Hey Christoph,
Thanks for the input. I was going over the tutorials and I think in my
case, the ibi_lammps should work if I just change the .in.data and
CG-CG.dist.tgt file. When I try to run this (even with the default spce.in
and spce.data file), I get this error:
sh run.sh
running csg_inverse --options "settings.xml"
Appending to existing logfile inverse.log
We are doing Method: ibi
Prepare (dir step_000)
Using initial guess from dist CG-CG.dist.tgt for CG-CG
step 0 done
Doing iteration 1 (dir step_001)
Simulation with lammps
################################################################################################################################################
#
#
# ERROR:
#
# Command/function lmp not found (when calling from csg_call you might need
to add --simprog option or set cg.inverse.program in the xml file) #
# For details see the logfile
/ccs/home/rdguha/votca/csg-tutorials/spce/ibi_lammps/inverse.log
#
#
#
################################################################################################################################################
run.sh: line 4: 2698557 Terminated csg_inverse --options
settings.xml
I have attached the settings.xml file with this email. Do you know what I
have to change and where for lammps to work?
Thanks
On Thu, Jul 8, 2021 at 12:43 PM Christoph Junghans <[email protected]>
wrote:
> On Thu, Jul 8, 2021 at 9:19 AM Rishabh Guha <[email protected]> wrote:
> >
> > I think there is an inconsistency here because these coordinates are
> straight from my LAMMPS data file:-
> > I have 500 beads in 500 molecules for the coarsegraining
> > > -20.153
> > > 0.534
> > > -24.577 -18.68
> > > 3.621
> > > -23.916
> > > an error occurred:
> > > coarse-grained bead is bigger than half the box
> > > (atoms N1 (id 18), O7 (id 22) , molecule 1).
> >
> > 18 1 1 -0.9187999963760376 -20.153000 0.534000 -24.577000
> > 22 1 7 -0.4959999918937683 -18.680000 3.621000 -23.916000
> >
> > Therefore, these are in Angstrom (not nm). So 3.621 - 0.534 is
> technically 0.3087 nm. Not sure why Votca is not doing the nm conversion
> here.
> You are right, I made a fix here:
> https://github.com/votca/csg/pull/697. We fixed it in the dump reader
> before, but seem to have missed it in the LAMMPS data reader.
>
> >
> > Anyways, I tried visualizing the .gro file in VMD and it looks fine.
> Nothing stands out. The initial file was 250 molecules of 2 different types
> of amino acids. Since I mapped each molecule to a single bead I now get 2
> different types of beads each being 250 in number.
> >
> > Can you please give me some pointers on how I proceed now. My aim is to
> generate a CG potential for these amino acid pairs based on RDF calculated
> from the atomistic trajectories. I have already calculated the RDF's from
> the atomistic trajectory but I don't know how I use it in VOTCA.
>
> The csg manual has more details here: https://www.votca.org/csg/index.html
> But in short, you will have to generate input files for Gromacs (or
> LAMMPS) that have everything but the potentials.
> csg_gmxtopol can be a good starting point even though it can only deal
> with one type of molecule, but I usually start with one of the
> tutorials go from there, if you have 2 kinds of molecules, have a look
> at the methanol-water or urea-water tutorials:
> https://github.com/votca/csg-tutorials
>
> Christoph
>
> >
> > I was trying to follow some discussion topics on the group and one of
> them mentions generating a CG topology file using cg_gmxtopol. When I try
> that I am getting this warning :-
> >
> > csg_gmxtopol --top topology.xml --cg "lysine.xml;methionine.xml" --out
> topol.top
> >
> > WARNING: The votca lammps data reader is only able to read lammps files
> formatted in the following styles:
> > angle
> > atom
> > bond
> > full
> > molecule
> >
> > These styles use the following formats in the atom block:
> > atom-ID molecule-ID atom-type charge x y z
> > atom-ID molecule-ID atom-type charge x y z nx ny nz
> > atom-ID molecule-ID atom-type x y z
> > atom-ID molecule-ID atom-type x y z nx ny nz
> > atom-ID atom-type x y z
> > atom-ID atom-type x y z nx ny nz
> >
> > I have 11000 beads in 500 molecules
> > I have 500 beads in 500 molecules for the coarsegraining
> > WARNING: cannot create topology for topology withmultiple molecules,
> using only first molecule
> >
> >
> >
> > On Thu, Jul 8, 2021 at 11:05 AM Christoph Junghans <[email protected]>
> wrote:
> >>
> >> On Thu, Jul 8, 2021 at 8:21 AM Rishabh Guha <[email protected]> wrote:
> >> >
> >> > Hey Christoph,
> >> >
> >> > First of all thanks for following up. Sorry this is gonna be a long
> email but I have some interesting observations based on your question.
