Dear Hello Gromacs users,
My system involves water molecules in a box of 5x5x5 nm3. When I was doing
the simulation for energy minimization I got n error message --
The optimal PME mesh load for parallel simulations is below 0.5
and for highly parallel simulations between 0.25 and 0.33,
for
Hi Mark,
Sorry that I don't get you. Can you explain a little bit for me? I just
wonder if Zn really moves out of active site, when I display multi box in
VMD, there shouldn't have another Zn bound in there.
Sincerely,
Hongtham
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> -Original Messages-
> From: "Mark Abraham"
> Sent Time: Tuesday, April 19, 2016
> To: gmx-us...@gromacs.org, gromacs.org_gmx-users@maillist.sys.kth.se
> Cc:
> Subject: Re: [gmx-users] Some simple questions about using -rerun in mdrun
> for energy between two groups
>
> Hi,
>
> Thi
> -Original Messages-
> From: "Justin Lemkul"
> Sent Time: Tuesday, April 19, 2016
> To: gmx-us...@gromacs.org
> Cc:
> Subject: Re: [gmx-users] Some simple questions about using -rerun in mdrun
> for energy between two groups
>
>
>
> On 4/18/16 1:19 PM, Sheng Bi wrote:
> > Dear GMX
Hi,
Convert the units and absorb the factor of two to the minus six. Compare
with other ions present in both representations of such force fields.
Mark
On Tue, 19 Apr 2016 02:21 Pedro Lacerda wrote:
> Hi Gromacs users,
>
> We are planning a simulation with a metallic (fe+2) attached on the
> p
Hi Gromacs users,
We are planning a simulation with a metallic (fe+2) attached on the
protein. The parameters found in [1] cannot be directly inserted on
ffnonbonded.itp because equation 1 of [1] and equation 4.5 of [2] are
slightly different.
Theoreticaly these Lennard-Jones parameters could be
Hi,
The operations you are doing are working differently on the different
ranges of values that the various groups take over the course of the
simulation. The only way to get a reliable result in all cases is to
actually say what you want - that these three things belong always
together.
Mark
On
HI Mark,
I don't get the reason why this happens to Zn since Protein and ligand are
fix well with trjconv options.
Would you please point to me particular reason for it? is it simply because
of visualization or there is really problem with simulation?
Thank you very much
Hongtham
On Mon, Apr 18,
You, my friend, are a genius. All worked, thanks tons.
Alex
On Mon, Apr 18, 2016 at 5:40 PM, Justin Lemkul wrote:
>
>
> On 4/18/16 7:39 PM, Alex wrote:
>
>> The atom groups, as they appear in the coordinate input, are:
>>
>> 1. DNA atoms (labeled DA, DC, etc)
>> 2. CNT atoms
>> 3. SOL
>> 4. Ion
On 4/18/16 7:39 PM, Alex wrote:
The atom groups, as they appear in the coordinate input, are:
1. DNA atoms (labeled DA, DC, etc)
2. CNT atoms
3. SOL
4. Ions
I tried the following (prod.tpr and traj_comp.xtc are the original tpr and
compressed trajectory, respectively):
step 1:
gmx convert-
The atom groups, as they appear in the coordinate input, are:
1. DNA atoms (labeled DA, DC, etc)
2. CNT atoms
3. SOL
4. Ions
I tried the following (prod.tpr and traj_comp.xtc are the original tpr and
compressed trajectory, respectively):
step 1:
gmx convert-tpr -s prod.tpr -o cnt_only.tpr
selec
On 4/18/16 7:27 PM, Alex wrote:
Yes, there are more atoms in the system, but only 2837 of them are labeled
"CNT.' Well, I could share the files with you, of course, but you're
running the latest version, aren't you? :)
As you might expect, yes.
Do the atom numbers of the CNT start from 1, o
Yes, there are more atoms in the system, but only 2837 of them are labeled
"CNT.' Well, I could share the files with you, of course, but you're
running the latest version, aren't you? :)
On Mon, Apr 18, 2016 at 5:23 PM, Justin Lemkul wrote:
>
>
> On 4/18/16 7:20 PM, Alex wrote:
>
>> Justin,
>>
>
On 4/18/16 7:20 PM, Alex wrote:
Justin,
I understand what you're saying, but for the life of me I can't understand
where this discrepancy is coming from, because the input coordinates have
2837 CNT atoms, and trjconv selector menu lists that number correctly.
Completely lost here. Are there an
Justin,
I understand what you're saying, but for the life of me I can't understand
where this discrepancy is coming from, because the input coordinates have
2837 CNT atoms, and trjconv selector menu lists that number correctly.
Completely lost here. Are there any alternatives to output (in mdp) th
On 4/18/16 6:17 PM, Alex wrote:
Hi all,
I've got a system that includes a group named "CNT" consisting of 2837
atoms. To save space, I am outputting (at a very high rate) a compressed
trajectory that contains only that group. The GMX version is 5.0.5. Here's
the relevant mdp excerpt:
nstxout
Dear all, is there an international workshop about Gromacs in America or
Europe the near future?.
