date:20170818


Hi Peter,

I'd imagine that in particular the CG angle parameters between beads may 
well be different if you determined them by mapping on to a single one 
of these surfactants in water, compared to mapping onto an ensemble of 
structures in an aggregated state as the hydrophobic chains would try to 
'fold up' and bury themselves away from the water. I haven't actually 
tried this though, that's just how I think it would probably be. Nice 
and easy to test anyway, if Emiliano really does need to parameterise 
this molecule.


Cheers

Tom

On 18/08/17 09:04, Peter Kroon wrote:

Hi Tom,


thanks for your thoughts :)

I want to respond to your sampling argument: I figured that a surfactant
in solution is "more free" to sample conformations due to sterics than
one in an aggregated state, and that sampling would therefore be faster.
Your point of sampling the bonded conformations from a solvated vs an
aggregated state is a powerful one though (then again, shouldn't the
difference in aggregated state vs solvated state come from the
non-bonded parameters? i.e. the bonded parameters should be the same for
both).


Peter


On 17-08-17 21:10, Piggot T. wrote:

Hi Peter/Emeliano,

I'm not sure I agree with some of what Peter says, but I guess it's probably a 
matter of taste. If it were me, I'd definitely want my atomistic simulations to 
behave properly before trying to develop CG parameters based upon these 
simulations. I know that the coarse-graining will lose some of the detail, but 
I'd want all of the detail in the atomistic simulations to be as accurate as 
possible to hopefully develop reasonable CG parameters with the appropriate 
detail lost but the underlying, correct, behaviour retained. You cannot be sure 
of this in your case here.

As for the sampling in the atomistic simulations, I guess you mean you could 
run one in a box a lot quicker as the system is smaller? With 50, you obviously 
have more surfactants in there to give you a lot more data for the 
parameterisaton and as a larger simulation size should scale better, you 
probably will get better sampling (in terms of stats) with the 50 in a box 
setup. Plus you get to also check, as Emeliano said, that the atomistic 
simulations behave sensibly and aggregate/form micelles, etc. (whatever this 
surfactant does). You can also look for differences in the CG bonds/angles 
depending upon what state the molecule is in (solvated, aggregated, etc.).  For 
this specific case, I guess this may not matter if it's only one bound to a 
protein though.

Anyway, regarding the original post, I would firstly ask is it really necessary 
to have this molecule in the simulations? I couldn't tell from the post why 
this was wanted to be included. Is it an important ligand, or is it just in the 
experimental structure as an artefact of the crystallisation 
conditions/procedure (which I suspect is quite likely)? If it's the latter, 
there is no need to go to all this effort. As for the LINCS warnings, it's hard 
to exactly say without seeing the topology/starting structure. It could well be 
that the ATB topology for things like the sugars isn't that great (the GROMOS 
sugar force fields are heavily optimised for things like dihedrals), or it 
could potentially be an issue with the starting structure of the system. If it 
were me, I would likely make the atomistic parameters manually through 
combining the building blocks available within the GROMOS force field.

Cheers

Tom


From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Peter Kroon 
[p.c.kr...@rug.nl]
Sent: 17 August 2017 12:03
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: Re: [gmx-users] surfactants simulation topology generation with 
Automated Topology Builder and lincs warnings

Hi Emeliano,


since you're just going to use the atomistic simulation to get some
parameters for your CG model, I don't think the differences will be
significant --- the approximations your are going to make in CG will be
larger anyway. I would even argue you'll be better off if you run just
one surfactant in water to get your bonded parameters, rather than 50,
since sampling will be better.

For further validation of your Martini model, you can (should) look at
some more macroscopic properties as well, such as dimerization free
energy and partition free energy.


Peter


On 17-08-17 11:18, edesantis wrote:

dear gromacs users,

I have a problem in the simulation of a surfactant, Octyl Glucose
Neopentyl Glycol, that is present in protein crystals.

my goal is to have a coarse grained model for this surfactant with
Martini ff.
to do that I have to generated an all atomistic simulation to use as a
reference to build the Martini topology.

I've downloaded the pdb file https://www3.rcsb.org/ligand/37X of the
surfactant and since there is not an existent ff for the all atom
simulation, I've generated it from ATB web

Re: [gmx-users] Error with MPICH

Hi,

If libmpich.so is available after building with --enabled-shared, then the
MPI wrapper compilers should take care of this. If you want more help, we
need to at least see how you called cmake, using mpicc and mpic++, and more
information about what was wrong than "it still doesn't work." :-)

Mark

On Fri, Aug 18, 2017 at 12:02 PM Souparno Adhikary 
wrote:

> Hi,
>
> I was installing GROMACS-5.1.4 with MPI option in the server. It yielded
> the following error,
>
> [  6%] Linking CXX shared library ../../lib/libgromacs_mpi.so
> /usr/bin/ld: /usr/local/lib/libmpich.a(allreduce.o): relocation R_X86_64_32
> against `.rodata.str1.8' can not be used when making a shared object;
> recompile with -fPIC
> /usr/local/lib/libmpich.a: could not read symbols: Bad value
> collect2: ld returned 1 exit status
> make[2]: *** [lib/libgromacs_mpi.so.1.4.0] Error 1
> make[1]: *** [src/gromacs/CMakeFiles/libgromacs.dir/all] Error 2
> make: *** [all] Error 2
>
> As the available suggestions on the internet suggested, I recompiled the
> mpich with --enable-shared option and also setting the CXXFLAGS as -fPIC.
> It still doesn't work.
>
> Can you please help?
>
> Souparno Adhikary,
> CHPC Lab,
> Department of Microbiology,
> University of Calcutta.
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
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Re: [gmx-users] ForceField of ethanol and the default parameters in Gromacs

Hi,

On Fri, Aug 18, 2017 at 6:14 AM ZUO Taisen  wrote:

>  Dear Gromacs developer:
>
>There is a topology file of ethanol in the OPLS FF of the new
> version of Gromacs (Gromacs2016 please see bellow). However, I did not see
> any bond, angle or dihedral parameters. Does this means that Gromacs use
> the default parameter?
>

Yes, please do some tutorial material where the structure of the .top file
is explained (also in the reference manual from GROMACS). The early
structure sets up the parameters from databases that are part of GROMACS.


>  If we want to compare this topology with the topology from
> literature, where should I find these top parameters in Gromacs one by one?
>

share/gromacs/top/*.ff


>  Is these default parameter accurate enough to simulate polymer like
> Polyethelene or Polystyrene?
>

No idea. You should approach such questions by reading and understanding
the philosophy behind the force fields.

