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
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
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
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.
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
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
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
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
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
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
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:
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
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
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
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
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
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
Hello, I am re-running some of our gromacs 3 simulations using gromacs
4, and as far as I can tell the gromacs 4 pull code, while very nicely
enhanced from gromacs 3, has also lost some functionality.
I am calculating the PMF of a peptide across a bilayer and, to
simplify the issue, what I
Run some more energy minimization (EM). Make sure that you have
constraints=none during EM (or I believe that you could also increase
the LINCS/SHAKE iterations to the appropriate number). Also, while
some people disagree in principle with me here, I also find in
practice that a
I haven't done it myself, but both of these methods appear as if they
could be implemented out of the box in gromacs.
On the use of orientational restraints and symmetry corrections in
alchemical free energy calculations. Mobley DL, Chodera JD, Dill KA.
Hi Justin, (comment to Berk below)
thanks for pointing out the g_wham problem. I am personally ok here as
I use a non-gromacs wham program.
Hi Berk,
unless I misunderstood, your suggestion does not yield the gromacs 3
behaviour that I am trying to reproduce with gromacs 4.
If I simply
Hi Berk, I am aware that pull_init=4.75 should pull to 4.75, not 1.0.
I was mixing results from my simulations as I was discussing, sorry.
Please allow me to restate the issue: If I am indeed pulling to 4.75
below group 0, then why is the force positive when group 1 has a
displacement of
I only now noticed Justin mail on g_wham.
You can probably also use pull_geometry=distance and pull_init=1,
if you starting structure has group1 close to 1 nm below group 0.
Agreed, although this will not work when the force constant is not
strong enough to inhibit any sampling 0 -- wherein
Hi Berk,
I do not mean the box 0, and I am aware about the pull distance
needing to be less than half of the smallest box length. Please allow
me describe a bit more rigorously what I need to avoid. I will use an
example that is totally fictitious, but is designed to emphasize the
First let me mention that I only scanned the mammoth manuscript
snippet. Nevertheless, I'll try to address your questions.
1. You are physically able to use spc in place of tip3p. Whether or
not that is a good idea is up to you to decide. Read the literature
including the spc, tip3p, and
Thank you very much Berk,
I'm not trying to be argumentative for arguments sake, but I just
can't see how exactly one would make pull_geometry=direction work in
this way. Although I think that I have shown the evidence for this in
my posts, if I am wrong here then clearly I misunderstand
Sorry for so disordered questions...
3. use the pull code. I don't know exactly what you want to do
here...perhaps harmonically restrain the distance between the two mentioned
groups to some specified value? No need to rename the water, just make an
index group.
The problem is that I don't know
Hi Berk,
I have done the tests and you are entirely correct. I have one further
question: If I simply want to pull to a relative displacement of -1.0
nm, is there any reason to prefer one of these methods, or are they
just overlapping implementations of different methods that also have
Hi Daniel,
I think you still need to read and attempt what has already been
suggested. To be more explicit:
trjconv -f a.xtc -o a_cluster.gro -e 0.001 -pbc cluster
grompp -f a.mdp -c a_cluster.gro -o a_cluster.tpr
trjconv -f a.xtc -o a_cluster.xtc -s a_cluster.tpr -pbc nojump
from:
Hi Daniel,
1a. I am confused about what is your vesicle. Is it everything that
you are showing in these images? Or perhaps it is only the cyan thing
that I can see sliced through in:
http://img109.imageshack.us/img109/8227/trajenddat.jpg
1b. I suspect that the cyan ring encircled by
There is no problem with the rhombic dodecahedron in and of itself.