> First of all if I try to do a topology dump using my pdb file I don't get a
> "size" of the box per say.
> >> >
> >> > I get this :- I have 8000 beads in 500 molecules
> >> > Boundary Condition: open
> >> >
> >> > Moreover the charges on my atoms are also 0 in the pdb file. I
> figured that for my case, using the LAMMPS data file I generate from my PDB
> file is a better candidate. When I use the LAMMPS data file, the
> identifiers change from 1:ALA:XX to 1:DUM:XX. I did all those changes and
> then if I do csg_dump I get:-
> >> >
> >> > I have 11000 beads in 500 molecules
> >> > Boundary Condition: orthorhombic
> >> > Box matix: 5.76509 0 0
> >> > 0 5.76509 0
> >> > 0 0 5.76509 (It was a different data set which has 11000
> molecules instead of 8000 so that is not an issue)
> >> >
> >> > Now my original LAMMPS data file actually gies from:
> >> > -28.825434 28.825434 xlo xhi
> >> > -28.825434 28.825434 ylo yhi
> >> > -28.825434 28.825434 zlo zhi
> >> >
> >> > So I guess VOTCA doesn't account for the negative coordinates and
> starts everything from 0.
> >> Well, 2x 28.825434 Angstroem = 5.76509 nm, so above it is correct.
> >> VOTCA uses minimum image convention when a box is given, so it is able
> >> deal with negative coordinates.
> >>
> >> >
> >> > I tried csg_map with this and I again got the previous error:
> >> > I have 11000 beads in 500 molecules
> >> > I have 500 beads in 500 molecules for the coarsegraining
> >> > -20.153
> >> > 0.534
> >> > -24.577 -18.68
> >> > 3.621
> >> > -23.916
> >> > an error occurred:
> >> > coarse-grained bead is bigger than half the box
> >> > (atoms N1 (id 18), O7 (id 22) , molecule 1).
> >> Half box length 2.88254 nm, but | 3.621 - 0.534 | (y difference of the
> >> two beads above) is 3.087nm and hence bigger than L/2, so the error
> >> message is correct as well.
> >>
> >> >
> >> > This time around I just increased the box size by a multiplier of 10
> in x,y and z and it worked:
> >> >
> >> > These styles use the following formats in the atom block:
> >> > atom-ID molecule-ID atom-type charge x y z
> >> > atom-ID molecule-ID atom-type charge x y z nx ny nz
> >> > atom-ID molecule-ID atom-type x y z
> >> > atom-ID molecule-ID atom-type x y z nx ny nz
> >> > atom-ID atom-type x y z
> >> > atom-ID atom-type x y z nx ny nz
> >> >
> >> > I have 11000 beads in 500 molecules
> >> > I have 500 beads in 500 molecules for the coarsegraining
> >> > Reading frame, timestep 5000000
> >> > writing coarse-grained trajectory to cg.gro
> >> >
> >> > I wanted to know whether increasing the box size is okay in this case.
> >> When you increase the box size you basically force the atoms in the
> >> 1st image of the periodic box.
> >> One problem with this method is that one could construct a case where
> >> a molecule would be broken into 2 pieces, when some atoms have
> >> coordinates on a different image than other atoms. Only way to know is
> >> to look at the output with vmd or pymol.
> >>
> >> Christoph
> >> >
> >> > Thanks again
> >> >
> >> > On Wed, Jul 7, 2021 at 6:35 PM Christoph Junghans <[email protected]>
> wrote:
> >> >>
> >> >> On Wed, Jul 7, 2021 at 2:18 PM Rishabh Guha <[email protected]> wrote:
> >> >> >
> >> >> > Hey Christoph,
> >> >> >
> >> >> > First of all in my pdb file the atoms are at:-
> >> >> > ATOM 1 CA ALA A 1 11.853 -2.654 0.787 1.00
> 0.00 C
> >> >> > ATOM 2 C ALA A 1 12.896 -2.967 -0.276 1.00
> 0.00 C
> >> >> >
> >> >> > Do you know why votca is dividing all the positions by 10?
