[gmx-users] domain decomposition error in the energy minimization step

[Qasim Pars]

Dear users,

I am trying to simulate a protein-ligand system including ~2 atoms with
waters using GROMACS-2016.1. The protocol I tried is forward state for the
free energy calculation. The best ligand pose used in the simulations was
got by AutoDock. At the beginning of the simulation GROMACS suffers from
domain decomposition error in the energy minimization step:

Fatal error:
There is no domain decomposition for 20 ranks that is compatible with the
given box and a minimum cell size of 1.7353 nm
Change the number of ranks or mdrun option -rdd
Look in the log file for details on the domain decomposition

I checked the complex structure visually. I don't see any distortion in the
structure. To check whether the problem is the number of nodes, I used 16
nodes:

gmx mdrun -v -deffnm em -nt 16

The energy minimization step was completed successfully. For the NVT step I
used 16 nodes again.

gmx mdrun -v -deffnm nvt -nt 16

After ~200 steps the system gave too many lincs warning.

Whereas there is no problem with wild type protein when it is simulated
without using -nt 16. These domain decomposition error and lincs warning
arise for complex structure.

By the way to keep the ligand in the active site of protein I use the bond,
angle and dihedral restraints under [ intermolecular_interactions ] section
in the top file.

[ intermolecular_interactions ]
[ bonds ]
  31317 10 0.294 0.29410.000  0.000 0.294
0.29410.000   4184.000

[ angle_restraints ]
  312   31317   313  1   140.445  0.000  1
140.445 41.840  1
  313171917  1   107.175  0.000  1
107.175 41.840  1

[ dihedral_restraints ]
  300   312   31317  156.245 0.000  0.000
56.245 0.000 41.840
  312   3131719  1-3.417 0.000  0.000
-3.417 0.000 41.840
  313171914  1  -110.822 0.000  0.000
-110.822 0.000 41.840

The mdp file used for the energy minimization is follows:

define  = -DFLEXIBLE
integrator  = steep
nsteps  = 5
emtol   = 1000.0
emstep  = 0.01
nstcomm = 100

; OUTPUT CONTROL
nstxout-compressed= 500
compressed-x-precision= 1000
nstlog= 500
nstenergy = 500
nstcalcenergy = 100

; BONDS
constraints = none

; NEIGHBOUR SEARCHING

cutoff-scheme= verlet
ns-type  = grid
nstlist  = 10
pbc  = xyz

; ELECTROSTATICS & EWALD
coulombtype  = PME
rcoulomb = 1.0
ewald_geometry   = 3d
pme-order= 4
fourierspacing   = 0.12

; VAN DER WAALS
vdwtype = Cut-off
vdw_modifier= Potential-switch
rvdw= 1.0
rvdw-switch = 0.9
DispCorr= EnerPres

; FREE ENERGY
free-energy  = yes
init-lambda  = 0
delta-lambda = 0
sc-alpha = 0.3
sc-power = 1
sc-sigma = 0.25
sc-coul  = yes
couple-moltype   = ligand
couple-intramol  = no
couple-lambda0   = vdw-q
couple-lambda1   = none
nstdhdl  = 100

I removed the free energy lines in the em.mdp and [
intermolecular_interactions ] section in the top file but GROMACS still
gives the domain decomposition error for the complex structure.

Will you please give suggestions on getting rid of the lincs warning and
domain decomposition messages?

I would appreciate any kind of help.

Thanks.

-- 
Qasim Pars
-- 
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] GROMACS IN CGYWIN

[Subashini .K]

Hi,


In cgywin, I typed this command


 source /usr/local/gromacs/bin/GMXRC

After that, cd  /way-to-the-required-directory/was given


But, when


; test

is given, it says,


-bash: syntax error near unexpected token `;'


Gromacs was installed following the instructions in this website

https://winmostar.com/en/gmx4wm_en_win.html


How to rectify it? Please help.

Thanks,
Subashini.K



From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on behalf of Mark Abraham 

Sent: Wednesday, January 11, 2017 12:30 AM
To: gmx-us...@gromacs.org; gromacs.org_gmx-users@maillist.sys.kth.se
Subject: Re: [gmx-users] ENERGY MINIMIZATION

Hi,

In a cygwin terminal, having source'd GMXRC (see the install guide), just
like you need to do under Linux.

Mark

On Tue, Jan 10, 2017 at 7:29 PM Subashini .K  wrote:

> Hi Gromacs users,
>
>
> I have installed gromacs in windows 7, 64 bit using cgywin.
>
>
> I want to use the em.mdp file to grompp and generate a .tpr file.
>
>
> In which terminal should the following commands be executed?
>
>
> ; to test
> ; grompp -f em.mdp -c test_GMX.gro -p test_GMX.top -o em.tpr -v
> ; mdrun -v -deffnm em
>
> Can someone tell me?
>
>
> Thanks,
>
> Subashini.K
>
>
> --
> 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.
-- 
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] protein XYZ dimension function of time

[atanu das]

Hi All,
Is there a simple way to calculate a protein's X, Y, and Z dimensions from a 
trajectory as a function of time (not the box vector, the protein dimensions as 
in how the protein spreads itself in the 3 directions as the simulation 
progresses)? I see that GROMACS has an option to estimate protein volume as a 
function of time, but I need to know how the individual dimensions change as a 
function of time. 
ThanksAtanu
-- 
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] rlist, rcolumb, and rvdw

[Mohsen Ramezanpour]

Dear gromacs users,

Reading through mailing list I found a nice discussion on the relation
between rlist, rcolumb, and rvdw:

https://www.mail-archive.com/gmx-users@gromacs.org/msg08387.html

https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2011-February/058507.html

If I understood correctly,

rcoulomb < rlist and rvdw < rlist is the most accurate way,

and
rlist=rcoulomb=rvdw is the commonly used way for these parameters.