Mark


>  Thank you very much!
>
> Sincerely yours,
> Taisen Zuo
>
>  ;
> ; Ethanol, Jorgensen et al. JACS 118 pp. 11225 (1996)
> ;
> [ moleculetype ]
> ; name  nrexcl
> ETH 3
>
> [ atoms ]
> ;   nrtype   resnr  residuatomcgnrcharge  mass
>  1   opls_157   1 ETH   C   1   -0.18
>  2   opls_156   1 ETH   H   1   0.06
>  3   opls_156   1 ETH   H   1   0.06
>  4   opls_156   1 ETH   H   1   0.06
>  5   opls_157   1 ETH   C   2   0.145
>  6   opls_156   1 ETH   H   2   0.06
>  7   opls_156   1 ETH   H   2   0.06
>  8   opls_154   1 ETH  OA   2   -0.683
>  9   opls_155   1 ETH  HO   2   0.418
>
> [ bonds ]
> ;  aiaj funct   c0   c1
>  1  5   1
>  3  1   1
>  4  1   1
>  2  1   1
>  7  5   1
>  6  5   1
>8  5   1
>  9  8   1
>
>  [ pairs ]
>  ; ij   func
>  2  6
>  2  7
>  2  8
>  3  6
>  3  7
>  3  8
>  4  6
>  4  7
>  4  8
>  1  9
>  6  9
>  7  9
> [ angles ]
> ;  aiajak funct   c0c1
> ; H3
>  2  1   5   1
>  3  1   5   1
>  4  1   5   1
> ;
>  4  1   3   1
>  4  1   2   1
> ;
>  3  1   2   1
> ;
>  1  5   7   1
>  1  5   6   1
>  1  5   8   1
> ;
>  5  8   9   1
> ;
>  6  5   7   1
>  6  5   8   1
> ;
>  7  5   8   1
> ;
> [ dihedrals ]
>  2  1   5  63
>  3  1   5  63
>  4  1   5  63
>  2  1   5  73
>  3  1   5  73
>  4  1   5  73
>  2  1   5  83
>  3  1   5  83
>  4  1   5  83
>  1  5   8  93
>  6  5   8  93
>  7  5   8  93
>
>
> --
> Taisen Zuo
>
> China Spallation Neutron Source，Institute of High Energy Physics， Chinese
> Academy of Science
> A1-510, Zhongziyuan road NO.1, Dongguan, Guangdong, PR China. 523770
> Tel: 86-0769-89156495
> Cell: 13650469795
>
>
> 左太森
> 中科院高能物理研究所中国散裂中子源
> 广东省东莞市大朗镇中子源路1号A1-510
> 邮编：523770
> 办公电话：86-0769-89156495
> 手机：13650469795
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
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Re: [gmx-users] Error with MPICH

2017-08-18 Thread Souparno Adhikary

My CMAKE was like this:

/root/cmake-3.9.1-Linux-x86_64/bin/cmake .. -DGMX_BUILD_OWN_FFTW=ON
-DREGRESSIONTEST_DOWNLOAD=ON -DGMX_MPI=ON
-DCMAKE_INSTALL_PREFIX=/usr/local/gromacs-5.1.4

I have compiled mpich2 with --enable-shared option.

Souparno Adhikary,
CHPC Lab,
Department of Microbiology,
University of Calcutta.

On Fri, Aug 18, 2017 at 6:01 PM, Mark Abraham 
wrote:

> Hi,
>
> If libmpich.so is available after building with --enabled-shared, then the
> MPI wrapper compilers should take care of this. If you want more help, we
> need to at least see how you called cmake, using mpicc and mpic++, and more
> information about what was wrong than "it still doesn't work." :-)
>
> Mark
>
> On Fri, Aug 18, 2017 at 12:02 PM Souparno Adhikary 
> wrote:
>
> > Hi,
> >
> > I was installing GROMACS-5.1.4 with MPI option in the server. It yielded
> > the following error,
> >
> > [  6%] Linking CXX shared library ../../lib/libgromacs_mpi.so
> > /usr/bin/ld: /usr/local/lib/libmpich.a(allreduce.o): relocation
> R_X86_64_32
> > against `.rodata.str1.8' can not be used when making a shared object;
> > recompile with -fPIC
> > /usr/local/lib/libmpich.a: could not read symbols: Bad value
> > collect2: ld returned 1 exit status
> > make[2]: *** [lib/libgromacs_mpi.so.1.4.0] Error 1
> > make[1]: *** [src/gromacs/CMakeFiles/libgromacs.dir/all] Error 2
> > make: *** [all] Error 2
> >
> > As the available suggestions on the internet suggested, I recompiled the
> > mpich with --enable-shared option and also setting the CXXFLAGS as -fPIC.
> > It still doesn't work.
> >
> > Can you please help?
> >
> > Souparno Adhikary,
> > CHPC Lab,
> > Department of Microbiology,
> > University of Calcutta.
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
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> > send a mail to gmx-users-requ...@gromacs.org.
> >
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Re: [gmx-users] Software inconsistency error: Lost particles while sorting

Hi,

There's not enough information for anybody to tell. Maybe you pulled too
hard, or with inappropriate settings.

Mark

On Thu, Aug 17, 2017 at 1:04 PM Alex Mathew  wrote:

> Dear all,
>
> I set up a simulation box, in which protein kept at the middle and one
> water molecule around the pore region of the protein. My aim is to pull
> water across the channel and get the energy diagram  (There are no other
> water molecules in the system). It shows an error while I execute the
> pull.tpr
>
> Software inconsistency error: Lost particles while sorting
>
> Can anyone tell me whats wrong here and any problem with my method?
> --
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Re: [gmx-users] problem in extending a simulation run

Hi,

On Fri, Aug 18, 2017 at 8:41 AM manindersingh rajawat <
rajawat.manindersi...@gmail.com> wrote:

> Dear all,
>
> I want extend a 100ns run to 150 ns. For this I use following commands:
>
> gmx convert-tpr -s md_100ns.tpr -extend 5 -o md_150ns.tpr
>
> gmx mdrun -v -deffnm md_150ns -c md_150ns.pdb
>
> But mdrun taken it as a new run


Sure. You implied that the checkpoint file was called md_150ns, but no such
file existed ;-)


> and began a full 150ns run:
> starting mdrun 'Protein in water'
> 7500 steps, 15.0 ps
>
> so i stopped it, and run with checkpoint input as following:
>
> gmx mdrun -v -s md_150ns.tpr -cpi state.cpt -c md_150ns.pdb
>
> Reading checkpoint file state.cpt generated: Fri Mar 24 05:39:47 2017
>
>
>   Version mismatch,
> current program: VERSION 5.0.6
> checkpoint file: VERSION 5.0.2
>

Generally you should continue simulations with the same version of GROMACS
you started, but there is unlikely to be a problem in this case.


>   Build time mismatch,
> current program: Mon Jul 27 05:11:28 UTC 2015
> checkpoint file: Fri Oct 24 17:49:05 UTC 2014
>
>   Build user mismatch,
> current program: buildd@lgw01-56 [CMAKE]
> checkpoint file: buildd@roseapple [CMAKE]
>
>   Build host mismatch,
> current program: Linux 3.19.0-23-generic x86_64
> checkpoint file: Linux 3.2.0-61-generic x86_64
>
> Gromacs patchlevel, binary or parallel settings differ from previous run.
> Continuation is exact, but not guaranteed to be binary identical.
>
> Using 1 MPI thread
> Using 4 OpenMP threads
> Compiled SIMD instructions: SSE2 (Gromacs could use AVX2_256 on this
> machine, which is better)
>

I would get GROMACS compiled properly for my expensive hardware so that it
runs more than twice as fast...