> >> >> VOTCA uses nm internally, and pdb is in Angstrom.
> >> >> >
> >> >> > Secondly these atoms show up as-
> >> >> > 0 Name 1:ALA:CA Type CA Mass 12.0107 Resnr 0 Resname ALA Charge 0
> >> >> > 1 Name 1:ALA:C Type C Mass 12.0107 Resnr 0 Resname ALA Charge 0
> >> >> > when I do csg_dump --top topology.xml and are mapped as 1:ALA:CA
> 1:ALA:C 1:ALA:N 1:ALA:H1 1:ALA:H2 1:ALA:CB 1:ALA:HA 1:ALA:HB1 1:ALA:HB2
> 1:ALA:HB3 1:ALA:O 1:ALA:OXT 1:ALA:HXT in the alanine.xml file.
> >> >> >
> >> >> > I do not see any issues in the mapping to be honest
> >> >> When you run csg_dump, what does it tell you the box size is?
> >> >>
> >> >> Christoph
> >> >> >
> >> >> > Regards
> >> >> >
> >> >> > On Wed, Jul 7, 2021 at 4:09 PM Christoph Junghans <
> [email protected]> wrote:
> >> >> >>
> >> >> >>
> >> >> >>
> >> >> >> On Wed, Jul 7, 2021, 14:05 Rishabh Guha <[email protected]> wrote:
> >> >> >>>
> >> >> >>> Hey Christoph,
> >> >> >>>
> >> >> >>> Thanks for the pointers. I tried to look closely into my mapping
> files and compared them with the pdb files, but nothing jumped out at me.
> Although I admit that it can easily be an oversight-I have just started
> using Votca today. I have attached all my files below. Does anything jump
> out at you? I am convinced that none of my atoms are than half the box
> length away
> >> >> >>
> >> >> >> The error says there is an atom at 1.1853
> >> >> >> -0.2654 0.0787 and one at 1.2896 -0.2967 -0.0276 that you are
> trying to map in a cg bead. These are the ones you have to look at
> carefully in the mapping file.
> >> >> >>
> >> >> >> Christoph
> >> >> >>
> >> >> >>>
> >> >> >>>
> >> >> >>> Regards
> >> >> >>>
> >> >> >>> On Wed, Jul 7, 2021 at 3:55 PM Christoph Junghans <
> [email protected]> wrote:
> >> >> >>>>
> >> >> >>>>
> >> >> >>>>
> >> >> >>>> On Wed, Jul 7, 2021 at 13:44 Rishabh Guha <[email protected]>
> wrote:
> >> >> >>>>>
> >> >> >>>>> Hey Christoph,
> >> >> >>>>>
> >> >> >>>>> Thanks for the help. I got to know about the csg_dump command
> as soon as I sent you the email. For some reason, csg_dump is categorizing
> all the atoms as the valine molecules as ALA as well, which is
> counterintuitive to me.
> >> >> >>>>
> >> >> >>>> yeah, there is a way to fix this, these are just unique
> identifiers so it doesn’t matter a lot what they are as long as they are
> unique. This artifact mainly stems from the fact that the pdb format misses
> some molecule information.