Note that editconf -d does not actually yield the -d that you ask it
to and that it errs on different sides of your request for different
box types. To prove this to yourself, run your starting structure
through editconf
Hi Li,
In my opiniun, what you propose is acceptable, but not rigorous, and
you will need to prove that there are no unexpected artifacts of
changing box size. For example, you should definitely run a couple of
your small box systems as larger boxes as well and show that you get
the same
We have the same desire on a large cluster in order to reduce the
number of file operations overall. In addition to Xavier's suggestion,
you can also write your .trr to memory:
mdrun -deffnm xx -t /dev/shm/xx.trr
or to the local disk:
mdrun -deffnm xx -t ${TMPDIR}/xx.trr
if those exist and
Hello,
I have just realized that an existing checkpoint file will not be used
as input to mdrun when its name is supplied via -deffnm but not
directly via -cpi. I suppose that this makes sense for backward
compatibility, and the mdrun -h -cpi state.cpt Input, Opt.
Checkpoint file
Thanks Berk,
I agree that a single file open action is not going to cause a lot of
system activity. We're simply trying to cut down wherever possible as
this is a large shared cluster where the activity of many users
distributed amongst 30K cores is overwhelming the GPFS. We have been
Sounds like a phase change. If that is the case, 10 ns is likely not
enough to expect equilibration considering that bilayers can take 50ns
(or even substantially longer) to equilibrate the area per lipid after
a phase change.
None of this is to contradict your intuition about a
Sorry, I don't use gromacs g_wham so I can't help you on the specifics
there. I don't know if the -zprof0 does anything special, but you know
that your PMF can be arbitrarily translated as dG is unknown to an
additive constant, right?
## assume rx coord in first column and dG in second
You did not state clearly what you want to do. In many cases you could
simply calculate the RDF using g_rdf and integrate to the first
minimum. If that doesn't suit you, here's another idea:
1) g_rdf - locate the first minimum
2) g_dist -dist to print all the atoms in group 2 that are closer
g_spatial -h
-or-
g_sdf -h
-- original message --
ai all...
Did anyone know how to do spatial distribution functions??? I have 125
ion pairs in my system. The problem is,
1)how I can I get the 3-D probability distributions of anion around
cation or cation around anion in my system?
I am doing umbrella sampling to calculate energy profile of an drug
passing through a ion channel by GROMACS3.3.
why not gmx 4?
In order to get right result, I need to choose a reasonable force
constant in my simulation, right? I know that, a reasonable force
constant should produce
Hello,
I am very interested to know exactly what has changed between gromacs
4.0.5 and 4.0.6/7. I understand that the test set is no longer useful
for gmx-4 (see quote below) and I'm not strongly motivated to update
my gromacs version when I don't know what bugs will be fixed and there
Thanks for taking the time Mark, this is quite useful. Especially Bug
354: switching from Berendsen to V-rescale doesn't work if -nosum is
used for those of us who don't follow the list every day.
-- original messagwe --
I started a 4.0.7 revisions list there and noted the issues that came
Thanks again Mark,
are you able to provide a bug number for Fixed bug with pull groups
using weights in parallel so that I can figure out exactly what the
problem was?
Separately, it seems like a decent idea to automate the production of
this list and its update on the website whenever a
I believe that Justin was suggesting that you move in the opposite
direction than to delete some waters.
The number density for water should be about 32.5 waters per cubic
nanometer, meaning that you should have nearly 1E6 water molecules in
a cubic box with sides of 31 nm, and 1095 water
You could also have a script that you optimize for your specific
system that knows the number of frames in the xtc based on the file
size and then trjconv -dump when your .xtc-polling script sees that it
has been updated? Your visualization program could then update based
on the output
In spite of the fact that I have never used g_lie, I have used a
variety of different techniques to calculate binding free energies,
and I would be astounded if it was possible to get the precision that
you desire with only 1 ns of sampling per state. Are you sure that the
reported
Hello,
does anybody have a reference for the -linacc method applied by
make_edi/mdrun? I have checked the references mentioned in make_edi -h
as well as the manual, but didn't find anything that matches -linacc
exactly.
