Re: [gmx-users] Center to center distance in cylindrical micelles

[Antonio Baptista]

You didn't give us much info about your system, so I will assume that your 
box is a rectangular prism and that all the cylinders are necessarily 
oriented along the z axis (e.g., because they are "infinite"/periodic). 
Since the center of mass (COM) of each cylinder must be a point on its 
axis, you simply need to compute the COMs of each cylinder and then 
compute any intended distances between their axes using just the xy 
components.



On Fri, 17 Aug 2018, Shan Jayasinghe wrote:


Hi All,

Does anyone know how to calculate distance between two adjacent cylinders
in a  hexagonal array?

Thank you.


On Sun, Aug 12, 2018 at 8:01 AM Shan Jayasinghe <
shanjayasinghe2...@gmail.com> wrote:


Hi,

Actually, I want to calculate the lattice parameter (distance between two
cylinders) of hexagonal phase. Appreciate, if you could help me.

Thank you.




On Sat, Aug 11, 2018 at 11:11 PM Mark Abraham 
wrote:


Hi,

A center is a point. I don't see how you would define a central point of
an
infinite cylinder.

Mark

On Sat, Aug 11, 2018, 14:47 Shan Jayasinghe 


wrote:


Hi,

I'm sorry for not providing the detail description of my system.

Actually

it is a hexagonal phase. Therefore, four cylindrical micelles can be

seen

in a cell. I want to calculate the center to center distance of two
cylindrical micelles.

On Sat, Aug 11, 2018 at 8:35 PM Mark Abraham 
wrote:


Hi,

There is an axis of each cylinder but the two won't be parallel so

there

is

no unique distance to measure. So I suggest thinking carefully about

what

you really want.

Mark

On Sat, Aug 11, 2018, 06:58 Shan Jayasinghe <

shanjayasinghe2...@gmail.com>

wrote:


Hi,

I tried to used gmx distance. However, I don't understand how can I

define

the center of the circle face of the cylinder to the same in the

other

cylindrical micelle.

Can anyone help me?
Thank you.


On Sat, Aug 11, 2018 at 9:33 AM Mark Abraham <

mark.j.abra...@gmail.com



wrote:


Hi,

Have you looked at the different tools available and considered

what

might

be useful for you?

Mark

On Fri, Aug 10, 2018, 07:34 Shan Jayasinghe <

shanjayasinghe2...@gmail.com>

wrote:


Dear Gromacs Users,

I want to calculate the center to center distance of two

cylindrical

micelles in my simulation. What gmx command should I use to

calculate

the

distance? Can anyone help me?

Thank you.
--
Gromacs Users mailing list

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

before

posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit


https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users

or

send a mail to gmx-users-requ...@gromacs.org.


--
Gromacs Users mailing list

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

before

posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit


https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users

or

send a mail to gmx-users-requ...@gromacs.org.




--
Best Regards
Shan Jayasinghe
--
Gromacs Users mailing list

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

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users

or

send a mail to gmx-users-requ...@gromacs.org.


--
Gromacs Users mailing list

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

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
send a mail to gmx-users-requ...@gromacs.org.




--
Best Regards
Shan Jayasinghe
--
Gromacs Users mailing list

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

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
send a mail to gmx-users-requ...@gromacs.org.


--
Gromacs Users mailing list

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

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
send a mail to gmx-users-requ...@gromacs.org.




--
Best Regards
Shan Jayasinghe




--
Best Regards
Shan Jayasinghe
--
Gromacs Users mailing list

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

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to 

Re: [gmx-users] gmx clustsize

[Justin Lemkul]

On 8/20/18 3:25 PM, Pandya, Akash wrote:

Hi all,

I am trying to find out how many clusters I have of my ligand during the course 
of my trajectory using gmx clustsize.

I type the following command and get an error message:


gmx clustsize -s glycine.tpr -f glycine.gro -nc nclust.xvg -hc histo-clust.xvg 
-mol




Program: gmx clustsize, version 2016.2
Source file: src/gromacs/fileio/matio.cpp (line 690)

Fatal error:
Lo: 0.00, Mid: 1.00, Hi: 1.00

For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors


Could anyone help me with this problem? I know for a fact that I don't just 
have one cluster of glycine (by inspection).


The clustsize program is for determining the physical size of a cluster 
of multiple molecules (think aggregated proteins or micelles). If you 
want to do structure-based clustering, that's gmx cluster.


-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.thelemkullab.com

==

--
Gromacs Users mailing list

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

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

[gmx-users] gmx clustsize

[Pandya, Akash]

Hi all,

I am trying to find out how many clusters I have of my ligand during the course 
of my trajectory using gmx clustsize.