> WARNING: This run will generate roughly 19040 Mb of data
>
> starting mdrun 'Protein in water'
> 7500 steps, 15.0 ps (continuing from step 5000, 10.0 ps).
> step 5600
>
> It starts well from the checkpoint, but due to little confusion i stopped
> it. and ran the following command:
>
> gmx mdrun -v -s md_150ns.tpr -cpi state_prev.cpt -c md_150ns.pdb
>
> It gives the following error
>
> Reading file md_150ns.tpr, VERSION 5.0.6 (single precision)
> Changing nstlist from 5 to 40, rlist from 1.2 to 1.223
>
>
> Reading checkpoint file state_prev.cpt generated: Fri Mar 24 05:36:56 2017
>
>
>   Version mismatch,
> current program: VERSION 5.0.6
> checkpoint file: VERSION 5.0.2
>
>   Build time mismatch,
> current program: Mon Jul 27 05:11:28 UTC 2015
> checkpoint file: Fri Oct 24 17:49:05 UTC 2014
>
>   Build user mismatch,
> current program: buildd@lgw01-56 [CMAKE]
> checkpoint file: buildd@roseapple [CMAKE]
>
>   Build host mismatch,
> current program: Linux 3.19.0-23-generic x86_64
> checkpoint file: Linux 3.2.0-61-generic x86_64
>
> Gromacs patchlevel, binary or parallel settings differ from previous run.
> Continuation is exact, but not guaranteed to be binary identical.
>
>
> ---
> Program gmx, VERSION 5.0.6
> Source code file:
> /build/gromacs-EDw7D5/gromacs-5.0.6/src/gromacs/gmxlib/checkpoint.c, line:
> 2204
>
> Fatal error:
> Failed to lock: md.log. Already running simulation?
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
>
> When i run the previous command, that is
>
> gmx mdrun -v -s md_150ns.tpr -cpi state.cpt -c md_150ns.pdb
>
> It starts giving the same error to this also.
>
> Reading checkpoint file state.cpt generated: Fri Mar 24 05:39:47 2017
>
>
>   Version mismatch,
> current program: VERSION 5.0.6
> checkpoint file: VERSION 5.0.2
>
>   Build time mismatch,
> current program: Mon Jul 27 05:11:28 UTC 2015
> checkpoint file: Fri Oct 24 17:49:05 UTC 2014
>
>   Build user mismatch,
> current program: buildd@lgw01-56 [CMAKE]
> checkpoint file: buildd@roseapple [CMAKE]
>
>   Build host mismatch,
> current program: Linux 3.19.0-23-generic x86_64
> checkpoint file: Linux 3.2.0-61-generic x86_64
>
> Gromacs patchlevel, binary or parallel settings differ from previous run.
> Continuation is exact, but not guaranteed to be binary identical.
>
>
> ---
> Program gmx, VERSION 5.0.6
> Source code file:
> /build/gromacs-EDw7D5/gromacs-5.0.6/src/gromacs/gmxlib/checkpoint.c, line:
> 2204
>
> Fatal error:
> Failed to lock: md.log. Already running simulation?
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
>
> Please help me to resolve it.
>

Don't have multiple simulations writing to md.log at the same time.

You'll also have fewer problems if you stop trying to manage your own file
names. If you want multiple parts that you have to manually recombine
later, use mdrun -noappend -s your.tpr -cpi. Otherwise mdrun -s yo

Re: [gmx-users] surfactants simulation topology generation with Automated Topology Builder and lincs warnings

2017-08-18 Thread edesantis


Hi,

thank you for both your suggestions,

as Tom, I also think that the structure of the surfactant could be 
modified by the presence of other surfactants in the aggregate form, 
maybe it is not and only the non bonded parameters can have a role in 
the formation of the aggregates (I am quite a beginner of these kind of 
simulation...)


anyway my all atomistic simulation has double purpose,
firstly, since it was the first time I used an ATB created topology, I 
wanted to see if the topology well reproduced the aggregations of these 
kind of surfactants,
and secondly, I want to use the bonds and angles distribution to 
parametrize my Martini model, and see again if also the Martini model 
can reproduce similar aggregates to those seen in the aa simulation




I've tried to continue the simulation using dt=0.00182 ps and after a 
while there are lincs warnings, so it smells like a bad parametrization 
of the all-atomistic topology, as Tom said.
till now I've always simulated standard proteins, so I don't know how to 
parametrize the force field for these small molecules, I am now trying 
PRODRG (once I have the token to use it), if you have other suggestion 
are welcome

for gromos sugar ff, do you have any reference??



for what concern the needed to introduce this kind of molecules,
I think it is quite necessary, these surfactants, use to solubilize the 
proteins in the crystal, are forming micelles around them and, since the 
final goal of my Martini simulation is the reproduce the diffuse 
scattering in the crystals, I think it is quite important to reproduce 
all the crystal components in order to have a system that is more 
similar to the real condition.




thank you again
Emiliano


On 2017-08-18 14:22, Thomas Piggot wrote:

Hi Peter,

I'd imagine that in particular the CG angle parameters between beads
may well be different if you determined them by mapping on to a single
one of these surfactants in water, compared to mapping onto an
ensemble of structures in an aggregated state as the hydrophobic
chains would try to 'fold up' and bury themselves away from the water.
I haven't actually tried this though, that's just how I think it would
probably be. Nice and easy to test anyway, if Emiliano really does
need to parameterise this molecule.

Cheers

Tom

On 18/08/17 09:04, Peter Kroon wrote:

Hi Tom,


thanks for your thoughts :)

I want to respond to your sampling argument: I figured that a 
surfactant

in solution is "more free" to sample conformations due to sterics than
one in an aggregated state, and that sampling would therefore be 
faster.

Your point of sampling the bonded conformations from a solvated vs an
aggregated state is a powerful one though (then again, shouldn't the
difference in aggregated state vs solvated state come from the
non-bonded parameters? i.e. the bonded parameters should be the same 
for

both).


Peter


On 17-08-17 21:10, Piggot T. wrote:

Hi Peter/Emeliano,

I'm not sure I agree with some of what Peter says, but I guess it's 
probably a matter of taste. If it were me, I'd definitely want my 
atomistic simulations to behave properly before trying to develop CG 
parameters based upon these simulations. I know that the 
coarse-graining will lose some of the detail, but I'd want all of the 
detail in the atomistic simulations to be as accurate as possible to 
hopefully develop reasonable CG parameters with the appropriate 
detail lost but the underlying, correct, behaviour retained. You 
cannot be sure of this in your case here.