For example, gromacs suggests that entire MD steps will be accepted
Than you Ran, this looks good. The method is basically the same with
the exception that Daidone et al. utilize a target structure as
opposed to a target eigenvector, although the difference here is
probably semantic.
I greatly appreciate it,
Chris.
-- original message --
Hi Chris,
Maybe
Can't you just do one of these:
echo 5 | pdb2gmx -f a.gro
or
pdb2gmx -f a.gro EOF
5
EOF
--original message--
Hi List,
is it possible to have the -merge option in pdb2gmx set to non-interactive?
I need to merge 8 copies of a protein into one definition (.top) because if
i don't do that all
What exactly did you try? Something like this?
pdb2gmx -f a.gro EOF
5
y
EOF
I have not done -merge myself, but I often pass in multiple
'command-line' arguments in a scripts, although it is necessary to run
it through on the command line once to see what the order of arguments
should be.
Hello,
does anybody know how to get an exclusive list of matching searches
while searching the gromacs mailing list using the new search tool?
I have tried:
essential dynamics Address not mapped
essential dynamics and Address not mapped
essential dynamics AND Address not mapped
essential
Hello,
In my hands, mdrun throws a segfault when passing the -ei flag to
mdrun and utilizing the sd integrator. I'll admit that I have only
tried this with a single system. Nevertheless, using -linacc vs.
-linfix makes no difference, neither does moving to constraints=none
or parallel
Hello,
When utilizing more than one eigenvector in make_edi -linfix, are the
eigenvector linearly combined with their eigenvalues as coefficients,
or does this combination occur in the absence of eigenvalues?
Thank you,
Chris.
--
gmx-users mailing listgmx-users@gromacs.org
Thank you Carsten for this information and for the sd/edi fix. This
actually makes a bunch of sense. I can effect the eigenvalues with
-linfix -linstep, and I see now that eigenvalues can not be sensibly
combined with -linacc in in its current incarnation.
Thank you,
Chris.
-- original
Hello,
I am having trouble getting make_edi -linfix to work with multiple
eigenvectors.
This works for a single EV:
$ echo 3 | make_edi -s ../../SETUP/makeTPR/edi.tpr -f
../../SETUP/makeEDI/eigenvec.trr -o testpositive.edi -linfix 1
-linstep 0.0001 -outfrq 50
And throws an error for:
Be careful when you draw conclusions from your results though. I
suggest that you start two simulations from different coordinates and
look at their convergence. In my hands, this type of thing can take
1 us to converge, and that's without any major conformational changes
in the
Hi Wende, please do not double post. If you are unsure if your post
got through, you can easily see the list at
http://lists.gromacs.org/pipermail/gmx-users/2009-December/date.html.
You did not put units beside 40, so I suppose that you mean 40 A,
whereas gromacs uses nm.
1. Make a box
Search:
trjconv pbc cluster
on the gromacs mailing list and take a look at the first hit.
Basically, you need to find a frame that *does* work with -pbc cluster
and then make a new .tpr based on the clustered .gro and then run
trjconv -pbc mol. Just ensure that this frame is as close to the
Hi Nisha,
Hetero-Atom Navi is a collection of heteroatoms culled from the PDB.
http://hetpdbnavi.nagahama-i-bio.ac.jp/index.php?mode=0
However, having only one heavy-atom, ammonia is unlikely to be
usefully extracted from this resource for use in atomistic MD.
You can easily make it
Hello,
I have just started working with the [ angle_restraints_z ] portion of
the code. My initial tests indicate that it works in my system.
However, in some cases I am getting a fatal error that a pair
interaction is too far apart to be calculated within domain
decomposition. Although
Hello,
I recently used mdrun -pd while attempting to solve my problems with
angle_restraints_z
(http://lists.gromacs.org/pipermail/gmx-users/2010-January/047785.html) since
I discovered that -noddcheck is not a valid solution to the missing
interactions problems with angle restraints.