2016-04-18 17:17 GMT-05:00 Alex :
> Hi all,
>
> I've got a system that includes a group named "CNT" consisting of 2837
> atoms. To save space, I am outputting (at a very high rate) a compressed
> tr
Hi all,
I've got a system that includes a group named "CNT" consisting of 2837
atoms. To save space, I am outputting (at a very high rate) a compressed
trajectory that contains only that group. The GMX version is 5.0.5. Here's
the relevant mdp excerpt:
nstxout = 1
nstcomm
On Mon, Apr 18, 2016 at 9:25 PM, Adam Huffman wrote:
> Hi Szilárd,
>
> Yes, it's certainly not worth a large effort to try and recover the
> information.
>
> Thanks for the link, which should be very useful.
>
> The next time you're looking at something like this, it might be worth
> trying to ca
Hi Szilárd,
Yes, it's certainly not worth a large effort to try and recover the information.
Thanks for the link, which should be very useful.
The next time you're looking at something like this, it might be worth
trying to capture what might be useful for others to run tests
themselves.
Thanks
Dear Mark:
I don't mean to carry this thread beyond its natural life, but I think the OP
is referring to improper dihedrals, harmonic type and not to improper
dihedrals, periodic type (or maybe I just don't get how "cos(n * phi + phi_0)"
is related to the harmonic type?)
Regarding an improper
On 4/18/16 1:36 PM, Xingcheng Lin wrote:
Hi,
Is there anyway in gromacs5.0 to get rid of the Verbosity output such as
"GROMACS is written by:..." when executing each Gromacs command?
Use -nocopyright -quiet.
-Justin
--
==
Justin A. Lemkul,
Hi,
Is there anyway in gromacs5.0 to get rid of the Verbosity output such as
"GROMACS is written by:..." when executing each Gromacs command?
Thank you,
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On 4/18/16 1:19 PM, Sheng Bi wrote:
Dear GMX Users
I have some questions when using -rerun in mdrun to get some specific energy
for my groups. Let me describe my question in this way.
I have a system containing some groups which include A and B and others. My
goal is to calculate the energy b
Hi,
This just works on the original trajectory if you use energy groups in the
rerun tpr. Whether the numbers are useful is another matter :-)
Mark
On Mon, 18 Apr 2016 18:27 Sheng Bi wrote:
> Dear GMX Users
> I have some questions when using -rerun in mdrun to get some specific
> energy for my
Thank you Justin, I understand the problems with PRODRG. I am switching to ATB
now but earlier, I performed similar study with different ligand using PRODRG,
and corrected charges according to the mentioned paper. No problem occured at
all. I understand all systems are different. I was surprised
Dear GMX Users
I have some questions when using -rerun in mdrun to get some specific energy
for my groups. Let me describe my question in this way.
I have a system containing some groups which include A and B and others. My
goal is to calculate the energy between A and B.
So Here is my steps:
fi
Hi,
I would further speculate that these differences are not even significant.
You can also try rotating the whole system with gmx editconf before you
generate the EM input, and that will be enough to change the order of the
floating point arithmetic, so that a different final energy minimum will
Hi Mark
I corrected the PRODRG charges according to the paper cited in tutorial. The
final energy after EM was -5.6. Anyhow, I will visualize em results and then
see what happens.
Thank you
Sent from my iPhone
> On 18-Apr-2016, at 9:37 pm, Mark Abraham wrote:
>
> Hi,
>
> The number of EM st
On 4/18/16 10:30 AM, Rakesh Sharan wrote:
Thanks very much Justin.
Actually I am minimization a series of configurations from an equilibrated
trajectory of bulk TIP4P/2005 (LINCS used as constraint algorithm). I need
So, to be clear, you altered the TIP4P topology to use a system of 3 constr
Hi,
The number of EM steps doesn't mean anything. The final energy can suggest
that something sensible happened, but the values depend on what your system
has in it. You also should visualize the result of the EM and see if that
fits with your chemical knowledge. PRODRG charges often won't produce
On 4/18/16 12:02 PM, suniba wrote:
Hello users I am doing protein-ligand MD using Gromos 43A1 and GROMACS 5.0.