> >> >> >>>>
> >> >> >>>>
> >> >> >>>>
> >> >> >>>>> But I did change my valine.xml file to:-
> >> >> >>>>>
> >> >> >>>>> <cg_molecule>
> >> >> >>>>> <name>VAL</name>
> >> >> >>>>> <ident>VAL</ident>
> >> >> >>>>> <topology>
> >> >> >>>>> <cg_beads>
> >> >> >>>>> <cg_bead>
> >> >> >>>>> <name>VAL</name>
> >> >> >>>>> <type>VAL</type>
> >> >> >>>>> <mapping>A</mapping>
> >> >> >>>>> <beads>
> >> >> >>>>> 1:ALA:CA 1:ALA:C 1:ALA:N 1:ALA:H1 1:ALA:H2 1:ALA:CB
> 1:ALA:HA 1:ALA:CG1 1:ALA:HG11 1:ALA:HG12 1:ALA:HG13 1:ALA:CG2 1:ALA:HB
> 1:ALA:HG21 1:ALA:HG22 1:ALA:HG23 1:ALA:O 1:ALA:OXT 1:ALA:HXT
> >> >> >>>>> </beads>
> >> >> >>>>> </cg_bead>
> >> >> >>>>> </cg_beads>
> >> >> >>>>> </topology>
> >> >> >>>>> <maps>
> >> >> >>>>> <map>
> >> >> >>>>> <name>A</name>
> >> >> >>>>> <weights>12 12 14 1 1 12 1 12 1 1 1 12 1 1 1 1 16 16
> 1</weights>
> >> >> >>>>> </map>
> >> >> >>>>> </maps>
> >> >> >>>>> </cg_molecule>
> >> >> >>>>>
> >> >> >>>>> Now, I get a different error,
> >> >> >>>>> I have 8000 beads in 500 molecules
> >> >> >>>>> I have 500 beads in 500 molecules for the coarsegraining
> >> >> >>>>> 1.1853
> >> >> >>>>> -0.2654
> >> >> >>>>> 0.0787 1.2896
> >> >> >>>>> -0.2967
> >> >> >>>>> -0.0276
> >> >> >>>>> an error occurred:
> >> >> >>>>> coarse-grained bead is bigger than half the box
> >> >> >>>>> (atoms CA (id 1), C (id 2) , molecule 1)
> >> >> >>>>>
> >> >> >>>>> Can you please tell me what I can change?
> >> >> >>>>
> >> >> >>>> this error means you are trying to map teo atoms that are more
> than half a box length away into one cg bead. The 6 number above are the
> positions.
> >> >> >>>>
> >> >> >>>> There can be multiple reasons for that error, most of the times
> it is a typo in the mapping file. If you are sure things are correct, you
> can always make the box bigger.
> >> >> >>>>
> >> >> >>>> Christoph
> >> >> >>>>>
> >> >> >>>>>
> >> >> >>>>>
> >> >> >>>>> On Wed, Jul 7, 2021 at 3:29 PM Christoph Junghans <
> [email protected]> wrote:
> >> >> >>>>>>
> >> >> >>>>>>
> >> >> >>>>>>
> >> >> >>>>>> On Wed, Jul 7, 2021 at 13:23 Rishabh Guha <[email protected]>
> wrote:
> >> >> >>>>>>>
> >> >> >>>>>>> Hello,
> >> >> >>>>>>>
> >> >> >>>>>>> I have an atomistic system consisting of 250 alanine and 250
> valine molecules. I am trying to use cg_map using the pdb file and the
> LAMMPS output trajectory, but I am getting an error:-
> >> >> >>>>>>> cannot find: <1:VAL:CA> in VAL
> >> >> >>>>>>> an error occurred:
> >> >> >>>>>>> mapping error: molecule 1:VAL:CA does not exist
> >> >> >>>>>>
> >> >> >>>>>> try to run “csg_dump --top topol.xml” and check how VOTCA
> labels things.
> >> >> >>>>>>
> >> >> >>>>>> Christoph
> >> >> >>>>>>
> >> >> >>>>>>>
> >> >> >>>>>>> My topology file looks like:-
> >> >> >>>>>>> <topology base="temp.pdb">
> >> >> >>>>>>> <molecules>
> >> >> >>>>>>> <clear/>
> >> >> >>>>>>> <define name="ALA" first="1" nbeads="13" nmols="250"/>
> >> >> >>>>>>> <define name="VAL" first="3251" nbeads="19" nmols="250"/>
> >> >> >>>>>>> </molecules>
> >> >> >>>>>>> </topology>
> >> >> >>>>>>>
> >> >> >>>>>>> My individual alanine and valine xml files are:-