I have determined that the proper solution here is to use particle
decomposition. -noddcheck simply delays the inevetable fatal LINCS
error. Nevertheless, mdrun -pd requires that one maintains whole
molecules in the starting conformation:
Your disk was full and the .xtc file could not be completely written,
therefore you have an incomplete frame. I think that you have answered
your own question here. If I was you, I would trjconv -e to get the
full trajectory minus the last incomplete frame for a good .xtc file.
There are
Hi Nisha,
you say And it runs minimization with bad contact errors, but I don't see any indication of that error message here.
Is it perhaps that your EM exits early and then your MD throws an error? In any event, please post complete error information
as output by gromacs.
Chris.
--
Mark already answered this:
http://lists.gromacs.org/pipermail/gmx-users/2010-January/047825.html
--original message --
HI
I am simulating the protein + ligand + water molecules system.
In the experimental work, the concentration of ligand is pretty low, say
under 20 mM (avearge 18 ligands
future users experiencing this problem can follow this thread at:
http://bugzilla.gromacs.org/show_bug.cgi?id=383
-- original message --
Hi,
Can you file a bugzilla and attach the tpr file?
Thanks,
Berk
Date: Tue, 5 Jan 2010 10:49:46 -0500
From: chris.neale at utoronto.ca
To: gmx-users at
Dear Sunny,
I replied a while ago, but it seems to have not made it to the list.
When using inflategro with gromacs3, you can run cycles like this:
1. inflategro.pl
2. mdrun (EM)
3. goto 1
When running with gromacs4, however, you must run cycles like this:
1. inflategro.pl
2. mdrun (EM)
3.
Hi Justin,
I just double checked and certainly the confout.gro from my EM run in
parallel with domain decomposition in mdrun is broken over periodic
boundaries.
I'm running gromacs-4.0.5 on a nehalem under openmpi. Here is my .mdp file
gpc-f101n084-$ cat em_pos.mdp
define=-DPOSRES_INDO
Hi Justin,
I can confirm that I see that code snippet in my md.c code, although
my tests indicate that this is not the end of the story.
I have now taken the output .gro, ran it through trjconv -pbc mol and
then ran mdrun again under a variety of conditions:
1. EM(steep) mdrun_mpi
Thanks Berk,
increasing -rdd from 1.0 to 2.5 has solved my problem. Note that the
actual distance between the two atoms in the angle restraint never
exceeds 0.9 nm, although this is a rather complex set of virtual atoms
based on the positions of other virtual atoms, each virtual atom in
Good idea Justin. I have posted as bug 386.
-- original message --
On 1/9/10 1:44 PM, chris.neale at utoronto.ca wrote:
Hi Justin,
I can confirm that I see that code snippet in my md.c code, although my
tests indicate that this is not the end of the story.
I have now taken the output .gro,
Try the doughnut mode in the newest version of the program -- it's
meant for exactly this situation.
http://www.csb.bit.uni-bonn.de/inflategro.html
-- original message --
Hello Gromacs Users,
I would like to run a simulation of a trimer in a DPPC membrane. I
really like the elegant solution
I have done a similar thing in the past (without using the pull code),
renaming the crystal waters around the protein so that they were
easier to track.
I eventually figured out that it was necessary for me to place the
waters sequentially in the .top file. e.g:
; This is OK
Protein 1
Probably you removed lipids from the gro but not from the top (which
you need to do as well).
Find a lipid atom name that occurs only once per molecule (In
non-united atom lipids I use P8)
grep P8 my.gro |wc -l
This will tell you how many lipids should appear in your top file.
Chris.
--
First, I doubt that you want a molecule with a partial charge.