Therefore, following Justin's tutorial, I used PRODRG for ligand topolgy. I
After doing my tutorial, you should *not* be using PRODRG for topologies, for
the reasons mentioned in t
Hi,
If you're trying to use such features, then you want to find out how they
are currently implemented and use those instead. Probably you don't care
about most of them. The defaults are all reasonably sensible, and if there
was some issue that you had to act upon, then you'd get an error or a
wa
Hello users
I am doing protein-ligand MD using Gromos 43A1 and GROMACS 5.0. Therefore,
following Justin's tutorial, I used PRODRG for ligand topolgy. I have drawn
ligand using chemdraw and minimized the structure using chem3D. However, during
energy minimization step in gromacs, the values conv
Hi all,
To calculate delta G of mutation I was following the following tutorial
http://www3.mpibpc.mpg.de/groups/de_groot/cecam2015/peptide_mutation/
However following outputs of grompp is confusing me
Ignoring obsolete mdp entry 'cpp'
Ignoring obsolete mdp entry 'domain-decomposition'
Ignoring
Dear All,
I want to calculate the potential of mean force of pore
formation in the lipid bilayer by using potential of mean constraint force
(PMCF) method. Can anybody suggest me how to use pull method to compute the
pmf of pore formation.
How to define the reaction coordinate of p
Thanks very much Justin.
Actually I am minimization a series of configurations from an equilibrated
trajectory of bulk TIP4P/2005 (LINCS used as constraint algorithm). I need
the final energy of the energy minimized structures, however, you can see
that depending on the choice of constrained algor
Dear gmx users,
I am using gmx wham to analyse umbrella sampling simulations. I have 30
positions along the reaction coordinate and therefore 30 tpr, pullf and pullx
files. Each of these files have 100,000 rows, as I save every ps.
When I try to execute wham with the command:
gmx wham -it tp
Ok thanks I will look into the tutorial!
J.
2016-04-18 16:02 GMT+02:00 Kroon, P.C. :
> @Michael: Yes, you are right, a protein is a protein. IIRC the martinize
> script does the same as pdb2gmx in this case.
> @James: It really sounds like you want to do DAFT.
> http://www.biotechnik.nat.uni-erla
Hi,
What were the actual commands, e.g. to grompp and trjconv that produced
such results? I think you've done something mutually inconsistent.
Mark
On Mon, Apr 18, 2016 at 3:22 PM abhishek khetan wrote:
> Dear gmx-users,
>
> I was analysing some trajectory files from a box of acetonitrile solv
@Michael: Yes, you are right, a protein is a protein. IIRC the martinize
script does the same as pdb2gmx in this case.
@James: It really sounds like you want to do DAFT.
http://www.biotechnik.nat.uni-erlangen.de/research/boeckmann/downloads/DAFT/index.shtml
seems to contain an tutorial. Otherwise,
Hi James,
My guess is that running a two (unbound) protein simulation with the MARTINI
force-field will be the same as if it was all atom. Build two separate protein
topologies (with Martini force-fields) as *.itp files to include in your *.top
and go from there. The topology file is what gromp
On 4/18/16 4:43 AM, gozde ergin wrote:
In Roux study they did 10 independent 1.5 ns production simulation and I did 15
ns simulation and divided it to 10 1.5ns simulations.
Osmotic pressure for 5M : My result 216.8 (+/- 0.2 bar)
Roux study 300(+/
On 4/18/16 9:05 AM, Nikhil Maroli wrote:
Hi thanks for your suggestion,
When i give both same name in mdp and top it gives an error
Atom index (123) in position_restraints out of bounds (1-122).
This probably means that you have inserted topology section "position_restraints
this is my topo
It seems like smth very complicated :)
I just need to put two different proteins in the system - one in the
membrane (A) and one in the water (B) and simulate it independently 10
times to collect statistics about associations of A and B during those
runs. The problems that I don't know how to put
Dear gmx-users,
I was analysing some trajectory files from a box of acetonitrile solvents
when i realised that despite using trjconv -pbc whole and then trjconv -pbc
no jump, the molecules appeared to be broken when visualising using pymol.
When i looked that the gro file, the final gro file was
Hi thanks for your suggestion,
When i give both same name in mdp and top it gives an error
Atom index (123) in position_restraints out of bounds (1-122).
This probably means that you have inserted topology section "position_restraints
this is my topology file structure
; Include forcefield para
Hi,
If you have a cluster of things that make sense to treat together then you
must tell the tool that, via using such an index group. We haven't yet
worked out to implement "do what I want" :-)
Mark
On Mon, 18 Apr 2016 13:40 HongTham wrote:
> Hello Gromacs users,
> I'm running a Zn bound prot
TI/FEP are appropriate when you have "small" changes between states.