As for the sampling in the atomistic simulations, I guess you mean 
you could run one in a box a lot quicker as the system is smaller? 
With 50, you obviously have more surfactants in there to give you a 
lot more data for the parameterisaton and as a larger simulation size 
should scale better, you probably will get better sampling (in terms 
of stats) with the 50 in a box setup. Plus you get to also check, as 
Emeliano said, that the atomistic simulations behave sensibly and 
aggregate/form micelles, etc. (whatever this surfactant does). You 
can also look for differences in the CG bonds/angles depending upon 
what state the molecule is in (solvated, aggregated, etc.).  For this 
specific case, I guess this may not matter if it's only one bound to 
a protein though.


Anyway, regarding the original post, I would firstly ask is it really 
necessary to have this molecule in the simulations? I couldn't tell 
from the post why this was wanted to be included. Is it an important 
ligand, or is it just in the experimental structure as an artefact of 
the crystallisation conditions/procedure (which I suspect is quite 
likely)? If it's the latter, there is no need to go to all this 
effort. As for the LINCS warnings, it's hard to exactly say without 
seeing the topology/starting structure. It could well be that the ATB 
topology for things like the sugars isn't that great (the GROMOS 
sugar force fields are heavily optimised for things like dih

Re: [gmx-users] RDF

2017-08-18 Thread Dan Gil

>
> I have come across people describing RDF analysis between water and water
> and I always wonder what does it means. RDF can be done between protein and
> water to know the distribution of water around protein with default center
> of mass(My little knowledge) and what co-ordination number contribute to
> RDF has always been a puzzle for me.
>

what do you mean by  two component system?
>

These questions be answered together at once. Imagine that a protein is
dissolved in water and urea solution. This system has 3 components (water,
urea, and protein). So there can be 6 RDFs: g_ww, g_uu, g_pp, g_wu, g_wp,
g_up. "w" means water, "u" means urea, "p" means protein (If there is only
one protein molecule, than g_pp should be zero).

Like you said, we can study the distribution of water around proteins. You
can also use RDFs far more things than just protein systems. It can be used
for salts in water, mixtures of organic solvents, etc.

Coordination number is related to the radial distribution function. This
Wikipedia page (https://en.wikipedia.org/wiki/Coordination_number) has a
one method of calculating the coordination number from RDFs. For example,
in a protein + water + urea system, you may be able to find the number of
water molecules and the number of urea molecules around the protein in each
solvation shell. These numbers are averages over time, not the actual
number at a moment in time. I think this method of calculating CN might be
a quick and easy way to see if its worth using better methods (e.g.
deconvoluting each solvation shell before integration). If your protein is
very large, I can imagine this being a more difficult problem, but I don't
know for sure.

On Fri, Aug 18, 2017 at 7:47 AM, RAHUL SURESH 
wrote:

> Hi Dan
>
> Thank you so much for you descriptive answers. I have few clarifications
> that I have posted here. I will go through the papers here.
>
> On Fri, Aug 18, 2017 at 5:01 PM, Dan Gil  wrote:
>
> > Hi Rahul,
> >
> > I can't find the exact papers right now, but I remember seeing some
> > inconsistency in how people name these functions especially the radial
> > distribution function and pair correlation functions.
> >
> > If we go far back into literature, we can see JG Kirkwood using pair
> > correlation functions as functions of both the distance and the relative
> > orientation between the pairs [The Journal of Chemical Physics 19, 774
> > (1951); doi: 10.1063/1.1748352]. I don't know if he is the "inventor" of
> > the RDF, but he was one of the earliest to use it extensively in
> theories.
> > When you average the pair correlation functions over the relative
> > orientations, you get the radial distribution function which is a
> function
> > of distance only.
>
>
> That was very informative. But as now it can be calculated as a whole
> easily using various tools.
>
>
> > I think I've seen newer papers use RDF/PCF/PDF somewhat
> > interchangeably although I can't find these right now... Most people mean
> > the RDF but you can always look at the data to know what they mean.
> >
>
> I have come across people describing RDF analysis between water and water
> and I always wonder what does it means. RDF can be done between protein and
> water to know the distribution of water around protein with default center
> of mass(My little knowledge) and what co-ordination number contribute to
> RDF has always been a puzzle for me.
>
> >
> > I never used surface distribution functions, hopefully someone else can
> > bring you up to date on that one (How is the surface defined?).
> >
>
> I will be happy if some one can explain SDF and any particular tool to
> analyze it.
>
> >
> > But there is also the spatial distribution functions, which now a
> function
> > in 3D spherical coordinates. It gives the average density of particles at
> > given (r, theta, phi). In this paper they normalize it by the bulk
> density,
> > I am not sure if everyone does the same. (doi: 10.1063/1.465158)
> >
>
> Thank you. I guess it can be calculated using gmx spatial
>
> >
> > I think "radial pair distribution function" is synonymous with the RDF
> like
> > you said.
> >
>
> Yeah VMD use it as Radial pair distribution function.
>
> >
> > Partial radial distribution function is for multicomponent systems. In a
> > single component system, there is only one RDF and that is the total RDF.
> > In a two component system,
>
>
> what do you mean by  two component system?
>
>
> > there are 3 (AA, AB, BB) partial radial
> > distribution functions.
> >
> > Hope that helps!
> >
> > Dan
> >
> > On Fri, Aug 18, 2017 at 2:19 AM, RAHUL SURESH 
> > wrote:
> >
> > > Radial Distribution Function, Surface Distribution Function(SDF),
> Radial
> > > Pair Distribution Function and Partial Radial Distribution Function.
> > >
> > > What makes the difference in all the four?
> > >
> > > Have gone through lot pages and literature. Somehow one or the other
> > piece
> > > of explanation confuses me.
> > >
> > > Can I have a short explanati

Re: [gmx-users] surfactants simulation topology generation with Automated Topology Builder and lincs warnings

You shouldn't use PRODRG, well the default output at least (e.g. see 
http://pubs.acs.org/doi/abs/10.1021/ci100335w).


The ATB is generally pretty good, and although it might not be perfect 
here (e.g. as you have sugars in your structure which have been pretty 
heavily optimised in different variants of the GROMOS force field; see 
http://onlinelibrary.wiley.com/doi/10.1002/jcc.24229/abstract and 
http://pubs.acs.org/doi/abs/10.1021/ct300479h amongst other papers), I'd 
be pretty surprised that the topology is causing LINCS warnings/crashes. 
If it were me, I'd definitely simply the situation to begin with and 
look at one of your surfactants in water. This will help you ensure your 
starting structure is fine and also allow you to determine exactly what 
bit of the system is causing the crashes.