I was wondering what would be the case if I want to change the cut-offs?

For instance, to use charmm36 in Groamcs, it is recommended to use 1.0-1.2

as the cut-off for LJ, and rlist=rcoulomb=rvdw

However, this setting might not result in good behaviour for some
lipid bilayers.

Therefore, I want to check if other cut-offs works better in gromacs.

If I change "1.2 nm" to "A nm" for rvdw, do I need to change rcolumb and
rlist to A as well? i.e. rlist=rcolumb=rvdw=A?

I am using following parameters already:

cutoff-scheme   = Verlet
nstlist   = 20
rlist  = *1.2*
coulombtype = *pme*
rcoulomb  = *1.2*
vdwtype   = Cut-off
vdw-modifier= *Force-switch*
rvdw_switch = *1.0*
rvdw= *1.2*

Thanks in advance for your comments
Cheers
Mohsen
-- 
*Rewards work better than punishment ...*
-- 
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] Fwd: LJ cut-offs

[Mohsen Ramezanpour]

Dear gromacs users,

Please let me know your opinion on the following question:
Thanks in advance for your comments


-- Forwarded message --
From: Mohsen Ramezanpour 
Date: Thu, Jan 5, 2017 at 5:20 PM
Subject: LJ cut-offs
To: Discussion list for GROMACS users 


Dear Gromacs users,

Every force field has been parametrized with a specific LJ cut-off which
must be the same for simulations using that force field.
However, I was wondering if there is any reason why people usually take
even numbers (e.g. 8-10, 8-12, 10-12 all with a difference of 2) for LJ
cut-offs in force field development?
Is there any rule that prohibit the use of 9-10, 9-11, or 11-12 for LJ
cut-off?

Thanks

Cheers
Mohsen





-- 
*Rewards work better than punishment ...*



-- 
*Rewards work better than punishment ...*
-- 
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] Creating a temperature gradient in water

[Alex]

Physics-wise, this is actually a pretty crazy scenario regardless of
implementation. A similar approach with crystals is something I have done
routinely, and it is considered far more palatable. With solids, restraints
are no longer required and you can generate your heat fluxes all you want.
Even then, fluxes at a given temperature T are accomplished via setting
thermostatted groups at T-dT and T+dT, where dT<< T. To give a sense of the
numbers, it'd be something like 295K and 305K for T = 300K, and even then
such things come under a lot of [well-deserved] scrutiny during reviews,
because with distances of tens to hundreds of nm, we'ra talking about
10^6-10^7 K/m in gradient.

Ibrahim is asking about not just an enormous gradient, but also a case with
phase difference between he thermostatted groups. I'd like to see a
visualization posted on youtube! : )

Good luck anyhow.

Alex

On Tue, Jan 10, 2017 at 12:05 PM, Mark Abraham 
wrote:

> Hi,
>
> Yes, as Alex says, you can get something done, but whether it is a
> reasonable model of reality is another matter. Having the "bath" groups at
> even wider temperature ranges, and analyzing only a subset of the data
> could help mitigate end effects from whatever regime generates the
> gradient. I would read carefully, and plan how I'm going to show my
> simulation is a model, and not just a computation :-)
>
> Mark
>
> On Tue, Jan 10, 2017 at 8:00 PM Alex  wrote:
>
> > I would like the asker to seriously read into what Mark has suggested to
> > help reduce the number of published papers with various degrees of setup
> > nonsense.
> > Mark's restraint strategy readily accomplishes the gradient, but creates
> > two partial "pistons" at the thermal boundaries due to restraints. If I
> was
> > to go for this, I'd use a really wide box. A really wide one.
> >
> > Alex
> >
> > On Tue, Jan 10, 2017 at 9:57 AM, Mark Abraham 
> > wrote:
> >
> > > Hi,
> > >
> > > Naturally one can only have a monotonic gradient over half of a
> periodic
> > > direction of a simulation cell, ie between two themostatted groups.
> Also,
> > > if you rely on the temperature coupling groups to implement that, then
> > > these are fixed at grompp time, so diffusion will tend to wreck the
> > intent.
> > > One could either use (flat-bottomed?) position restraints to keep the
> two
> > > groups localized, or periodically stop the simulation and use gmx
> select
> > to
> > > re-create index groups with the desired spatial locality. Obviously,
> the
> > > remaining water should not be coupled to a thermostat.
> > >
> > > Mark
> > >
> > > On Tue, Jan 10, 2017 at 5:44 PM Alex  wrote:
> > >
> > > > Erik,
> > > >
> > > > Even with PBC, something like Ibrahim's scenario is possible in
> > principle
> > > > (T_1 in the region at the center of the box, T_2 at the edges).
> > However,
> > > > can this geometry-based thermostatting for fluids be accomplished in
> > GMX?
> > > >
> > > > Alex
> > > >
> > > > On Tue, Jan 10, 2017 at 8:15 AM, Erik Marklund <
> > erik.markl...@kemi.uu.se
> > > >
> > > > wrote:
> > > >
> > > > > Dear Ibrahim,
> > > > >
> > > > > Do you use pbc? If so, how does that work with your gradient?
> > > > >
> > > > > Kind regards,
> > > > > Erik
> > > > >
> > > > > > On 10 Jan 2017, at 15:00, ibrahim khalil <
> > > > ibrahim.khalil.c...@gmail.com>
> > > > > wrote:
> > > > > >
> > > > > > Dear gromacs users,
> > > > > >
> > > > > > I have a simulation box containing nothing but water (TIP3P). I
> > want
> > > to
> > > > > > create a temperature gradient within water (ie. 300K in the left
> > side
> > > > and
> > > > > > 500K in the right side of the simulation box).
> > > > > >
> > > > > > I have successfully applied different temperatures to different
> > > groups
> > > > in
> > > > > > my other simulations (for example, different temperatures for
> water
> > > and
> > > > > > proteins).
> > > > > >
> > > > > > How can apply different temperatures within the same group of
> > liquids
> > > > (in
> > > > > > my case, water)?
> > > > > >
> > > > > > Thanks in advance.
> > > > > > --
> > > > > > 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
> > > > > 

Re: [gmx-users] Creating a temperature gradient in water

[Mark Abraham]

Hi,

Yes, as Alex says, you can get something done, but whether it is a
reasonable model of reality is another matter. Having the "bath" groups at
even wider temperature ranges, and analyzing only a subset of the data
could help mitigate end effects from whatever regime generates the
gradient. I would read carefully, and plan how I'm going to show my
simulation is a model, and not just a computation :-)

Mark

On Tue, Jan 10, 2017 at 8:00 PM Alex  wrote:

> I would like the asker to seriously read into what Mark has suggested to
> help reduce the number of published papers with various degrees of setup
> nonsense.
> Mark's restraint strategy readily accomplishes the gradient, but creates
> two partial "pistons" at the thermal boundaries due to restraints. If I was
> to go for this, I'd use a really wide box. A really wide one.
>
> Alex
>
> On Tue, Jan 10, 2017 at 9:57 AM, Mark Abraham 
> wrote:
>
> > Hi,
> >
> > Naturally one can only have a monotonic gradient over half of a periodic
> > direction of a simulation cell, ie between two themostatted groups. Also,
> > if you rely on the temperature coupling groups to implement that, then
> > these are fixed at grompp time, so diffusion will tend to wreck the
> intent.
> > One could either use (flat-bottomed?) position restraints to keep the two
> > groups localized, or periodically stop the simulation and use gmx select
> to
> > re-create index groups with the desired spatial locality. Obviously, the
> > remaining water should not be coupled to a thermostat.
> >
> > Mark
> >
> > On Tue, Jan 10, 2017 at 5:44 PM Alex  wrote:
> >
> > > Erik,
> > >
> > > Even with PBC, something like Ibrahim's scenario is possible in
> principle
> > > (T_1 in the region at the center of the box, T_2 at the edges).
> However,
> > > can this geometry-based thermostatting for fluids be accomplished in
> GMX?
> > >
> > > Alex
> > >
> > > On Tue, Jan 10, 2017 at 8:15 AM, Erik Marklund <
> erik.markl...@kemi.uu.se
> > >
> > > wrote:
> > >
> > > > Dear Ibrahim,
> > > >
> > > > Do you use pbc? If so, how does that work with your gradient?
> > > >
> > > > Kind regards,
> > > > Erik
> > > >
> > > > > On 10 Jan 2017, at 15:00, ibrahim khalil <
> > > ibrahim.khalil.c...@gmail.com>
> > > > wrote:
> > > > >
> > > > > Dear gromacs users,
> > > > >
> > > > > I have a simulation box containing nothing but water (TIP3P). I
> want
> > to
> > > > > create a temperature gradient within water (ie. 300K in the left
> side
> > > and
> > > > > 500K in the right side of the simulation box).
> > > > >
> > > > > I have successfully applied different temperatures to different
> > groups
> > > in
> > > > > my other simulations (for example, different temperatures for water
> > and
> > > > > proteins).
> > > > >
> > > > > How can apply different temperatures within the same group of
> liquids
> > > (in
> > > > > my case, water)?
> > > > >
> > > > > Thanks in advance.
> > > > > --
> > > > > 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.
> > > >
> > > --
> > > 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.
> >
> --
> 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
> 

Re: [gmx-users] ENERGY MINIMIZATION

[Mark Abraham]

Hi,

In a cygwin terminal, having source'd GMXRC (see the install guide), just
like you need to do under Linux.