> >> >> >>>>>>> Alanine-
> >> >> >>>>>>> <cg_molecule>
> >> >> >>>>>>> <name>ALA</name>
> >> >> >>>>>>> <ident>ALA</ident>
> >> >> >>>>>>> <topology>
> >> >> >>>>>>> <cg_beads>
> >> >> >>>>>>> <cg_bead>
> >> >> >>>>>>> <name>ALA</name>
> >> >> >>>>>>> <type>ALA</type>
> >> >> >>>>>>> <mapping>A</mapping>
> >> >> >>>>>>> <beads>
> >> >> >>>>>>> 1:ALA:CA 1:ALA:C 1:ALA:N 1:ALA:H1 1:ALA:H2
> 1:ALA:CB 1:ALA:HA 1:ALA:HB1 1:ALA:HB2 1:ALA:HB3 1:ALA:O 1:ALA:OXT 1:ALA:HXT
> >> >> >>>>>>> </beads>
> >> >> >>>>>>> </cg_bead>
> >> >> >>>>>>> </cg_beads>
> >> >> >>>>>>> </topology>
> >> >> >>>>>>> <maps>
> >> >> >>>>>>> <map>
> >> >> >>>>>>> <name>A</name>
> >> >> >>>>>>> <weights>12 12 14 1 1 12 1 1 1 1 16 16 1</weights>
> >> >> >>>>>>> </map>
> >> >> >>>>>>> </maps>
> >> >> >>>>>>> </cg_molecule>
> >> >> >>>>>>>
> >> >> >>>>>>> Valine
> >> >> >>>>>>> <cg_molecule>
> >> >> >>>>>>> <name>VAL</name>
> >> >> >>>>>>> <ident>VAL</ident>
> >> >> >>>>>>> <topology>
> >> >> >>>>>>> <cg_beads>
> >> >> >>>>>>> <cg_bead>
> >> >> >>>>>>> <name>VAL</name>
> >> >> >>>>>>> <type>VAL</type>
> >> >> >>>>>>> <mapping>A</mapping>
> >> >> >>>>>>> <beads>
> >> >> >>>>>>> 1:VAL:CA 1:VAL:C 1:VAL:N 1:VAL:H1 1:VAL:H2
> 1:VAL:CB 1:VAL:HA 1:VAL:CG1 1:VAL:HG11 1:VAL:HG12 1:VAL:HG13 1:VAL:CG2
> 1:VAL:HB 1:VAL:HG21 1:VAL:HG22 1:VAL:HG23 1:VAL:O 1:VAL:OXT 1:VAL:HXT
> >> >> >>>>>>> </beads>
> >> >> >>>>>>> </cg_bead>
> >> >> >>>>>>> </cg_beads>
> >> >> >>>>>>> </topology>
> >> >> >>>>>>> <maps>
> >> >> >>>>>>> <map>
> >> >> >>>>>>> <name>A</name>
> >> >> >>>>>>> <weights>12 12 14 1 1 12 1 12 1 1 1 12 1 1 1 1 16 16
> 1</weights>
> >> >> >>>>>>> </map>
> >> >> >>>>>>> </maps>
> >> >> >>>>>>> </cg_molecule>
> >> >> >>>>>>>
> >> >> >>>>>>> I have attached the pdb file for further reference.
> >> >> >>>>>>>
> >> >> >>>>>>> Can anyone please help me with this?
> >> >> >>>>>>>
> >> >> >>>>>>> --
> >> >> >>>>>>> Join us on Slack: https://join.slack.com/t/votca/signup
> >> >> >>>>>>> ---
> >> >> >>>>>>> You received this message because you are subscribed to the
> Google Groups "votca" group.
> >> >> >>>>>>> To unsubscribe from this group and stop receiving emails
> from it, send an email to [email protected].
> >> >> >>>>>>> To view this discussion on the web visit
> https://groups.google.com/d/msgid/votca/3c0b76f3-ff3a-4013-8b74-d366e1e9c865n%40googlegroups.com
> .
> >> >> >>>>>>
> >> >> >>>>>> --
> >> >> >>>>>> Christoph Junghans
> >> >> >>>>>> Web: http://www.compphys.de
> >> >> >>>>>>
> >> >> >>>>>> --
> >> >> >>>>>> Join us on Slack: https://join.slack.com/t/votca/signup
> >> >> >>>>>> ---
> >> >> >>>>>>
> >> >> >>>>>> You received this message because you are subscribed to a
> topic in the Google Groups "votca" group.
> >> >> >>>>>> To unsubscribe from this topic, visit
> https://groups.google.com/d/topic/votca/C3L0xhdUs6s/unsubscribe.
> >> >> >>>>>> To unsubscribe from this group and all its topics, send an
> email to [email protected].
> >> >> >>>>>> To view this discussion on the web visit
> https://groups.google.com/d/msgid/votca/CAHG27e7WZfOD2xdHy1AWWob7zNtdr5cBpYydNGp0WmA9sfqO9w%40mail.gmail.com
> .