Cheers

Tom

On 18/08/17 14:10, edesantis wrote:

Hi,

thank you for both your suggestions,

as Tom, I also think that the structure of the surfactant could be 
modified by the presence of other surfactants in the aggregate form, 
maybe it is not and only the non bonded parameters can have a role in 
the formation of the aggregates (I am quite a beginner of these kind 
of simulation...)


anyway my all atomistic simulation has double purpose,
firstly, since it was the first time I used an ATB created topology, I 
wanted to see if the topology well reproduced the aggregations of 
these kind of surfactants,
and secondly, I want to use the bonds and angles distribution to 
parametrize my Martini model, and see again if also the Martini model 
can reproduce similar aggregates to those seen in the aa simulation




I've tried to continue the simulation using dt=0.00182 ps and after a 
while there are lincs warnings, so it smells like a bad 
parametrization of the all-atomistic topology, as Tom said.
till now I've always simulated standard proteins, so I don't know how 
to parametrize the force field for these small molecules, I am now 
trying PRODRG (once I have the token to use it), if you have other 
suggestion are welcome

for gromos sugar ff, do you have any reference??



for what concern the needed to introduce this kind of molecules,
I think it is quite necessary, these surfactants, use to solubilize 
the proteins in the crystal, are forming micelles around them and, 
since the final goal of my Martini simulation is the reproduce the 
diffuse scattering in the crystals, I think it is quite important to 
reproduce all the crystal components in order to have a system that is 
more similar to the real condition.




thank you again
Emiliano


On 2017-08-18 14:22, Thomas Piggot wrote:

Hi Peter,

I'd imagine that in particular the CG angle parameters between beads
may well be different if you determined them by mapping on to a single
one of these surfactants in water, compared to mapping onto an
ensemble of structures in an aggregated state as the hydrophobic
chains would try to 'fold up' and bury themselves away from the water.
I haven't actually tried this though, that's just how I think it would
probably be. Nice and easy to test anyway, if Emiliano really does
need to parameterise this molecule.

Cheers

Tom

On 18/08/17 09:04, Peter Kroon wrote:

Hi Tom,


thanks for your thoughts :)

I want to respond to your sampling argument: I figured that a 
surfactant

in solution is "more free" to sample conformations due to sterics than
one in an aggregated state, and that sampling would therefore be 
faster.

Your point of sampling the bonded conformations from a solvated vs an
aggregated state is a powerful one though (then again, shouldn't the
difference in aggregated state vs solvated state come from the
non-bonded parameters? i.e. the bonded parameters should be the same 
for

both).


Peter


On 17-08-17 21:10, Piggot T. wrote:

Hi Peter/Emeliano,

I'm not sure I agree with some of what Peter says, but I guess it's 
probably a matter of taste. If it were me, I'd definitely want my 
atomistic simulations to behave properly before trying to develop 
CG parameters based upon these simulations. I know that the 
coarse-graining will lose some of the detail, but I'd want all of 
the detail in the atomistic simulations to be as accurate as 
possible to hopefully develop reasonable CG parameters with the 
appropriate detail lost but the underlying, correct, behaviour 
retained. You cannot be sure of this in your case here.


As for the sampling in the atomistic simulations, I guess you mean 
you could run one in a box a lot quicker as the system is smaller? 
With 50, you obviously have more surfactants in there to give you a 
lot more data for the parameterisaton and as a larger simulation 
size should scale better, you probably will get better sampling (in 
terms of stats) with the 50 in a box setup. Plus you get to also 
check, as Emeliano said, that the atomistic simulations behave 
sensibly and aggregate/form micelles, etc. (whatever this 
surfactant does). You can also look for differences in the CG 
bonds/an

[gmx-users] umbrella sample Question

2017-08-18 Thread yujie liu


Hello，gromacs user

I am a novice, I met some problems when I do this tutorial to learn umbrella 
sample, at 
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/05_pull.html.
 I am using gromacs 5.1.4 and the summary_distances.dat file is not  complete 
while carrying out  ‘perl distances.pl’. Some values of distance between COM of 
Chain_A and Chain_B are empty and some distxxx.xvg files still existing. In 
fact, I checked out some distxxx.xvg and found which existed a value of 
distance but why these values can’t write into summary_distances.dat completely 
by commend ‘perl distances.pl’ ?  There is someone met with the situation??

Thanks 

Yours Liu.
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

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Re: [gmx-users] surfactants simulation topology generation with Automated Topology Builder and lincs warnings


Hi Emiliano,

So I had a spare 5 mins and I found your molecule on the ATB:

https://atb.uq.edu.au/molecule.py?molid=223816#panel-md

Simulating one of these in water doesn't give me any problems with a 2 
fs timestep, so you should check the starting structure of your system 
and also your simulation procedures.


Cheers

Tom

On 18/08/17 14:46, Thomas Piggot wrote:
You shouldn't use PRODRG, well the default output at least (e.g. see 
http://pubs.acs.org/doi/abs/10.1021/ci100335w).


The ATB is generally pretty good, and although it might not be perfect 
here (e.g. as you have sugars in your structure which have been pretty 
heavily optimised in different variants of the GROMOS force field; see 
http://onlinelibrary.wiley.com/doi/10.1002/jcc.24229/abstract and 
http://pubs.acs.org/doi/abs/10.1021/ct300479h amongst other papers), 
I'd be pretty surprised that the topology is causing LINCS 
warnings/crashes. If it were me, I'd definitely simply the situation 
to begin with and look at one of your surfactants in water. This will 
help you ensure your starting structure is fine and also allow you to 
determine exactly what bit of the system is causing the crashes.


Cheers

Tom

On 18/08/17 14:10, edesantis wrote:

Hi,

thank you for both your suggestions,

as Tom, I also think that the structure of the surfactant could be 
modified by the presence of other surfactants in the aggregate form, 
maybe it is not and only the non bonded parameters can have a role in 
the formation of the aggregates (I am quite a beginner of these kind 
of simulation...)


anyway my all atomistic simulation has double purpose,
firstly, since it was the first time I used an ATB created topology, 
I wanted to see if the topology well reproduced the aggregations of 
these kind of surfactants,
and secondly, I want to use the bonds and angles distribution to 
parametrize my Martini model, and see again if also the Martini model 
can reproduce similar aggregates to those seen in the aa simulation




I've tried to continue the simulation using dt=0.00182 ps and after a 
while there are lincs warnings, so it smells like a bad 
parametrization of the all-atomistic topology, as Tom said.
till now I've always simulated standard proteins, so I don't know how 
to parametrize the force field for these small molecules, I am now 
trying PRODRG (once I have the token to use it), if you have other 
suggestion are welcome

for gromos sugar ff, do you have any reference??



for what concern the needed to introduce this kind of molecules,
I think it is quite necessary, these surfactants, use to solubilize 
the proteins in the crystal, are forming micelles around them and, 
since the final goal of my Martini simulation is the reproduce the 
diffuse scattering in the crystals, I think it is quite important to 
reproduce all the crystal components in order to have a system that 
is more similar to the real condition.




thank you again
Emiliano


On 2017-08-18 14:22, Thomas Piggot wrote:

Hi Peter,

I'd imagine that in particular the CG angle parameters between beads
may well be different if you determined them by mapping on to a single
one of these surfactants in water, compared to mapping onto an
ensemble of structures in an aggregated state as the hydrophobic
chains would try to 'fold up' and bury themselves away from the water.
I haven't actually tried this though, that's just how I think it would
probably be. Nice and easy to test anyway, if Emiliano really does
need to parameterise this molecule.