Mark

On Tue, Jan 10, 2017 at 7:29 PM Subashini .K  wrote:

> Hi Gromacs users,
>
>
> I have installed gromacs in windows 7, 64 bit using cgywin.
>
>
> I want to use the em.mdp file to grompp and generate a .tpr file.
>
>
> In which terminal should the following commands be executed?
>
>
> ; to test
> ; grompp -f em.mdp -c test_GMX.gro -p test_GMX.top -o em.tpr -v
> ; mdrun -v -deffnm em
>
> Can someone tell me?
>
>
> Thanks,
>
> Subashini.K
>
>
> --
> 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] ENERGY MINIMIZATION

[Subashini .K]

Hi Gromacs users,


I have installed gromacs in windows 7, 64 bit using cgywin.


I want to use the em.mdp file to grompp and generate a .tpr file.


In which terminal should the following commands be executed?


; to test
; grompp -f em.mdp -c test_GMX.gro -p test_GMX.top -o em.tpr -v
; mdrun -v -deffnm em

Can someone tell me?


Thanks,

Subashini.K


-- 
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] MMPBSA - with water molecules in the binding site

[Gabriela Aucar]

Dear gromacs users,

I have 100ns of production run of a Protein-Ligand Complex, and I want to
perform an MMPBSA calculation including water molecules of the binding
site. Can I do that with g_mmbpsa tool ? I tried to obtain a new trajectory
with the water molecules of the binding site, and the protein and ligand
with VMD but I didn't succeed.

Any help will be apprecieated

Thanks in advance,

M. Gabriela
-- 
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] Adding FE2+ parameters

[Hannes Loeffler]

On Tue, 10 Jan 2017 12:19:15 -0500
Justin Lemkul  wrote:

> On 1/10/17 12:09 PM, CROUZY Serge 119222 wrote:
> > Hello Hannes
> >
> > I'm perfectly aware how you need to be careful in using metal
> > parameters - checking for which solvent and which coordination they
> > have been created for. In my case structural metal coordinated to
> > protein amino acids... I did try to see in Li/Merz parameters which
> > line could resemble the parameters in Gromacs for Zn2+ but with no
> > success - This brings me back to the original question, where do Zn
> > parameters in Gromacs 54a7 come from ?  Knowing this I could try
> > deduce parameters for Fe2+ 
> 
> This came up recently, and the best answer that I found was: these
> parameters have simply always existed in GROMOS.  The only reference
> I could find was the GROMOS manual itself, which requires payment of
> a license fee to even read.  If that's not correct, someone please
> speak up!

I can only correct you about the availability of GROMOS.  Since the mid
last year the source code and the manual are available from their web
page.  There only seems the need for a license when one wants to use it
in connection with CPMD.


Cheers,
Hannes.
-- 
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] Adding FE2+ parameters

[Mark Abraham]

Hi,

They've been there in the GROMOS forcefield implementations in GROMACS ever
since Peter Tieleman's commit in 1999. If GROMOS themselves have never
documented them, then that is worrying to the point of "do something else."
A publication using any transition-metal parameterization without detailed
commentary about why it might be a valid model would get at least a "please
explain" from me as a reviewer...

Mark

On Tue, Jan 10, 2017 at 6:19 PM Justin Lemkul  wrote:

>
>
> On 1/10/17 12:09 PM, CROUZY Serge 119222 wrote:
> > Hello Hannes
> >
> > I'm perfectly aware how you need to be careful in using metal parameters
> - checking for which solvent and which coordination they have been created
> for.
> > In my case structural metal coordinated to protein amino acids...
> > I did try to see in Li/Merz parameters which line could resemble the
> parameters in Gromacs for Zn2+ but with no success - This brings me back to
> the original question, where do Zn parameters in Gromacs 54a7 come from ?
> Knowing this I could try deduce parameters for Fe2+
> >
>
> This came up recently, and the best answer that I found was: these
> parameters
> have simply always existed in GROMOS.  The only reference I could find was
> the
> GROMOS manual itself, which requires payment of a license fee to even
> read.  If
> that's not correct, someone please speak up!
>
> -Justin
>
> > Thanx
> >
> > Serge Crouzy PhD HDR
> > Groupe de Modélisation et Chimie Théorique
> > Laboratoire de Chimie et Biologie des Métaux
> > Institut de Biosciences et Biotechnologies de Grenoble
> > CEA Grenoble  UMR  CEA/CNRS/UJF 5249
> > 17, rue des martyrs
> > 38054 Grenoble Cedex 9
> > Bat. K  pièce 110
> > Tel (33)0438782963
> > Fax (33)0438785487
> > http://big.cea.fr/drf/big/CBM/GMCT
> >
> >
> >
> >
> > -Message d'origine-
> > De : gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:
> gromacs.org_gmx-users-boun...@maillist.sys.kth.se] De la part de Hannes
> Loeffler
> > Envoyé : mardi 10 janvier 2017 17:38
> > À : gromacs.org_gmx-users@maillist.sys.kth.se
> > Cc : gmx-us...@gromacs.org
> > Objet : Re: [gmx-users] Adding FE2+ or FE3+ into the system
> >
> > What are you planning to do with those parameters?
> >
> > You could have a look into the Li/Merz parameters (and papers!)
> available with the AmberTools (may not have been converted yet to Gromacs
> formats and the 12-6-4 sets would need support in the code).
> > Generally, you should be wary when using simple ion force fields and
> check carefully how they have been parameterised and what for.
> > Distinguishing different valencies of the same transition metal atom
> with only vdW/Coulomb parameters will most likely not capture their complex
> chemistry.
> >
> >
> > On Tue, 10 Jan 2017 16:24:47 +
> > CROUZY Serge 119222  wrote:
> >
> >> I'm interested as well in knowing how to get decent parameters for
> >> Fe2+
> >>
> >> From gromacs-5.1.2/share/top/gromos54a7.ff/ffnonbonded.itp
> >> We have Zn2+  (What is a reference for these parameters ?)
> >>
> >> name   bondtype   mass   charge   ptype CA
> >> ;name  at.num   mass  charge  ptype   c6   c12
> >> ZN2+   30  0.000  0.000 A  0.0004182025  9.4400656e-09
> >>
> >> From which I deduced
> >> if LJ = v(rij)=C(12)/r12 - C(6)/r6 = A/r^12 -C/r^6 to be compared to
> >> the standard V=4*eps*[(sig/r)^12 - (sig/r)^6] A =4*eps*sig^12
> >> C=4*eps*sig^6
> >> sig = (A/C)^1/6
> >> eps=C^2 / (4 A)
> >> For Zn sig=0.168112  eps=4.631677 kJ/mol
> >>
> >> But no Fe2+
> >>
> >> Regards
> >>
> >> Serge Crouzy PhD HDR
> >> Groupe de Modélisation et Chimie Théorique Laboratoire de Chimie et
> >> Biologie des Métaux Institut de Biosciences et Biotechnologies de
> >> Grenoble CEA Grenoble  UMR  CEA/CNRS/UJF 5249 17, rue des martyrs
> >> 38054 Grenoble Cedex 9
> >> Bat. K  pièce 110
> >> Tel (33)0438782963
> >> Fax (33)0438785487
> >> http://big.cea.fr/drf/big/CBM/GMCT
> >>
> >>
> >>
> >> -Message d'origine-
> >> De : gromacs.org_gmx-users-boun...@maillist.sys.kth.se
> >> [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] De la part
> >> de liming_52 Envoyé : mardi 10 janvier 2017 16:54 À :
> >> gmx-us...@gromacs.org Objet : [gmx-users] Adding FE2+ or FE3+ into
> >> the system
> >>
> >> Dear gromacs users,
> >>
> >> I want to compare the protein in the buffers with FE2+ and FE3+,
> >> respectively.
> >>
> >> How can I add FE2+ or FE3+ into the system? What is the command?
> >>
> >> Thanks in advance.
> >>
> >>
> >>
> >>
> >>
> >> --
> >>
> >> With my best wishes,
> >> Ming Li, PhD
> >> Chinese Academy of Agricultural Sciences, Beijing, China
> >
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201

Re: [gmx-users] REg MD results

[Justin Lemkul]

On 1/10/17 3:07 AM, Parul Raj Srivastava wrote:

Dear Sir,

On analysing each chain separately,though the rmsd is stable but the rmsf
is not beginning from the origin and suddenly rising from the centre of
falling off towards the end.



RMSF is a per-residue quantity, not a time series.  There's no reason to expect 
it to start at the origin of the plot.  If a residue has an RMSF of zero, it 
never moved.


-Justin


Regards,
Parul Raj Srivastava,
M.Tech.Computational Biology,
Anna University,Chennai-600025

On Sun, Jan 8, 2017 at 1:44 AM, Justin Lemkul  wrote:




On 1/7/17 5:14 AM, Parul Raj Srivastava wrote:


I have given an MD run for a quaternary protein structure by taking 2
chains at a time for the MD run.The rmsf graph so obtained is showing
erratic behaviour,please find attached graph.Is this result justified or
incorrect??



The list does not accept attachments.  If you want to share an image,
upload it to a file-sharing service and provide a link.

Often it is just easier to create index groups for each chain and analyze
them separately.  This eliminates most confusion associated with
residue-specific analyses like RMSF.

-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
--
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.



--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
--
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] Adding FE2+ parameters

[Justin Lemkul]

On 1/10/17 12:09 PM, CROUZY Serge 119222 wrote:

Hello Hannes

I'm perfectly aware how you need to be careful in using metal parameters - 
checking for which solvent and which coordination they have been created for.
In my case structural metal coordinated to protein amino acids...
I did try to see in Li/Merz parameters which line could resemble the parameters 
in Gromacs for Zn2+ but with no success - This brings me back to the original 
question, where do Zn parameters in Gromacs 54a7 come from ?  Knowing this I 
could try deduce parameters for Fe2+



This came up recently, and the best answer that I found was: these parameters 
have simply always existed in GROMOS.  The only reference I could find was the 
GROMOS manual itself, which requires payment of a license fee to even read.  If 
that's not correct, someone please speak up!


