
my posts on that topic via searching for opls and ber
To wrap up combination of the OPLS-AA forcefield with the Berger lipids,
I have posted a detailed description of the motivation, method, and
testing. Much of the methods there will be used in a paper at some point
in time so please do not copy the text directly for your own use.
http://www.pom
Check the archives. I posted a summary of one possible solution less
than 8 hours ago. You will receive more assistance if you demonstrate
that you are trying to help yourself. If you still don't find the
answer that you are looking for then you need to be *way* more
detailed in your questi
Yes, the LO LO in atom type should be as Justin has mentioned.
Sudheer, please note that the original post that you quote below actually
includes an example for LO LO
"LO LO 115.9994 0.000 A2.96000e-01 8.87864e-01"
Also note that similar information is available i
There is no need to post twice, I saw your first post. Your level of questions
indicates that you still do not understand the topology file format. It is
essential that you understand exactly how it works and what is going on or else
you are more likely to have errors in your simulation. I am h
Where is lipid.itp and your other forcefield files. Check that they
are identical between your two clusters. This appears to be a problem
with files and not with the installation. If you can't figure it out,
you will need to post your topology at the very least and also post
'grep LO ffopls
While the previously posted script seems like a valid approach, the
usefulness of -sort depends entirely on how long your trajectory is. If
you only sort once at the beginning, then after <<10ns your waters will
be mostly redistributed and I think that you will have totally lost the
benifits of
Thanks a lot for your suggestion. I wanted to calculate lateral
diffusion co-efficient for lipid, so it needs a long run. I understand
I should give more time on making
this working. I have already downloaded g_desort.c, and was successful
upto some steps, but not the whole. If I get doubts furthe
Are you using united atom lipids? If so, you may want to reconsider
attempting this. If not, you'll be more likely to get further
assistance if you provide quite a bit more information and demonstrate
that you invested some time trying to solve this.
-- original message --
Yes, I looked in
Hello,
I find that trjconv and g_order 3.3.2 don't properly find the frame to
which I would like to seek via -b. I initially discovered this based on
the output to the command line from g_order about which frame is being
processed, and I have further confirmed that the incorrect frame is
actu
I use tip4p/opls/berger combination and it works well for me. I have never used tip5p. I suggest that you build your membrane and run
one control simulation (sounds like you would lean toward using spc for this) and then one simulation with tip5p. Check order parameters and
area per lipid while us
Indeed, 3.3.3 works well. Thanks David and Berk.
Chris.
Chris Neale wrote:
/ Hello,
/>/
/>/ I find that trjconv and g_order 3.3.2 don't properly find the frame to
/>/ which I would like to seek via -b. I initially discovered this based on
/>/ the output to the command
Is it possible for the moderators to change some setting that
would automatically word-wrap all posts on the mailing list
archive?
Many of my posts end up spanning more than the horizontal
space on one screen when viewed from the mailing list
archive. I try to remember to add hard returns on each
That sentence could definitely use some massaging. Try this:
Whether one needs to correct for this contribution depends on what the
pmf should represent. When one wants to pull a substrate into a protein,
this entropic term indeed contributes to the work to get the substrate
into the protein. Thi
Probably you would benefit from putting down your simulation and
spending the next week reading. search the literature for membrane
simulations in the absence of proteins, read it, and duplicate the
tests for simulations matching experiment that you see.
--original message --
Hi
I have re
I don't have a problem, per se, but would like to discuss the problems
that may, or may not, arise when mixing force fields.
It is clear to me why one would not want to calculate the free energy
of binding for two proteins, one using the amber ff and the other
using the opls ff; also it is
Thanks Soo Mei, that might be interesting. I couldn't access it
either. I think it is a book (http://www.springer.com/series/7651)
MacKerell's website indicates that it is not yet in press, although I
am not sure how recently that was updated:
Guvench, O. and MacKerell, A.D., Jr., ?Comparis
To some extent, it depends on your interconnect and the number of atoms in the simulations that you will be doing. If you are using gigabit ethernet, then you may not scale very well beyond 8 cores on these dual node quad cores and so there is an argument to be made for 10% faster. However, if you
Please post again, this time turn off your html formatting in your
email. It is too difficult for me to read with all of the
characters.
Also, please be more explicit about what the problem is. Is your area
per lipid too small? It seems that way, but I did not use DMPC myself.
I use POP
1. You really must figure out your email issue. Go to
http://www.gromacs.org/pipermail/gmx-users/2008-May/034065.html to see
what some of us have to wade through to assist you.
2. Avoid changing your subject line when continuing a discussion
3. Did you address Marks comment about " define =
Please don't post to the users list and the developers list
simultaneously with the same question. I think this is more
appropriately a users list question. I guess if you also get a reply
on the developers list then it pays to post to both, but the idea is
to put it only in one space.
H
I noticed this typo in ions.itp under the FF_OPLS section. It appears to
have been present at least from 3.2.1 to 3.3.3
(the atom name for LI+ is NA)
[ moleculetype ]
; molname nrexcl
LI+ 1
[ atoms ]
; idat type res nr residu name at name cg nr charge
ma
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