Cheers

Tom

On 18/08/17 09:04, Peter Kroon wrote:

Hi Tom,


thanks for your thoughts :)

I want to respond to your sampling argument: I figured that a 
surfactant

in solution is "more free" to sample conformations due to sterics than
one in an aggregated state, and that sampling would therefore be 
faster.

Your point of sampling the bonded conformations from a solvated vs an
aggregated state is a powerful one though (then again, shouldn't the
difference in aggregated state vs solvated state come from the
non-bonded parameters? i.e. the bonded parameters should be the 
same for

both).


Peter


On 17-08-17 21:10, Piggot T. wrote:

Hi Peter/Emeliano,

I'm not sure I agree with some of what Peter says, but I guess 
it's probably a matter of taste. If it were me, I'd definitely 
want my atomistic simulations to behave properly before trying to 
develop CG parameters based upon these simulations. I know that 
the coarse-graining will lose some of the detail, but I'd want all 
of the detail in the atomistic simulations to be as accurate as 
possible to hopefully develop reasonable CG parameters with the 
appropriate detail lost but the underlying, correct, behaviour 
retained. You cannot be sure of this in your case here.


As for the sampling in the atomistic simulations, I guess you mean 
you could run one in a box a lot quicker as the system is smaller? 
With 50, you obviously have more surfactants in there to give you 
a lot more data for the pa

Re: [gmx-users] surfactants simulation topology generation with Automated Topology Builder and lincs warnings

2017-08-18 Thread edesantis


thanks a lot Tom,

I've used gromocs 53a6 ff, the united atom topology and the original 
pdb,

do you used the same parameters?


should I use the optimised geometry file??


thank again for your precious help

Emiliano



On 2017-08-18 17:26, Thomas Piggot wrote:

Hi Emiliano,

So I had a spare 5 mins and I found your molecule on the ATB:

https://atb.uq.edu.au/molecule.py?molid=223816#panel-md

Simulating one of these in water doesn't give me any problems with a 2
fs timestep, so you should check the starting structure of your system
and also your simulation procedures.

Cheers

Tom

On 18/08/17 14:46, Thomas Piggot wrote:
You shouldn't use PRODRG, well the default output at least (e.g. see 
http://pubs.acs.org/doi/abs/10.1021/ci100335w).


The ATB is generally pretty good, and although it might not be perfect 
here (e.g. as you have sugars in your structure which have been pretty 
heavily optimised in different variants of the GROMOS force field; see 
http://onlinelibrary.wiley.com/doi/10.1002/jcc.24229/abstract and 
http://pubs.acs.org/doi/abs/10.1021/ct300479h amongst other papers), 
I'd be pretty surprised that the topology is causing LINCS 
warnings/crashes. If it were me, I'd definitely simply the situation 
to begin with and look at one of your surfactants in water. This will 
help you ensure your starting structure is fine and also allow you to 
determine exactly what bit of the system is causing the crashes.


Cheers

Tom

On 18/08/17 14:10, edesantis wrote:

Hi,

thank you for both your suggestions,

as Tom, I also think that the structure of the surfactant could be 
modified by the presence of other surfactants in the aggregate form, 
maybe it is not and only the non bonded parameters can have a role in 
the formation of the aggregates (I am quite a beginner of these kind 
of simulation...)


anyway my all atomistic simulation has double purpose,
firstly, since it was the first time I used an ATB created topology, 
I wanted to see if the topology well reproduced the aggregations of 
these kind of surfactants,
and secondly, I want to use the bonds and angles distribution to 
parametrize my Martini model, and see again if also the Martini model 
can reproduce similar aggregates to those seen in the aa simulation




I've tried to continue the simulation using dt=0.00182 ps and after a 
while there are lincs warnings, so it smells like a bad 
parametrization of the all-atomistic topology, as Tom said.
till now I've always simulated standard proteins, so I don't know how 
to parametrize the force field for these small molecules, I am now 
trying PRODRG (once I have the token to use it), if you have other 
suggestion are welcome

for gromos sugar ff, do you have any reference??



for what concern the needed to introduce this kind of molecules,
I think it is quite necessary, these surfactants, use to solubilize 
the proteins in the crystal, are forming micelles around them and, 
since the final goal of my Martini simulation is the reproduce the 
diffuse scattering in the crystals, I think it is quite important to 
reproduce all the crystal components in order to have a system that 
is more similar to the real condition.




thank you again
Emiliano


On 2017-08-18 14:22, Thomas Piggot wrote:

Hi Peter,

I'd imagine that in particular the CG angle parameters between beads
may well be different if you determined them by mapping on to a 
single

one of these surfactants in water, compared to mapping onto an
ensemble of structures in an aggregated state as the hydrophobic
chains would try to 'fold up' and bury themselves away from the 
water.
I haven't actually tried this though, that's just how I think it 
would

probably be. Nice and easy to test anyway, if Emiliano really does
need to parameterise this molecule.

Cheers

Tom

On 18/08/17 09:04, Peter Kroon wrote:

Hi Tom,


thanks for your thoughts :)

I want to respond to your sampling argument: I figured that a 
surfactant
in solution is "more free" to sample conformations due to sterics 
than
one in an aggregated state, and that sampling would therefore be 
faster.
Your point of sampling the bonded conformations from a solvated vs 
an
aggregated state is a powerful one though (then again, shouldn't 
the

difference in aggregated state vs solvated state come from the
non-bonded parameters? i.e. the bonded parameters should be the 
same for

both).


Peter


On 17-08-17 21:10, Piggot T. wrote:

Hi Peter/Emeliano,

I'm not sure I agree with some of what Peter says, but I guess 
it's probably a matter of taste. If it were me, I'd definitely 
want my atomistic simulations to behave properly before trying to 
develop CG parameters based upon these simulations. I know that 
the coarse-graining will lose some of the detail, but I'd want all 
of the detail in the atomistic simulations to be as accurate as 
possible to hopefully develop reasonable CG parameters with the 
appropriate detail lost but the underlying, correct, behaviour 
retained. You can

Re: [gmx-users] surfactants simulation topology generation with Automated Topology Builder and lincs warnings

I used the optimised pdb but I can't imagine it would change anything. I 
also used the united-atom topology and the GROMOS 54A7 force field files 
(the ones from the ATB the also include the parameters for the HS14 atom 
type). I'm pretty sure (IIRC) that there aren't any force field changes 
from 53A6 to 54A7 so as to have influenced your simulations of the molecule.


Cheers

Tom

On 18/08/17 16:39, edesantis wrote:

thanks a lot Tom,

I've used gromocs 53a6 ff, the united atom topology and the original pdb,
do you used the same parameters?


should I use the optimised geometry file??


thank again for your precious help

Emiliano



On 2017-08-18 17:26, Thomas Piggot wrote:

Hi Emiliano,

So I had a spare 5 mins and I found your molecule on the ATB:

https://atb.uq.edu.au/molecule.py?molid=223816#panel-md

Simulating one of these in water doesn't give me any problems with a 2
fs timestep, so you should check the starting structure of your system
and also your simulation procedures.