I type the following command and get an error message:


gmx clustsize -s glycine.tpr -f glycine.gro -nc nclust.xvg -hc histo-clust.xvg 
-mol




Program: gmx clustsize, version 2016.2
Source file: src/gromacs/fileio/matio.cpp (line 690)

Fatal error:
Lo: 0.00, Mid: 1.00, Hi: 1.00

For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors


Could anyone help me with this problem? I know for a fact that I don't just 
have one cluster of glycine (by inspection).

Thank you,

Akash

-- 
Gromacs Users mailing list

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

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] [Install error] What can I do this situation?

[Szilárd Páll]

On Mon, Aug 20, 2018 at 2:54 PM 김나연  wrote:

> There is error messages. TT
> 1) What can I do??
>

Install manually. The installation warnings suggest that you are risking
strange failures (due to mixing C++ libraries).


> 2) If this process succeeds, can I do GPU calculations in mdrun?
>

Yes, if the homebrew package was built with GPU support.


> 3) I think gromacs only supports gcc.


That's not correct.


> But I heard that installing gcc and home-brew at the same time will result
> in an unknown error. Is that right?
>

No idea. Have you tried?

Error Messages (In fact, installation messages)
>
> iMac-pro:Desktop$ brew install gromacs
> Updating Homebrew...
> ==> Auto-updated Homebrew!
> Updated 1 tap (homebrew/core).
> No changes to formulae.
>
> ==> Installing dependencies for gromacs: fftw, gsl
> ==> Installing gromacs dependency: fftw
> ==> Downloading
> https://homebrew.bintray.com/bottles/fftw-3.3.8.high_sierra.bottle.tar.gz
> 
> 100.0%
> ==> Pouring fftw-3.3.8.high_sierra.bottle.tar.gz
>   /usr/local/Cellar/fftw/3.3.8: 52 files, 10.8MB
> ==> Installing gromacs dependency: gsl
> ==> Downloading
> https://homebrew.bintray.com/bottles/gsl-2.5.high_sierra.bottle.tar.gz
> 
> 100.0%
> ==> Pouring gsl-2.5.high_sierra.bottle.tar.gz
>   /usr/local/Cellar/gsl/2.5: 271 files, 9.2MB
> ==> Installing gromacs
> ==> Downloading
> https://homebrew.bintray.com/bottles/gromacs-2018.2.high_sierra.bottle.tar.gz
> 
> 100.0%
> ==> Pouring gromacs-2018.2.high_sierra.bottle.tar.gz
> Warning: gromacs dependency gcc was built with a different C++ standard
> library (libstdc++ from clang). This may cause problems at runtime.
> ==> Caveats
> GMXRC and other scripts installed to:
>   /usr/local/share/gromacs
>
> Bash completion has been installed to:
>   /usr/local/etc/bash_completion.d
>
> zsh completions have been installed to:
>   /usr/local/share/zsh/site-functions
> ==> Summary
>   /usr/local/Cellar/gromacs/2018.2: 705 files, 20.4MB
> ==> Caveats
> ==> gromacs
> GMXRC and other scripts installed to:
>   /usr/local/share/gromacs
>
> Bash completion has been installed to:
>   /usr/local/etc/bash_completion.d
>
> zsh completions have been installed to:
>   /usr/local/share/zsh/site-functions
>
>
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
-- 
Gromacs Users mailing list

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

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

[gmx-users] [Install error] What can I do this situation?

[김나연]

There is error messages. TT
1) What can I do??
2) If this process succeeds, can I do GPU calculations in mdrun? 
3) I think gromacs only supports gcc. But I heard that installing gcc and 
home-brew at the same time will result in an unknown error. Is that right?


Error Messages (In fact, installation messages)

iMac-pro:Desktop$ brew install gromacs
Updating Homebrew...
==> Auto-updated Homebrew!
Updated 1 tap (homebrew/core).
No changes to formulae.

==> Installing dependencies for gromacs: fftw, gsl
==> Installing gromacs dependency: fftw
==> Downloading 
https://homebrew.bintray.com/bottles/fftw-3.3.8.high_sierra.bottle.tar.gz
 100.0%
==> Pouring fftw-3.3.8.high_sierra.bottle.tar.gz
  /usr/local/Cellar/fftw/3.3.8: 52 files, 10.8MB
==> Installing gromacs dependency: gsl
==> Downloading 
https://homebrew.bintray.com/bottles/gsl-2.5.high_sierra.bottle.tar.gz
 100.0%
==> Pouring gsl-2.5.high_sierra.bottle.tar.gz
  /usr/local/Cellar/gsl/2.5: 271 files, 9.2MB
==> Installing gromacs
==> Downloading 
https://homebrew.bintray.com/bottles/gromacs-2018.2.high_sierra.bottle.tar.gz
 100.0%
==> Pouring gromacs-2018.2.high_sierra.bottle.tar.gz
Warning: gromacs dependency gcc was built with a different C++ standard
library (libstdc++ from clang). This may cause problems at runtime.
==> Caveats
GMXRC and other scripts installed to:
  /usr/local/share/gromacs