-Justin


Thanx

Serge Crouzy PhD HDR
Groupe de Modélisation et Chimie Théorique
Laboratoire de Chimie et Biologie des Métaux
Institut de Biosciences et Biotechnologies de Grenoble
CEA Grenoble  UMR  CEA/CNRS/UJF 5249
17, rue des martyrs
38054 Grenoble Cedex 9
Bat. K  pièce 110
Tel (33)0438782963
Fax (33)0438785487
http://big.cea.fr/drf/big/CBM/GMCT




-Message d'origine-
De : gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] De la part de Hannes 
Loeffler
Envoyé : mardi 10 janvier 2017 17:38
À : gromacs.org_gmx-users@maillist.sys.kth.se
Cc : gmx-us...@gromacs.org
Objet : Re: [gmx-users] Adding FE2+ or FE3+ into the system

What are you planning to do with those parameters?

You could have a look into the Li/Merz parameters (and papers!) available with 
the AmberTools (may not have been converted yet to Gromacs formats and the 
12-6-4 sets would need support in the code).
Generally, you should be wary when using simple ion force fields and check 
carefully how they have been parameterised and what for.
Distinguishing different valencies of the same transition metal atom with only 
vdW/Coulomb parameters will most likely not capture their complex chemistry.


On Tue, 10 Jan 2017 16:24:47 +
CROUZY Serge 119222  wrote:


I'm interested as well in knowing how to get decent parameters for
Fe2+

From gromacs-5.1.2/share/top/gromos54a7.ff/ffnonbonded.itp
We have Zn2+  (What is a reference for these parameters ?)

name   bondtype   mass   charge   ptype CA
;name  at.num   mass  charge  ptype   c6   c12
ZN2+   30  0.000  0.000 A  0.0004182025  9.4400656e-09

From which I deduced
if LJ = v(rij)=C(12)/r12 - C(6)/r6 = A/r^12 -C/r^6 to be compared to
the standard V=4*eps*[(sig/r)^12 - (sig/r)^6] A =4*eps*sig^12
C=4*eps*sig^6
sig = (A/C)^1/6
eps=C^2 / (4 A)
For Zn sig=0.168112  eps=4.631677 kJ/mol

But no Fe2+

Regards

Serge Crouzy PhD HDR
Groupe de Modélisation et Chimie Théorique Laboratoire de Chimie et
Biologie des Métaux Institut de Biosciences et Biotechnologies de
Grenoble CEA Grenoble  UMR  CEA/CNRS/UJF 5249 17, rue des martyrs
38054 Grenoble Cedex 9
Bat. K  pièce 110
Tel (33)0438782963
Fax (33)0438785487
http://big.cea.fr/drf/big/CBM/GMCT



-Message d'origine-
De : gromacs.org_gmx-users-boun...@maillist.sys.kth.se
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] De la part
de liming_52 Envoyé : mardi 10 janvier 2017 16:54 À :
gmx-us...@gromacs.org Objet : [gmx-users] Adding FE2+ or FE3+ into
the system

Dear gromacs users,

I want to compare the protein in the buffers with FE2+ and FE3+,
respectively.

How can I add FE2+ or FE3+ into the system? What is the command?

Thanks in advance.





--

With my best wishes,
Ming Li, PhD
Chinese Academy of Agricultural Sciences, Beijing, China




--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
--
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] Adding a new(modefied) fatty acid to charm 36 force field.

[Justin Lemkul]

On 1/10/17 4:49 AM, Tushar Ranjan Moharana wrote:

Hi All,
I want to understand the interaction of a fatty acid to various amino acid
side chain while it forms a covalent link with the hydroxyle group of the
serine. For that I wanted to add covalently linked serine-fatty acid as a
different amino acid so the pdb2gmx can generate the topology. For the
above reason I made the required complex in pdb format and converted to
mol2 format and generated .itp file from swissparam server. My plan was to
copy the [ atom ]  and [ bond ] section of the .itp to aminoacid.rtp under
the new amino acid with suitable modifications and add it to
residuetype.dat with type protein.

While trying the above, I did the same thing with only serine
(unmodefied).  The [ atom ] and [ bond ] section of the .itp generated by
swissparam looks completly different from that of serine mentioned in
aminoacid.rtp. This is giving me a fishy smell about what I am doing.
Kindly enlighten me about my mistakes and the correct protocol to do the
same. Following are the entry of  the [ atom ] and [ bond ] section of the
aminoacid.rtp and .itp that I have generated.



Given that serine and fatty acids already exist in CHARMM, you only need to work 
with the linker (presumably an ester).  There are some parameters for such 
species already in CHARMM so you should look to see what's available already, 
and then proceed with parametrizing, e.g. methylacetate and building the rest of 
the residue from stock building blocks.