> >> >> >>>>>
> >> >> >>>>>
> >> >> >>>>>
> >> >> >>>>> --
> >> >> >>>>> Rishabh Debraj Guha(PhD student)
> >> >> >>>>>
> >> >> >>>>> Graduate Research Assistant
> >> >> >>>>> Mechanical and Aerospace Engineering
> >> >> >>>>> North Carolina State University
> >> >> >>>>> Contact:- +1-347-205-2280
> >> >> >>>>>
> >> >> >>>>> --
> >> >> >>>>> Join us on Slack: https://join.slack.com/t/votca/signup
> >> >> >>>>> ---
> >> >> >>>>> You received this message because you are subscribed to the
> Google Groups "votca" group.
> >> >> >>>>> To unsubscribe from this group and stop receiving emails from
> it, send an email to [email protected].
> >> >> >>>>> To view this discussion on the web visit
> https://groups.google.com/d/msgid/votca/CAFKQktCXqB_zefYDpusjSBnLkt%2B77vfkgnU-dovocsFsiiKUow%40mail.gmail.com
> .
> >> >> >>>>
> >> >> >>>> --
> >> >> >>>> Christoph Junghans
> >> >> >>>> Web: http://www.compphys.de
> >> >> >>>>
> >> >> >>>> --
> >> >> >>>> Join us on Slack: https://join.slack.com/t/votca/signup
> >> >> >>>> ---
> >> >> >>>> You received this message because you are subscribed to a topic
> in the Google Groups "votca" group.
> >> >> >>>> To unsubscribe from this topic, visit
> https://groups.google.com/d/topic/votca/C3L0xhdUs6s/unsubscribe.
> >> >> >>>> To unsubscribe from this group and all its topics, send an
> email to [email protected].
> >> >> >>>> To view this discussion on the web visit
> https://groups.google.com/d/msgid/votca/CAHG27e6Kjvwxvv4suXuuqLSQ57AJeh_Vi-CepLi4A%3DXb9MmzWg%40mail.gmail.com
> .
> >> >> >>>
> >> >> >>>
> >> >> >>>
> >> >> >>> --
> >> >> >>> Rishabh Debraj Guha(PhD student)
> >> >> >>>
> >> >> >>> Graduate Research Assistant
> >> >> >>> Mechanical and Aerospace Engineering
> >> >> >>> North Carolina State University
> >> >> >>> Contact:- +1-347-205-2280
> >> >> >>>
> >> >> >>> --
> >> >> >>> Join us on Slack: https://join.slack.com/t/votca/signup
> >> >> >>> ---
> >> >> >>> You received this message because you are subscribed to the
> Google Groups "votca" group.
> >> >> >>> To unsubscribe from this group and stop receiving emails from
> it, send an email to [email protected].
> >> >> >>> To view this discussion on the web visit
> https://groups.google.com/d/msgid/votca/CAFKQktBEGaPFAtudiU20y7Y-0pwe1jS2XXnvShd0kyXvfBLuOQ%40mail.gmail.com
> .
> >> >> >>
> >> >> >> --
> >> >> >> Join us on Slack: https://join.slack.com/t/votca/signup
> >> >> >> ---
> >> >> >> You received this message because you are subscribed to a topic
> in the Google Groups "votca" group.
> >> >> >> To unsubscribe from this topic, visit
> https://groups.google.com/d/topic/votca/C3L0xhdUs6s/unsubscribe.
> >> >> >> To unsubscribe from this group and all its topics, send an email
> to [email protected].
> >> >> >> To view this discussion on the web visit
> https://groups.google.com/d/msgid/votca/CAHG27e4ypf5Po8_zKmhBSbSTW_xgGBu09Bmj6Nsh8KdQtYJN-Q%40mail.gmail.com
> .
> >> >> >
> >> >> >
> >> >> >
> >> >> > --
> >> >> > Rishabh Debraj Guha(PhD student)
> >> >> >
> >> >> > Graduate Research Assistant
> >> >> > Mechanical and Aerospace Engineering
> >> >> > North Carolina State University
> >> >> > Contact:- +1-347-205-2280
> >> >> >
> >> >> > --
> >> >> > Join us on Slack: https://join.slack.com/t/votca/signup
> >> >> > ---
> >> >> > You received this message because you are subscribed to the Google
> Groups "votca" group.