Bash completion has been installed to:
  /usr/local/etc/bash_completion.d

zsh completions have been installed to:
  /usr/local/share/zsh/site-functions
==> Summary
  /usr/local/Cellar/gromacs/2018.2: 705 files, 20.4MB
==> Caveats
==> gromacs
GMXRC and other scripts installed to:
  /usr/local/share/gromacs

Bash completion has been installed to:
  /usr/local/etc/bash_completion.d

zsh completions have been installed to:
  /usr/local/share/zsh/site-functions



-- 
Gromacs Users mailing list

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

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] Getting ligand's topology

[Justin Lemkul]

On 8/20/18 2:40 AM, Mahdi Sobati Nezhad wrote:

thanks for your taking time. and so on for a begginer like me there is no
any way


Well, there is if you're willing to invest the time in learning some 
challenging concepts and some new software. But no one should expect 
that for any given ligand, there is a perfect tool for magically giving 
you a perfect topology. That's rarely the case.


-Justin


On Mon, 20 Aug 2018 00:29 Justin Lemkul,  wrote:



On 8/19/18 10:20 AM, RAHUL SURESH wrote:

Hi.

First, I feel grimaces users may not entertain other discussions in

grimace

forum. You can directly mail me if it’s something apart from gromacs.

Then, I am not sure about other servers.

Looking at your str file, I would say that it definitely need some work

on

our molecule. As I said before try zinc database.

I don't see how the ZINC database is relevant. Either the .mol2
submitted to the CGenFF server is valid or it is not.

CGenFF is nice in that it tells you the potential problems with the
ligand topology. AFAIK, no other servers do. You get a "black box"
output that you're supposed to trust. The areas pinpointed by CGenFF
should be examined carefully. The parameters may actually be fine, but
the penalties are there to tell the user when there is a functional
group that is not well described by existing molecules in the CGenFF
database, from which the analogies are made.

There is a CGenFF tutorial available online that walks a user through
the whole process. It requires subdividing a molecule into units that
can be parametrized easily; large molecules should always be broken down
into manageable pieces that have all the necessary degrees of freedom.

The tutorial materials can be accessed here:
http://mackerell.umaryland.edu/~kenno/cgenff/download.php

CHARMM/CGenFF parametrization assumes some familiarity with QM
calculations (geometry optimizations, potential energy scans,
interaction energies) but the methodology is published in great detail,
and the CGenFF paper itself is a worked example of how to parametrize a
molecule. While the developers have made every effort to make the
methodology publicly available, ligand parametrization and refinement is
still an advanced concept that is best suited for experienced users, as
knowledge of fundamental principles of MD, QM, and empirical energy
functions is required.

-Justin


Thank you


On Sun, 19 Aug 2018 at 1:37 PM, Mahdi Sobati Nezhad <
mahdisobatinez...@gmail.com> wrote:


thanks.
if I use MATCH server or swissparam, I can trust to their results?!

And this is my error when I use CGenFF:
"readmol2 warning: non-unique atoms were renamed. Now processing

molecule

mae ..."

And this is my output of penalty:

* Toppar stream file generated by * CHARMM General Force Field (CGenFF)
program version 2.2.0 * For use with CGenFF version 4.0 * read rtf card
append * Topologies generated by * CHARMM General Force Field (CGenFF)
program version 2.2.0 * 36 1 ! "penalty" is the highest penalty score of
the associated parameters. ! Penalties lower than 10 indicate the

analogy

is fair; penalties between 10 ! and 50 mean some basic validation is
recommended; penalties higher than ! 50 indicate poor analogy and

mandate

extensive validation/optimization. RESI mae 0.000 ! param penalty=

198.400

; charge penalty= 142.287 GROUP ! CHARGE CH_PENALTY ATOM C1 CG2R61

0.227 !

0.000 ATOM C2 CG2R61 -0.117 ! 2.688 ATOM C3 CG2R61 -0.003 ! 5.191 ATOM

C4

CG2R61 -0.117 ! 2.688 ATOM C5 CG2R61 0.227 ! 0.000 ATOM C6 CG2R61 0.217

!