-Justin


aminoacid.rtp entry

[ SER ]
 [ atoms ]
N NH1 -0.47 0
HN H 0.31 1
CA CT1 0.07 2
HA HB 0.09 3
CB CT2 0.05 4
HB1 HA 0.09 5
HB2 HA 0.09 6
OG OH1 -0.66 7
HG1 H 0.43 8
C C 0.51 9
O O -0.51 10
 [ bonds ]
CB CA
OG CB
N HN
N CA
C CA
C +N
CA HA
CB HB1
CB HB2
OG HG1
O C
 [ impropers ]
N -C CA HN
C CA +N O
 [ cmap ]
-C N CA C +N


Modifiedserine.itp entry


[ atoms ]
; nr type resnr resid atom cgnr charge mass
   1 CR   1 MSER CA  1  0.3310  12.0110
   2 C=O  1 MSER C   2  0.6590  12.0110
   3 O=C  1 MSER O   3 -0.5700  15.9994
   4 CR   1 MSER CB  4  0.2800  12.0110
   5 NR   1 MSER N01 5 -0.9900  14.0067
   6 OR   1 MSER O01 6 -0.6500  15.9994
   7 OR   1 MSER O02 7 -0.6800  15.9994
   8 HOCO 1 MSER H01 8  0.5000   1.0079
   9 HNR  1 MSER H02 9  0.3600   1.0079
  10 HCMM 1 MSER H0310  0.   1.0079
  11 HCMM 1 MSER H0411  0.   1.0079
  12 HCMM 1 MSER H0512  0.   1.0079
  13 HNR  1 MSER H0613  0.3600   1.0079
  14 HOR  1 MSER H0714  0.4000   1.0079

[ bonds ]
; ai aj fu b0 kb, b0 kb
  8   6 1 0.09810  445818.6  0.09810  445818.6
 11   4 1 0.10930  287014.9  0.10930  287014.9
  9   5 1 0.10190  390836.6  0.10190  390836.6
  6   2 1 0.13550  349343.9  0.13550  349343.9
 14   7 1 0.09720  469365.3  0.09720  469365.3
  4  12 1 0.10930  287014.9  0.10930  287014.9
  4   7 1 0.14180  303937.5  0.14180  303937.5
  4   1 1 0.15080  256422.3  0.15080  256422.3
  2   3 1 0.12220  779866.6  0.12220  779866.6
  2   1 1 0.14920  252327.8  0.14920  252327.8
  5  13 1 0.10190  390836.6  0.10190  390836.6
  5   1 1 0.14510  306165.0  0.14510  306165.0
  1  10 1 0.10930  287014.9  0.10930  287014.9



--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
--
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] Adding FE2+ or FE3+ into the system

[Justin Lemkul]

On 1/10/17 12:08 PM, liming_52 wrote:

Thanks  for your apply. Since the protein I simulated could bind FE ions.
I want to compare the affinity difference of FE3+ and FE2+ to the protein. How 
can I solve this problem?


The central challenge here is that, simply put, there is no good way to 
represent these with existing empirical force fields.  Your best bet is probably 
QM/MM of some sort, because representing a transition metal (which is strongly 
polarizable, induces charge transfer, and has a particular coordination 
geometry) is not really reasonable to expect using an additive force field model.


There are some parameter sets (e.g. one developed for CHARMM: 
dx.doi.org/10.1021/jp309150r) based solely on hydration properties, but that's 
not enough necessarily to study interactions with proteins with any real level 
of confidence.


-Justin


Could you send me the link of the paper you mentioned?





--

With my best wishes,
Ming Li, PhD
Chinese Academy of Agricultural Sciences, Beijing, China



At 2017-01-11 00:37:49, "Hannes Loeffler"  wrote:

What are you planning to do with those parameters?

You could have a look into the Li/Merz parameters (and papers!)
available with the AmberTools (may not have been converted yet to
Gromacs formats and the 12-6-4 sets would need support in the code).
Generally, you should be wary when using simple ion force fields and
check carefully how they have been parameterised and what for.
Distinguishing different valencies of the same transition metal atom
with only vdW/Coulomb parameters will most likely not capture their
complex chemistry.


On Tue, 10 Jan 2017 16:24:47 +
CROUZY Serge 119222  wrote:


I'm interested as well in knowing how to get decent parameters for
Fe2+

From gromacs-5.1.2/share/top/gromos54a7.ff/ffnonbonded.itp
We have Zn2+  (What is a reference for these parameters ?)

name   bondtype   mass   charge   ptype CA
;name  at.num   mass  charge  ptype   c6   c12
ZN2+   30  0.000  0.000 A  0.0004182025  9.4400656e-09

From which I deduced
if LJ = v(rij)=C(12)/r12 - C(6)/r6 = A/r^12 -C/r^6
to be compared to the standard V=4*eps*[(sig/r)^12 - (sig/r)^6]
A =4*eps*sig^12
C=4*eps*sig^6
sig = (A/C)^1/6
eps=C^2 / (4 A)
For Zn sig=0.168112  eps=4.631677 kJ/mol

But no Fe2+

Regards

Serge Crouzy PhD HDR
Groupe de Modélisation et Chimie Théorique
Laboratoire de Chimie et Biologie des Métaux
Institut de Biosciences et Biotechnologies de Grenoble
CEA Grenoble  UMR  CEA/CNRS/UJF 5249
17, rue des martyrs
38054 Grenoble Cedex 9
Bat. K  pièce 110
Tel (33)0438782963
Fax (33)0438785487
http://big.cea.fr/drf/big/CBM/GMCT



-Message d'origine-
De : gromacs.org_gmx-users-boun...@maillist.sys.kth.se
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] De la part
de liming_52 Envoyé : mardi 10 janvier 2017 16:54 À :
gmx-us...@gromacs.org Objet : [gmx-users] Adding FE2+ or FE3+ into
the system

Dear gromacs users,

I want to compare the protein in the buffers with FE2+ and FE3+,
respectively.