Cheers

Tom

On 18/08/17 14:46, Thomas Piggot wrote:
You shouldn't use PRODRG, well the default output at least (e.g. see 
http://pubs.acs.org/doi/abs/10.1021/ci100335w).


The ATB is generally pretty good, and although it might not be 
perfect here (e.g. as you have sugars in your structure which have 
been pretty heavily optimised in different variants of the GROMOS 
force field; see 
http://onlinelibrary.wiley.com/doi/10.1002/jcc.24229/abstract and 
http://pubs.acs.org/doi/abs/10.1021/ct300479h amongst other papers), 
I'd be pretty surprised that the topology is causing LINCS 
warnings/crashes. If it were me, I'd definitely simply the situation 
to begin with and look at one of your surfactants in water. This 
will help you ensure your starting structure is fine and also allow 
you to determine exactly what bit of the system is causing the crashes.


Cheers

Tom

On 18/08/17 14:10, edesantis wrote:

Hi,

thank you for both your suggestions,

as Tom, I also think that the structure of the surfactant could be 
modified by the presence of other surfactants in the aggregate 
form, maybe it is not and only the non bonded parameters can have a 
role in the formation of the aggregates (I am quite a beginner of 
these kind of simulation...)


anyway my all atomistic simulation has double purpose,
firstly, since it was the first time I used an ATB created 
topology, I wanted to see if the topology well reproduced the 
aggregations of these kind of surfactants,
and secondly, I want to use the bonds and angles distribution to 
parametrize my Martini model, and see again if also the Martini 
model can reproduce similar aggregates to those seen in the aa 
simulation




I've tried to continue the simulation using dt=0.00182 ps and after 
a while there are lincs warnings, so it smells like a bad 
parametrization of the all-atomistic topology, as Tom said.
till now I've always simulated standard proteins, so I don't know 
how to parametrize the force field for these small molecules, I am 
now trying PRODRG (once I have the token to use it), if you have 
other suggestion are welcome

for gromos sugar ff, do you have any reference??



for what concern the needed to introduce this kind of molecules,
I think it is quite necessary, these surfactants, use to solubilize 
the proteins in the crystal, are forming micelles around them and, 
since the final goal of my Martini simulation is the reproduce the 
diffuse scattering in the crystals, I think it is quite important 
to reproduce all the crystal components in order to have a system 
that is more similar to the real condition.




thank you again
Emiliano


On 2017-08-18 14:22, Thomas Piggot wrote:

Hi Peter,

I'd imagine that in particular the CG angle parameters between beads
may well be different if you determined them by mapping on to a 
single

one of these surfactants in water, compared to mapping onto an
ensemble of structures in an aggregated state as the hydrophobic
chains would try to 'fold up' and bury themselves away from the 
water.
I haven't actually tried this though, that's just how I think it 
would

probably be. Nice and easy to test anyway, if Emiliano really does
need to parameterise this molecule.

Cheers

Tom

On 18/08/17 09:04, Peter Kroon wrote:

Hi Tom,


thanks for your thoughts :)

I want to respond to your sampling argument: I figured that a 
surfactant
in solution is "more free" to sample conformations due to sterics 
than
one in an aggregated state, and that sampling would therefore be 
faster.
Your point of sampling the bonded conformations from a solvated 
vs an

aggregated state is a powerful one though (then again, shouldn't the
difference in aggregated state vs solvated state come from the
non-bonded parameters? i.e. the bonded parameters should be the 
same for

both).


Peter


On 17-08-17 21:10, Piggot T. wrote:

Hi Peter/Emeliano,

I'm not sure I agree with some of what Peter says, but I guess 
it's probably a matter of taste. If it were me, I'd d

Re: [gmx-users] surfactants simulation topology generation with Automated Topology Builder and lincs warnings

Letting the simulation run for a bit longer, I also get LINCS warnings 
after several ns. The issues seem to arise for the sugar part of the 
molecule. This doesn't hugely surprise me, as this part of the ATB 
topology is quite odd with the non-polar hydrogens included for the 
sugar rings (unlike in the normal sugar/carbohydrate GROMOS force fields).


You probably will need to go down the route that I suggested previously 
and manually make the topology though a combination of building blocks 
available within the GROMOS force field(s).


Cheers

Tom

On 18/08/17 16:52, Thomas Piggot wrote:
I used the optimised pdb but I can't imagine it would change anything. 
I also used the united-atom topology and the GROMOS 54A7 force field 
files (the ones from the ATB the also include the parameters for the 
HS14 atom type). I'm pretty sure (IIRC) that there aren't any force 
field changes from 53A6 to 54A7 so as to have influenced your 
simulations of the molecule.


Cheers

Tom

On 18/08/17 16:39, edesantis wrote:

thanks a lot Tom,

I've used gromocs 53a6 ff, the united atom topology and the original 
pdb,

do you used the same parameters?


should I use the optimised geometry file??


thank again for your precious help

Emiliano



On 2017-08-18 17:26, Thomas Piggot wrote:

Hi Emiliano,

So I had a spare 5 mins and I found your molecule on the ATB:

https://atb.uq.edu.au/molecule.py?molid=223816#panel-md

Simulating one of these in water doesn't give me any problems with a 2
fs timestep, so you should check the starting structure of your system
and also your simulation procedures.

Cheers

Tom

On 18/08/17 14:46, Thomas Piggot wrote:
You shouldn't use PRODRG, well the default output at least (e.g. 
see http://pubs.acs.org/doi/abs/10.1021/ci100335w).


The ATB is generally pretty good, and although it might not be 
perfect here (e.g. as you have sugars in your structure which have 
been pretty heavily optimised in different variants of the GROMOS 
force field; see 
http://onlinelibrary.wiley.com/doi/10.1002/jcc.24229/abstract and 
http://pubs.acs.org/doi/abs/10.1021/ct300479h amongst other 
papers), I'd be pretty surprised that the topology is causing LINCS 
warnings/crashes. If it were me, I'd definitely simply the 
situation to begin with and look at one of your surfactants in 
water. This will help you ensure your starting structure is fine 
and also allow you to determine exactly what bit of the system is 
causing the crashes.