0.000 ATOM H1 HGR61 0.115 ! 0.000 ATOM H2 HGR61 0.115 ! 0.000 ATOM O1

OG301

-0.391 ! 0.000 ATOM O2 OG301 -0.391 ! 0.000 ATOM O3 OG301 -0.391 ! 0.000
ATOM C7 CG331 -0.100 ! 0.000 ATOM H3 HGA3 0.090 ! 0.000 ATOM H4 HGA3

0.090

! 0.000 ATOM H5 HGA3 0.090 ! 0.000 ATOM C8 CG331 -0.100 ! 0.000 ATOM H6
HGA3 0.090 ! 0.000 ATOM H7 HGA3 0.090 ! 0.000 ATOM H8 HGA3 0.090 ! 0.000
ATOM C9 CG331 -0.100 ! 0.000 ATOM H9 HGA3 0.090 ! 0.000 ATOM H10 HGA3

0.090

! 0.000 ATOM H11 HGA3 0.090 ! 0.000 ATOM C10 CG3C51 0.317 ! 142.287

ATOM N1

NG3C51 -0.343 ! 101.066 ATOM C11 CG321 -0.072 ! 70.919 ATOM H12 HGA2

0.090

! 2.500 ATOM H13 HGA2 0.090 ! 2.500 ATOM C12 CG2R53 0.464 ! 90.248 ATOM

N2

NG2R50 -0.515 ! 21.469 ATOM N3 NG3C51 -0.417 ! 87.522 ATOM H14 HGP1

0.341 !

3.424 ATOM C13 CG321 0.028 ! 26.713 ATOM H15 HGA2 0.090 ! 2.659 ATOM N4
NG3N1 -0.689 ! 58.305 ATOM C14 CG2R61 0.140 ! 19.097 ATOM C15 CG2R61

-0.110

! 13.488 ATOM C16 CG2R61 0.036 ! 13.718 ATOM C17 CG2R61 -0.112 ! 0.000

ATOM

H16 HGR61 0.115 ! 0.000 ATOM C18 CG2R61 0.071 ! 0.000 ATOM C19 CG2R61
-0.089 ! 0.000 ATOM H17 HGR61 0.115 ! 0.000 ATOM S SG311 -0.210 !

105.411

ATOM H18 HGP3 0.160 ! 4.359 ATOM H19 HGR62 0.144 ! 0.000 ATOM Cl1 CLGR1
-0.152 ! 2.500 ATOM Cl2 CLGR1 -0.167 ! 0.000 ATOM HXT1 HGA1 0.090 !

5.954

ATOM HXT2 HGA2 0.090 ! 2.659 ATOM HN HGP1 0.394 ! 9.368 ATOM LP1 LPH

0.050

! on Cl1 ATOM LP2 LPH 0.050 ! on Cl2


Thanks for your taking time


On Sat, 18 Aug 2018 22:31 RAHUL 

Re: [gmx-users] Combining position restraints with Parrinello-Rahman pressure coupling leads to instabilities

[Justin Lemkul]

On 8/20/18 6:52 AM, Naba wrote:

Dear Gromacs users and developers,

I am using Gromacs 2018.2.
Following the membrane protein simulation tutorial, I am planning to run
long simulations of a tetramer that needs larger lipid bilayer than 128
lipids as described in the tutorial. So, I have replicated the
pre-equilibrated POPC bilayer of 128 lipids from lipidbook (
https://lipidbook.bioch.ox.ac.uk/lipid/) to get a larger bilayer of 512
lipids using genconf. Moreover, I have extended gromos54a7_lipid.ff
forcefield to Berger lipid parameters for long membrane protein
simulations. I have set 10 ns for NVT and 20 ns for NPT equilibration.
NVT simulation ran successfully, but when I reached to NPT equilibration,
grompp showed me a note like the following:
"You are combining position restraints with Parrinello-Rahman pressure
   coupling, which can lead to instabilities. If you really want to combine
   position restraints with pressure coupling, we suggest to use Berendsen
   pressure coupling instead."


I think this note is a bit imprecise. grompp is guessing that the 
combination of Parrinello-Rahman and restraints implies equilibration, 
and it should really say so, or otherwise do a more rigorous check to 
see if velocities are being generated. In principle, there shouldn't be 
anything wrong with this approach, but Parrinello-Rahman *usually* isn't 
the best choice for equilibration.



When I used Berendsen pressure coupling, grompp terminated with a warning
as:
"Using Berendsen pressure coupling invalidates the true ensemble for the
   thermostat"


This only matters for production runs. The Berendsen method should never 
be used for actual data collection. For equilibration, it's perfectly 
fine because you're going to throw this time out, anyway.


-Justin


What to do with this? Can I proceed with the note using Parrinello-Rahman
pressure coupling? Please help.