Second, just because the bonds, angles, and LJ parameters will be
generated doesn't mean they will be correct. What are the N-H bond
lengths of ammonia? Are those the same as the ones that you are
including here? Take a look at
I think the notes from grompp are pretty clear. You need to redivide
your charge groups so that they contain fewer atoms. You can do this
in the .top or .itp file and you can find out how to do that in the
manual. Feel free to post your original and charge-group-modified
topologies back
From what I can find, it seems that you are correct to assume that
frozen coordinates should not be scaled:
http://lists.gromacs.org/pipermail/gmx-users/2002-July/002054.html
and, from the online manual:
freezegrps:
Groups that are to be frozen (i.e. their X, Y, and/or Z position
Hello,
I have a run that was working fine under parallel mdrun -pd and when I
then switched to domain decomposition I got:
Fatal error:
The size of the domain decomposition grid (1) does not match the
number of nodes (8). The total number of nodes is 8
while running like this:
Hi Stefan and Pär,
I believe that the latest response had the wrong subject, so I am
changing it back.
Pär, two comments:
First, does that option really exist?
$ /scratch/cneale/GPC/exe/intel/gromacs-4.0.7/exec/bin/pdb2gmx -h z
21; cat z|grep nochargegrp|wc -l
Second, I am not
That's why I said if you know what you're doing :)
ok, fair enough.
The name flag is listed as [no]chargegrp
I still don't see it (see below), is this [no]chargegrp new in the cvs ?
I'm pretty sure that you're not referring to [no]lys, etc.
$
implicit solvent has apparently been implemented in the openMM
modification of gromacs, although that is still in beta and is not to
be trusted for production runs without doing your own testing. I have
not tried it myself.
You can obtain it here:
https://simtk.org/home/openmm
-- original
Please provide actual gromacs output and tell us where it is from. I
know it's sad, but not all of us can recall what the gromacs 3.3.3
.pdo file format looked like. So please include a sufficiently large
portion of the file to help us recall. If, on the other hand, these
values that you
Sounds like a bubble. Do some NpT equilibration by adding pressure
coupling. That's going to be difficult with your freeze groups though.
Basically, you need to find a way to get the correct solution density
between the graphite layers.
-- original message --
Hi all,
Is there anyone who
1. Is your system is properly minimized
2. If you take the output from a 500 ps run with 0.25 fs timestep and
start a 1 fs timestep run, is that new run stable?
3. What are atoms 62 and 80?
**4. Why is there a 1-4 between atoms 62 and 80 if you have only water
and a 42 atom solute?
5. What
Dear Giuseppe:
I don't think your method of showing the change is very good since it
introduces unnecessary variables (e.g. did you use the correct files
for the second run).
What I am looking for is raw -pd pull.pdo data from the first run. I
found no such file in the body of the email
Dear Giuseppe:
*** What I am looking for is raw -pd pull.pdo data from the first run. ***
It looks like you did not define a name for -pd:
mpiexec -n $NSLOTS mdrun_mpi -np 1 -v -s start_res.tpr -o output_res -c
output_conf -pi pull.ppa -pn mdgrp1.ndx -po pullout -pdo pullout1 *
so based on
1. Is your system is properly minimized
Of course, it is, based on the energy values.
Don't be so sure! Although since your 0.25 fs timestep -- 1 fs
timestep transition crashes you are likely correct here.
**4. Why is there a 1-4 between atoms 62 and 80 if you have only water
and a 42
Dear Giuseppe:
OK, those are the forces. They seem pretty huge and massively
fluctuating, although I use umbrella sampling myself so this might be
quite normal for constraint sampling (something for you to look into).
The only thing that comes to mind is that your running up against a
Dear Vitaly:
Justin raises the point well, so that should be addressed first. If,
however, you still have problems then there's the only thing that I
can think of:
1. put a single solute in a large vacuum box and use the sd
integrator. Can you reproduce the problem?
2. Remove the
All the directives are correct. Chris just mistyped saying
[ molecules ]
CIP 3
instead of
[ moleculetype ]
CIP 3
that I orginally send him.
Not true. I meant exactly what I typed. I am referring to the section
that occurs at the end of your .top file:
It sometimes looks like
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