Cheers

Tom

On 18/08/17 14:10, edesantis wrote:

Hi,

thank you for both your suggestions,

as Tom, I also think that the structure of the surfactant could be 
modified by the presence of other surfactants in the aggregate 
form, maybe it is not and only the non bonded parameters can have 
a role in the formation of the aggregates (I am quite a beginner 
of these kind of simulation...)


anyway my all atomistic simulation has double purpose,
firstly, since it was the first time I used an ATB created 
topology, I wanted to see if the topology well reproduced the 
aggregations of these kind of surfactants,
and secondly, I want to use the bonds and angles distribution to 
parametrize my Martini model, and see again if also the Martini 
model can reproduce similar aggregates to those seen in the aa 
simulation




I've tried to continue the simulation using dt=0.00182 ps and 
after a while there are lincs warnings, so it smells like a bad 
parametrization of the all-atomistic topology, as Tom said.
till now I've always simulated standard proteins, so I don't know 
how to parametrize the force field for these small molecules, I am 
now trying PRODRG (once I have the token to use it), if you have 
other suggestion are welcome

for gromos sugar ff, do you have any reference??



for what concern the needed to introduce this kind of molecules,
I think it is quite necessary, these surfactants, use to 
solubilize the proteins in the crystal, are forming micelles 
around them and, since the final goal of my Martini simulation is 
the reproduce the diffuse scattering in the crystals, I think it 
is quite important to reproduce all the crystal components in 
order to have a system that is more similar to the real condition.




thank you again
Emiliano


On 2017-08-18 14:22, Thomas Piggot wrote:

Hi Peter,

I'd imagine that in particular the CG angle parameters between beads
may well be different if you determined them by mapping on to a 
single

one of these surfactants in water, compared to mapping onto an
ensemble of structures in an aggregated state as the hydrophobic
chains would try to 'fold up' and bury themselves away from the 
water.
I haven't actually tried this though, that's just how I think it 
would

probably be. Nice and easy to test anyway, if Emiliano really does
need to parameterise this molecule.

Cheers

Tom

On 18/08/17 09:04, Peter Kroon wrote:

Hi Tom,


thanks for your thoughts :)

I want to respond to your sampling argument: I figured that a 
surfactant
in solution

Re: [gmx-users] Use of providing -ix pullx.xvg in WHAM




On 8/17/17 9:38 AM, jay patil wrote:

Hello Experts,
What property we can calculate by providing -ix pullx.xvg through gmx WHAM 
command. Like -if pullf.xvg can give PMF.


You get a PMF.  There are just two different ways to get it, but that's 
all gmx wham does.



Is there way to calculate diffusivity using WHAM command or any other command.


Look at gmx msd.

-Justin

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Re: [gmx-users] CHARMM36 & Gromacs




On 8/17/17 10:18 AM, Mateusz Marianski wrote:

Dear All,

Seems like a trivial issue, but google is not helpful here. I intend 
to run simulations of (branched) carbohydrates in GROMACS 5.x.x using 
CHARMM36 FF (params from 
http://mackerell.umaryland.edu/charmm_ff.shtml). In principle, all 
building blocks are there, but I have no idea how to generate a 
topology file that includes proper glycosidic linkages between the 
subunits. The rtp file contains only 'complete' carbohydrates and I 
don't see any hints about creating glycosidic bonds (linear or branched).


Any help (preferably some tutorial?) here?



You'll have to go into the actual CHARMM force field files (specifically 
top_all36_carb.rtf) and look for the patches that will be used to link 
the monomers (PRES entries).  Those specify changes to atom types and 
charges.  Then you'll need to construct a new .rtp file for the entire 
carbohydrate.  GROMACS is not very good at doing things that are 
branched.  You can try to employ specbond.dat but I suspect that will 
fail given the extent of changes that have to be made.


The other alternative is to use CHARMM-GUI to prepare a topology. As 
long as your residue and atom names are CHARMM-compliant, it should 
generate the system (even files in GROMACS format) just fine.


-Justin

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Re: [gmx-users] Regarding naming dipeptide in charmm36 Forcefield




On 8/18/17 1:13 AM, Dilip H N wrote:

Thank you sir.,
1] If so thn, is there any other possible way such that i can get a peptide
(two aminoacids linked) and thn simulate it in CHARMM FF.. ?? (or) in
alanine dipeptide case which is the residue name in the .rtp file..?? and
how can i remove the n-methyl and  acetyl groups in order to get only
alanine dipeptide...


This doesn't make any sense to me.  The capping groups are what make 
alanine dipeptide (ALAD) what it is, not removing them.


If you need to *generate* coordinates, then that's another matter. 
Plenty of software can do that (see links on gromacs.org).



2] Or should i modify modify any aminoacid (eg., glycine into diglycine)
into a peptide to run the simulation, and if so thn how can i take care of
charges in the peptide (since thee will be removal of H2O molecule between
them and diglycine case there will be some net charge resulting )..
I am running out of ideasSo any suggestions are welcome


Have you run pdb2gmx to process a simple protein or polypeptide? This is 
done for you.  Each amino acid is defined.  If you supply a coordinate 
file with a GLY-GLY peptide, pdb2gmx does everything you need.


-Justin

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Justin A. Lemkul, Ph.D.
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Virginia Tech Department of Biochemistry

303 Engel Hall
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Re: [gmx-users] How to convert C6&C12 from GROMOS54a7 to sigma&epsilon for OPLSAA




On 8/18/17 3:43 AM, Ming Tang wrote:

Dear all,

I want to calculate sigma&epsilon for OPLSAA.ff from C6&C12 developed based on 
GROMOS54a7.ff.

 From the manual, I got the equations:



C12 = Sigma^(6)*C6
C6 = 4*sigma^(6)*epsilon
However, I found sigma and epsilon are different in OPLSAA and AMBER, and that 
C6&C12 from GROMOS and sigma&epsilon from OPLSAA do not match these equations. 
Could anybody give me some guidance?


Mathematically speaking, you can certainly transform one to another, but 
you shouldn't do it.  GROMOS parameters aren't guaranteed to mix with 
any other force field, so convention wisdom is to not waste time trying 
to do it.  Force fields are self-consistent entities. Mixing and 
matching yields a physical model of unknown (likely junk) quality.


-Justin

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Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
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Re: [gmx-users] umbrella sample Question

On 8/18/17 10:54 AM, yujie liu wrote:

Hello，gromacs user

I am a novice, I met some problems when I do this tutorial to learn umbrella
sample, at
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/05_pull.html.
I am using gromacs 5.1.4 and the summary_distances.dat file is not complete
while carrying out ‘perl distances.pl’. Some values of distance between COM of
Chain_A and Chain_B are empty and some distxxx.xvg files still existing. In
fact, I checked out some distxxx.xvg and found which existed a value of
distance but why these values can’t write into summary_distances.dat completely
by commend ‘perl distances.pl’ ? There is someone met with the situation??

People keep telling me that this happens and no one follows up with a
solution. I'd love to solve it once and for all, because I can never
reproduce the problem.

Run gmx distance yourself, not from the script. Something will fail and
you'll get a clear error message that can be used to diagnose the
issue. Without that, it's impossible to help.

-Justin

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

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Re: [gmx-users] How to convert C6&C12 from GROMOS54a7 to sigma&epsilon for OPLSAA

2017-08-18 Thread Ming Tang

Dear Justin,

So happy to see your reply. Thanks for your explanation. The nonbonded 
parameters were developed under GROMOS.ff. I actually used GROMOS.ff for my 
simulations, but I found this force field is not suitable for my protein 
(BMP2), as it unfolded the alpha helix structure which did not happen under 
OPLSAA.ff. Thus, I want to convert the modified C6&C12 under GROMOS to 
sigma&epsilon for OPLSAA, and then run my simulations using OPLSAA.

Thanks,
Ming
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Re: [gmx-users] How to convert C6&C12 from GROMOS54a7 to sigma&epsilon for OPLSAA