Following is the mdp parameters I have used:

title   = NPT Equilibration for KALP15-DPPC
define  = -DPOSRES  ; position restrain the protein
; Run parameters
integrator  = md; leap-frog integrator
nsteps  = 1000; 2 * 1000 = 2 ps (20 ns)
dt  = 0.002 ; 2 fs
cutoff-scheme = verlet
; Output control
nstxout = 2500   ; save coordinates every 5 ps
nstvout = 2500   ; save velocities every 5 ps
nstenergy   = 2500   ; save energies every 5 ps
nstlog  = 2500   ; update log file every 5 ps
; Bond parameters
continuation= yes   ; Restarting after NVT
constraint_algorithm= lincs ; holonomic constraints
constraints = all-bonds ; all bonds (even heavy atom-H bonds)
constrained
lincs_iter  = 1 ; accuracy of LINCS
lincs_order = 4 ; also related to accuracy
; Neighborsearching
ns_type = grid  ; search neighboring grid cels
nstlist = 5 ; 10 fs
rlist   = 1.2   ; short-range neighborlist cutoff (in nm)
rcoulomb= 1.2   ; short-range electrostatic cutoff (in nm)
rvdw= 1.2   ; short-range van der Waals cutoff (in nm)
; Electrostatics
coulombtype = PME   ; Particle Mesh Ewald for long-range
electrostatics
pme_order   = 4 ; cubic interpolation
fourierspacing  = 0.16  ; grid spacing for FFT
; Temperature coupling is on
tcoupl  = Nose-Hoover   ; More accurate thermostat
tc-grps = Protein_POPC  Water_and_ions  ; two coupling groups -
more accurate
tau_t   = 0.5   0.5 ; time constant, in ps
ref_t   = 300   300 ; reference temperature,
one for each group, in K
; Pressure coupling is on
pcoupl  = Berendsen ; Pressure coupling on in NPT
pcoupltype  = semiisotropic ; uniform scaling of x-y box vectors,
independent z
tau_p   = 5.0   ; time constant, in ps
ref_p   = 1.0   1.0 ; reference pressure, x-y, z (in bar)
compressibility = 4.5e-54.5e-5  ; isothermal compressibility, bar^-1
; Periodic boundary conditions
pbc = xyz   ; 3-D PBC
; Dispersion correction
DispCorr= EnerPres  ; account for cut-off vdW scheme
; Velocity generation
gen_vel = no; Velocity generation is off
; COM motion removal
; These options remove motion of the protein/bilayer relative to the
solvent/ions
nstcomm = 1
comm-mode   = Linear
comm-grps   = Protein_POPC Water_and_ions
; Scale COM of reference coordinates
refcoord_scaling = com
nstcalcenergy = 1
nhchainlength = 1


Thank in advance.

Regards,

Nabajyoti Goswami

Research Associate
Bioinformatics Infrastructure Facility
Department of Animal Biotechnology
College of Veterinary Science
Khanapara,Guwahati 781022
Assam, India


--
==

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) 

[gmx-users] Combining position restraints with Parrinello-Rahman pressure coupling leads to instabilities

[Naba]

Dear Gromacs users and developers,

I am using Gromacs 2018.2.
Following the membrane protein simulation tutorial, I am planning to run
long simulations of a tetramer that needs larger lipid bilayer than 128
lipids as described in the tutorial. So, I have replicated the
pre-equilibrated POPC bilayer of 128 lipids from lipidbook (
https://lipidbook.bioch.ox.ac.uk/lipid/) to get a larger bilayer of 512
lipids using genconf. Moreover, I have extended gromos54a7_lipid.ff
forcefield to Berger lipid parameters for long membrane protein
simulations. I have set 10 ns for NVT and 20 ns for NPT equilibration.
NVT simulation ran successfully, but when I reached to NPT equilibration,
grompp showed me a note like the following:
"You are combining position restraints with Parrinello-Rahman pressure
  coupling, which can lead to instabilities. If you really want to combine
  position restraints with pressure coupling, we suggest to use Berendsen
  pressure coupling instead."

When I used Berendsen pressure coupling, grompp terminated with a warning
as:
"Using Berendsen pressure coupling invalidates the true ensemble for the
  thermostat"

What to do with this? Can I proceed with the note using Parrinello-Rahman
pressure coupling? Please help.