Whether you delete/create all of a molecule or just part of it doesn't
matter that much. So a relative simulation between a glycated and
non-glycated sounds quite reasonable to me. Of course, this will become
increasingly more d
Hello Gromacs users,
I'm running a Zn bound protein - ligand complex simulation. I solvated
whole system in a dodecahedron box. I also meet the problems with boundary
effects. I try to use the gmx trjconv with option -pbc mol -ur compact
-center to fix the problem. However, it doesn't work. The pro
Hi Mark,
I will give that a thorough read. I was wondering if you could possibly
comment on whether TI is an appropriate tool for calculating the free
energy difference between two states, A―> non-glycated side chain, and b―>
glycated side chain? Most examples given focus on the inclusion/exclusio
Hi,
On Thu, 14 Apr 2016 21:10 Christopher Neale
wrote:
> Where? I took a look at v5.1.2 manual section 4.2.12 and could not find
> it, hence my suggestion to test it out. I note that there is indeed some
> definition in section 4.2.13: "Proper dihedral angles are defined according
> to the IUPAC/
Hi,
Off-list Ali sent me a link to his movie - this does indeed show the ligand
diffusing out gradually, rather than "jumping" in a discrete step. Such an
event would be very rare for a lot of bound ligands with a suitable model
physics, so if it's reproducible then you have problems with the mode
Hi,
Also you might consider pmx
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4365728/ for such topology
generation. There is further work in the pipeline, so do get in touch with
Bert if there's something of interest.
Mark
On Mon, Apr 18, 2016 at 11:56 AM Nash, Anthony wrote:
> From the site, “
From the site, “..or the free energy of a mutation of a side chain.”
I think this is what I am after. Many thanks for the link.
Anthony
On 18/04/2016 10:42, "gromacs.org_gmx-users-boun...@maillist.sys.kth.se on
behalf of Hannes Loeffler"
wrote:
>A good starting point is http://www.alchemistr
A good starting point is http://www.alchemistry.org/ which has quite a
lot of detail on relative alchemical free energy simulations (not only
TI).
On Mon, 18 Apr 2016 09:27:02 +
"Nash, Anthony" wrote:
> Hi all,
>
> I¹m looking for a guide on performing TI between a protein in its
> crystal
Hi all,
I¹m looking for a guide on performing TI between a protein in its crystal
periodicity with a particular residue (state A), to the same system but
with a different residue (state B).
I¹m currently using
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free
_energy/01_
Hi Mark,
I guess so because a lot of studies cite this study also their results are
almost identical with the experimental one.
> On 18 Apr 2016, at 10:46, Mark Abraham wrote:
>
> Are they known to produce these observables accurately
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Hi,
Are they known to produce these observables accurately? Might a wrong
distribution of KE affect them?
Mark
On Fri, 15 Apr 2016 12:00 gozde ergin wrote:
> Hi Mark,
>
> I use Berendsen for T and P-coupl.
> Do you think I should change them?
>
> > On 15 Apr 2016, at 11:55, Mark Abraham wrote
In Roux study they did 10 independent 1.5 ns production simulation and I did 15
ns simulation and divided it to 10 1.5ns simulations.
Osmotic pressure for 5M : My result 216.8 (+/- 0.2 bar)
Roux study 300(+/- 10 bar)
Hi,
What statistical error do you (and they) measure? How many replicates have
each of you done?
Mark
On Mon, 18 Apr 2016 10:25 gozde ergin wrote:
> Hi Justin,
>
> I corrected the nonbonded settings as your suggestion ;
>
> ; Bond parameters
> continuation = no
> constraint_algorithm =
Hi Justin,
I corrected the nonbonded settings as your suggestion ;
; Bond parameters
continuation = no
constraint_algorithm = shake
constraints = h-bonds
shake_tol= 0.0001
cutoff-scheme = Verlet
vdwtype = cutoff
vdw-modifier = force-switch
rvdw-switch = 1.0
Hi,
I assume you want to study the binding of your water soluble protein to
your membrane(protein). DAFT was created to do just this. DOI:
10.1021/ct5010092
Peter
On Fri, Apr 15, 2016 at 3:37 PM, James Starlight
wrote:
> Dear Gromacs users!
>
> I am looking for some tutorial for the MARTINI si
You defined in .top file as POSRES_Protein so in .mdp file you should call as
define = -DPOSRES_Protein.
The names in .top and .mdp should match
On 18 Apr 2016, at 08:46, Nikhil Maroli wrote:
>
> Dear all,
> i wanted to include position restrain to cyclic peptide nanotube c-alpha
> atoms
Hi Brett,
If you have all the necessary .itp files and if your .top file is generated
correctly, yes it works.
> On 18 Apr 2016, at 09:23, Brett wrote:
>
> Dear All,
>
>
> Does GROMACS work if the force field for ligand part is GAFF force field?
>
>
> Brett
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Dear All,
Does GROMACS work if the force field for ligand part is GAFF force field?
Brett
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