> >> >> > To unsubscribe from this group and stop receiving emails from it,
> send an email to [email protected].
> >> >> > To view this discussion on the web visit
> https://groups.google.com/d/msgid/votca/CAFKQktBH-gARMiCQR%2BdJVudO95mHB5ZZkf6odZJDxmp6U2a-nQ%40mail.gmail.com
> .
> >> >>
> >> >>
> >> >>
> >> >> --
> >> >> Christoph Junghans
> >> >> Web: http://www.compphys.de
> >> >>
> >> >> --
> >> >> Join us on Slack: https://join.slack.com/t/votca/signup
> >> >> ---
> >> >> You received this message because you are subscribed to a topic in
> the Google Groups "votca" group.
> >> >> To unsubscribe from this topic, visit
> https://groups.google.com/d/topic/votca/C3L0xhdUs6s/unsubscribe.
> >> >> To unsubscribe from this group and all its topics, send an email to
> [email protected].
> >> >> To view this discussion on the web visit
> https://groups.google.com/d/msgid/votca/CAHG27e58qQRPUVC07BnJTeMtkm5StheQQTxsSQsDo_fOQz8Lcw%40mail.gmail.com
> .
> >> >
> >> >
> >> >
> >> > --
> >> > Rishabh Debraj Guha(PhD student)
> >> >
> >> > Graduate Research Assistant
> >> > Mechanical and Aerospace Engineering
> >> > North Carolina State University
> >> > Contact:- +1-347-205-2280
> >> >
> >> > --
> >> > Join us on Slack: https://join.slack.com/t/votca/signup
> >> > ---
> >> > You received this message because you are subscribed to the Google
> Groups "votca" group.
> >> > To unsubscribe from this group and stop receiving emails from it,
> send an email to [email protected].
> >> > To view this discussion on the web visit
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> .
> >>
> >>
> >>
> >> --
> >> Christoph Junghans
> >> Web: http://www.compphys.de
> >>
> >> --
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> .
> >
> >
> >
> > --
> > Rishabh Debraj Guha(PhD student)
> >
> > Graduate Research Assistant
> > Mechanical and Aerospace Engineering
> > North Carolina State University
> > Contact:- +1-347-205-2280
> >
> > --
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> .
>
>
>
> --
> Christoph Junghans
> Web: http://www.compphys.de
>
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> .
>
--
Rishabh Debraj Guha(PhD student)
Graduate Research Assistant
Mechanical and Aerospace Engineering
North Carolina State University
Contact:- +1-347-205-2280
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<cg>
<!-- example for a non-bonded interaction entry -->
<non-bonded>
<!-- name of the interaction -->
<name>CG-CG</name>
<!-- types involved in this interaction -->
<type1>Bead1</type1>
<type2>Bead1</type2>
<!-- dimension + grid spacing of tables for calculations -->
<min>0.0</min>
<max>0.9</max>
<step>0.01</step>
<inverse>
<!-- target distribution (rdf) -->
<target>CG-CG.dist.tgt</target>
<lammps>
<!-- name of the table for lammps run -->
<table>CG_CG.pot</table>
<!-- nm to angstrom -->
<scale>10</scale>
<!-- kJ/mol to kcal/mol -->
<y_scale>0.239006</y_scale>
<table_begin>0.20</table_begin>
<table_bins>0.002</table_bins>
</lammps>
</inverse>
</non-bonded>
<!-- general options for inverse script -->
<inverse>
<!-- votca units 300*0.00831451 kJ/mol -->
<kBT>2.49435</kBT>
<!-- use lammps as simulation program -->
<program>lammps</program>
<!-- lammps specific options -->
<lammps>
<!-- lammps script to run !-->
<script>spce.in</script>
<!-- topology to be used by csg_stat !-->
<topol>spce.data</topol>
<!-- traj file created by lammps !-->
<traj>traj.dump</traj>
</lammps>
<initial_configuration>maindir</initial_configuration>
<!-- these files are copied for each new run -->
<filelist>spce.data spce.in</filelist>
<!-- do so many iterations -->
<iterations_max>300</iterations_max>
<!-- ibi: inverse biltzmann imc: inverse monte carlo -->
<method>ibi</method>
</inverse>
</cg>