Following is the mdp parameters I have used:

title   = NPT Equilibration for KALP15-DPPC
define  = -DPOSRES  ; position restrain the protein
; Run parameters
integrator  = md; leap-frog integrator
nsteps  = 1000; 2 * 1000 = 2 ps (20 ns)
dt  = 0.002 ; 2 fs
cutoff-scheme = verlet
; Output control
nstxout = 2500   ; save coordinates every 5 ps
nstvout = 2500   ; save velocities every 5 ps
nstenergy   = 2500   ; save energies every 5 ps
nstlog  = 2500   ; update log file every 5 ps
; Bond parameters
continuation= yes   ; Restarting after NVT
constraint_algorithm= lincs ; holonomic constraints
constraints = all-bonds ; all bonds (even heavy atom-H bonds)
constrained
lincs_iter  = 1 ; accuracy of LINCS
lincs_order = 4 ; also related to accuracy
; Neighborsearching
ns_type = grid  ; search neighboring grid cels
nstlist = 5 ; 10 fs
rlist   = 1.2   ; short-range neighborlist cutoff (in nm)
rcoulomb= 1.2   ; short-range electrostatic cutoff (in nm)
rvdw= 1.2   ; short-range van der Waals cutoff (in nm)
; Electrostatics
coulombtype = PME   ; Particle Mesh Ewald for long-range
electrostatics
pme_order   = 4 ; cubic interpolation
fourierspacing  = 0.16  ; grid spacing for FFT
; Temperature coupling is on
tcoupl  = Nose-Hoover   ; More accurate thermostat
tc-grps = Protein_POPC  Water_and_ions  ; two coupling groups -
more accurate
tau_t   = 0.5   0.5 ; time constant, in ps
ref_t   = 300   300 ; reference temperature,
one for each group, in K
; Pressure coupling is on
pcoupl  = Berendsen ; Pressure coupling on in NPT
pcoupltype  = semiisotropic ; uniform scaling of x-y box vectors,
independent z
tau_p   = 5.0   ; time constant, in ps
ref_p   = 1.0   1.0 ; reference pressure, x-y, z (in bar)
compressibility = 4.5e-54.5e-5  ; isothermal compressibility, bar^-1
; Periodic boundary conditions
pbc = xyz   ; 3-D PBC
; Dispersion correction
DispCorr= EnerPres  ; account for cut-off vdW scheme
; Velocity generation
gen_vel = no; Velocity generation is off
; COM motion removal
; These options remove motion of the protein/bilayer relative to the
solvent/ions
nstcomm = 1
comm-mode   = Linear
comm-grps   = Protein_POPC Water_and_ions
; Scale COM of reference coordinates
refcoord_scaling = com
nstcalcenergy = 1
nhchainlength = 1


Thank in advance.

Regards,

Nabajyoti Goswami

Research Associate
Bioinformatics Infrastructure Facility
Department of Animal Biotechnology
College of Veterinary Science
Khanapara,Guwahati 781022
Assam, India
-- 
Gromacs Users mailing list

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

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] force/time application for pull

[Rakesh Mishra]

So, Dear Justin and Mark

Basically in Gromacs pulling using umbrella sampling.  Force corresponding
to the distance increment
during constant velocity pulling becomes like.
F= k(vt-x)
k=spring constant
v= constant velocity
t=time
x= distance between pulled group and reference group.

The force file (f/t) which we get  corresponds  that the force that feels
by system when distance increase.
And the sudden drop of force nearly zero corresponds that the strands (here
the case of dsDNA/siRNA)
are ruptured or melted (like force induced melting).

On Mon, Aug 13, 2018 at 6:14 PM, Mark Abraham 
wrote:

> Hi,
>
> Can you please share a link to something that indicates why this would be a
> good tool for modeling such experimental pulling scenarios? Making the case
> for implementing such a feature would benefit from that.
>
> Mark
>
> On Mon, Aug 13, 2018, 13:42 Rakesh Mishra  wrote:
>
> > Hello Mark,
> >
> > Thank for  your clarification. Gromacs pulling has simple protocol for
> > pulling
> > using umbrella sampling. Where one can only get f/t and x/t . here t is
> > linearly
> > increases for both cases of force and distance. That actually not full
> fill
> > the need of
> > experimental pulling.
> >
> >
> > On Mon, Aug 13, 2018 at 3:26 PM Mark Abraham 
> > wrote:
> >
> > > Hi,
> > >
> > > It's possible, but there is no code written for it.
> > >
> > > Mark
> > >
> > > On Mon, Aug 13, 2018, 12:47 Rakesh Mishra  wrote:
> > >
> > > > Dear Justin.
> > > >
> > > > Thanks for your kind  advise.
> > > > But why don't it is not  possible to apply the constant force which
> > > should
> > > > increases linearly (at each instant of time delta)
> > > > like at
> > > > t1 -f1
> > > > t2-f2
> > > > .
> > > > .
> > > > tn-fn
> > > >
> > > > and corresponding to that force we get extension for each increment
> of
> > > > time in Gromacs. This is more relevant in order to map
> > > > experimental work of unzipping or axial pulling of nucleic acid like
> > > > DNA/RNA/protein.  Is it possible to build this protocol in Gromacs.
> > > >
> > > > On Thu, Aug 9, 2018 at 5:30 PM Justin Lemkul 
> wrote:
> > > >
> > > > >
> > > > >
> > > > > On 8/9/18 6:37 AM, Rakesh Mishra wrote:
> > > > > > Dear all,
> > > > > >
> > > > > > Can anyone shed some light as ,Is it possible to apply force/time
> > for
> > > > > > pulling in gromacs. Means I want to pull my system in step wise .
> > eg.
> > > > > >0 - t1 force applied f1
> > > > > >t1+dt  to t2 force f2
> > > > > >t2+dt  to t3 force f3
> > > > > >.
> > > > > >.
> > > > > >.
> > > > > >tn-1 +dt  to tn force fn
> > > > > >   Is it possible.
> > > > >
> > > > > Not in a single run. You would have to run a simulation for
> interval
> > 0
> > > -
> > > > > dt, generate a new .tpr file for the time period of (t1+dt) - t2, e
> >  2Bdt)+-+t2,+e=gmail=g>
> > tc.
> > > > >
> > > > > -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.thelemkullab.com
> > > > >
> > > > > ==
> > > > >
> > > > > --
> > > > > Gromacs Users mailing list
> > > > >
> > > > > * Please search the archive at
> > > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > > > > posting!
> > > > >
> > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > > > >
> > > > > * For (un)subscribe requests visit
> > > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> > or
> > > > > send a mail to gmx-users-requ...@gromacs.org.
> > > > >
> > > >
> > > >
> > > > --
> > > >
> > > > *With Best-Rakesh Kumar Mishra*
> > > > *  (RA)CSD  SINP Kolkata, India*
> > > >
> > > > *E-mail - rakesh.mis...@saha.ac.in  *
> > > >
> > > > *Phone n. +91 9473662491, +918777496532*
> > > > --
> > > > Gromacs Users mailing list
> > > >
> > > > * Please search the archive at
> > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > > > posting!
> > > >
> > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > > >
> > > > * For (un)subscribe requests visit
> > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> or
> > > > send a mail to gmx-users-requ...@gromacs.org.
> > > >
> > > --
> > > Gromacs Users mailing list
> > >
> > > * Please search the archive at
> > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > > posting!
> > >
> > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > >
> > > * For (un)subscribe requests visit
> > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > > send a mail to 

[gmx-users] lipid relaxation time

[Neda Rafiee]

Dear All,
I have a question regarding relaxation time for lipids in simulation. I will be 
thankful if anyone can help me with this. Actually I want to find the 
relaxation time so that I can estimate the required time for equilibration 
before starting production MD. Does anyone know which parameter should be 
considered as a sign of enough equilibration. I mean when we can say the lipid 
is relaxed and it is in equilibration?
Thanks in advance.
Neda
-- 
Gromacs Users mailing list

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

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] Getting ligand's topology

[Mahdi Sobati Nezhad]

thanks for your taking time. and so on for a begginer like me there is no
any way

On Mon, 20 Aug 2018 00:29 Justin Lemkul,  wrote:

>
>
> On 8/19/18 10:20 AM, RAHUL SURESH wrote:
> > Hi.
> >
> > First, I feel grimaces users may not entertain other discussions in
> grimace
> > forum. You can directly mail me if it’s something apart from gromacs.
> >
> > Then, I am not sure about other servers.
> >
> > Looking at your str file, I would say that it definitely need some work
> on
> > our molecule. As I said before try zinc database.
>
> I don't see how the ZINC database is relevant. Either the .mol2
> submitted to the CGenFF server is valid or it is not.
>
> CGenFF is nice in that it tells you the potential problems with the
> ligand topology. AFAIK, no other servers do. You get a "black box"
> output that you're supposed to trust. The areas pinpointed by CGenFF
> should be examined carefully. The parameters may actually be fine, but
> the penalties are there to tell the user when there is a functional
> group that is not well described by existing molecules in the CGenFF
> database, from which the analogies are made.
>
> There is a CGenFF tutorial available online that walks a user through
> the whole process. It requires subdividing a molecule into units that
> can be parametrized easily; large molecules should always be broken down
> into manageable pieces that have all the necessary degrees of freedom.
>
> The tutorial materials can be accessed here:
> http://mackerell.umaryland.edu/~kenno/cgenff/download.php
>
> CHARMM/CGenFF parametrization assumes some familiarity with QM
> calculations (geometry optimizations, potential energy scans,
> interaction energies) but the methodology is published in great detail,
> and the CGenFF paper itself is a worked example of how to parametrize a
> molecule. While the developers have made every effort to make the
> methodology publicly available, ligand parametrization and refinement is
> still an advanced concept that is best suited for experienced users, as
> knowledge of fundamental principles of MD, QM, and empirical energy
> functions is required.
>
> -Justin
>
> > Thank you
> >
> >
> > On Sun, 19 Aug 2018 at 1:37 PM, Mahdi Sobati Nezhad <
> > mahdisobatinez...@gmail.com> wrote:
> >
> >> thanks.
> >> if I use MATCH server or swissparam, I can trust to their results?!
> >>
> >> And this is my error when I use CGenFF:
> >> "readmol2 warning: non-unique atoms were renamed. Now processing
> molecule
> >> mae ..."
> >>
> >> And this is my output of penalty:
> >>
> >> * Toppar stream file generated by * CHARMM General Force Field (CGenFF)
> >> program version 2.2.0 * For use with CGenFF version 4.0 * read rtf card
> >> append * Topologies generated by * CHARMM General Force Field (CGenFF)
> >> program version 2.2.0 * 36 1 ! "penalty" is the highest penalty score of
> >> the associated parameters. ! Penalties lower than 10 indicate the
> analogy
> >> is fair; penalties between 10 ! and 50 mean some basic validation is
> >> recommended; penalties higher than ! 50 indicate poor analogy and
> mandate
> >> extensive validation/optimization. RESI mae 0.000 ! param penalty=
> 198.400
> >> ; charge penalty= 142.287 GROUP ! CHARGE CH_PENALTY ATOM C1 CG2R61
> 0.227 !
> >> 0.000 ATOM C2 CG2R61 -0.117 ! 2.688 ATOM C3 CG2R61 -0.003 ! 5.191 ATOM
> C4
> >> CG2R61 -0.117 ! 2.688 ATOM C5 CG2R61 0.227 ! 0.000 ATOM C6 CG2R61 0.217
> !
> >> 0.000 ATOM H1 HGR61 0.115 ! 0.000 ATOM H2 HGR61 0.115 ! 0.000 ATOM O1
> OG301
> >> -0.391 ! 0.000 ATOM O2 OG301 -0.391 ! 0.000 ATOM O3 OG301 -0.391 ! 0.000
> >> ATOM C7 CG331 -0.100 ! 0.000 ATOM H3 HGA3 0.090 ! 0.000 ATOM H4 HGA3
> 0.090
> >> ! 0.000 ATOM H5 HGA3 0.090 ! 0.000 ATOM C8 CG331 -0.100 ! 0.000 ATOM H6
> >> HGA3 0.090 ! 0.000 ATOM H7 HGA3 0.090 ! 0.000 ATOM H8 HGA3 0.090 ! 0.000
> >> ATOM C9 CG331 -0.100 ! 0.000 ATOM H9 HGA3 0.090 ! 0.000 ATOM H10 HGA3
> 0.090
> >> ! 0.000 ATOM H11 HGA3 0.090 ! 0.000 ATOM C10 CG3C51 0.317 ! 142.287
> ATOM N1
> >> NG3C51 -0.343 ! 101.066 ATOM C11 CG321 -0.072 ! 70.919 ATOM H12 HGA2
> 0.090
> >> ! 2.500 ATOM H13 HGA2 0.090 ! 2.500 ATOM C12 CG2R53 0.464 ! 90.248 ATOM
> N2
> >> NG2R50 -0.515 ! 21.469 ATOM N3 NG3C51 -0.417 ! 87.522 ATOM H14 HGP1
> 0.341 !
> >> 3.424 ATOM C13 CG321 0.028 ! 26.713 ATOM H15 HGA2 0.090 ! 2.659 ATOM N4
> >> NG3N1 -0.689 ! 58.305 ATOM C14 CG2R61 0.140 ! 19.097 ATOM C15 CG2R61
> -0.110
> >> ! 13.488 ATOM C16 CG2R61 0.036 ! 13.718 ATOM C17 CG2R61 -0.112 ! 0.000
> ATOM
> >> H16 HGR61 0.115 ! 0.000 ATOM C18 CG2R61 0.071 ! 0.000 ATOM C19 CG2R61
> >> -0.089 ! 0.000 ATOM H17 HGR61 0.115 ! 0.000 ATOM S SG311 -0.210 !
> 105.411
> >> ATOM H18 HGP3 0.160 ! 4.359 ATOM H19 HGR62 0.144 ! 0.000 ATOM Cl1 CLGR1
> >> -0.152 ! 2.500 ATOM Cl2 CLGR1 -0.167 ! 0.000 ATOM HXT1 HGA1 0.090 !
> 5.954
> >> ATOM HXT2 HGA2 0.090 ! 2.659 ATOM HN HGP1 0.394 ! 9.368 ATOM LP1 LPH
> 0.050
> >> ! on Cl1 ATOM LP2 LPH 0.050 ! on Cl2
> >>
> >>
> >> Thanks for your taking time
> >>
> >>
> >> On Sat, 18 Aug 2018 22:31 RAHUL