How can I add FE2+ or FE3+ into the system? What is the command?

Thanks in advance.





--

With my best wishes,
Ming Li, PhD
Chinese Academy of Agricultural Sciences, Beijing, China


--
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.


--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
--
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] Topology parameters for ligand

[Justin Lemkul]

On 1/10/17 4:05 AM, tasneem kausar wrote:

Thank You for your reply

The system under my study has positive charge. There are 3 positive charges
on the protein and one on drug molecule. How these charges will be handled.



Like any others.  A non-zero formal charge of a species does not preclude you 
from doing free energy calculations.


-Justin



On Mon, Jan 9, 2017 at 6:37 PM, Justin Lemkul  wrote:




On 1/9/17 2:31 AM, tasneem kausar wrote:


I got it.

I have looked at the input files for the T4-lysozyme tutorial available at
alchemistry.org. They have defined state A and state B. I am using
GROMACS-5.1.4 for these calculation. So as mentioned in gromacs manual
decoupling parameters are taken from the mdp options, like by defining
[lambda-moltype] in mdp file. As I know from the tutorials and manual the
solvation free energy of the ligand can calculated.

From the alchemistry.org input files, the topology parameters of ligand
are
inserted in protein topology named as complex.top.

If I follow the same protocol without defining the state B of the ligand
in
topology, how the ligand molecule will be decoulped in complex.



An explicit B-state is necessary for a relative free energy calculation,
in which one molecule is transformed into another.

For any absolute free energy calculation (solvation, binding, etc) then
you do not need to define a B-state, and just couple the physical
parameters to lambda to turn them on/off.

-Justin





On Sun, Jan 8, 2017 at 10:21 PM, Justin Lemkul  wrote:




On 1/7/17 10:29 PM, tasneem kausar wrote:

Thank you for your reply


In last section of your tutorial you have suggested some changes to made
in
mdp file. That can be used for solvation free energies.
For free energy calculation of protein drug complex, is it only lambda
restraint to be defined?


Along with a complex system of [intermolecular_interactions] that

preserve
the relative orientation of the ligand.  This is a very complex
calculation
in practice.  See examples on alchemistry.org and in the literature in
works by Roux, Im, Karplus, etc.  My tutorial is not very useful for such
calculations; it is extremely basic relative to what is needed to carry
out
a binding free energy calculation.  I only mentioned it there because so
many people asked about it and I wanted to clear up any confusion.

-Justin


On 8 Jan 2017 01:45, "Justin Lemkul"  wrote:






On 1/7/17 6:05 AM, tasneem kausar wrote:

Dear all



I am following Justin's tutorial methane in water for free energy
calculation. I am using Gromacs-5.1.4. The charges of methane in
topology
are set to zero. So following the same protocol, is it relevant to set
the
charges at zero in topology of the drug. I am confused because in
tutorial
of Sander (ethanol in water) charges are present in the topology file.

Please tell me the difference in both the tutorials and how can I
apply
it
to drug that I want to study.


The charges in my tutorial are set to zero because the stated goal of


that
tutorial is to reproduce *only the LJ portion of the hydration free
energy*
to match a published paper.  This creates a very simple, robust system.
If
you want to calculate a real, meaningful hydration or binding free
energy,
charge transformation is required.

-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
--
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.


--

==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
--
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.



--
==

Justin A. Lemkul, Ph.D.
Ruth L. 

Re: [gmx-users] Error in leaprc.ff14SB (Amber14)

[Justin Lemkul]

On 1/10/17 12:18 AM, Subashini .K wrote:

Hi Gromacs users,



While using the tleap of AmberTools 15,


we give the following command


 source /home/admin/amber14/dat/leap/cmd/leaprc.ff14SB




However, the following error is shown in cgywin command prompt


-bash: logFile: command not found
-bash: addAtomTypes: command not found
-bash: /home/admin/amber14/dat/leap/cmd/leaprc.ff14SB: line 209: syntax error: 
unexpected end of file


How to fix it?



Ask on the AMBER mailing list.

-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
--
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] Adding FE2+ parameters

[CROUZY Serge 119222]

Hello Hannes

I'm perfectly aware how you need to be careful in using metal parameters - 
checking for which solvent and which coordination they have been created for.
In my case structural metal coordinated to protein amino acids... 
I did try to see in Li/Merz parameters which line could resemble the parameters 
in Gromacs for Zn2+ but with no success - This brings me back to the original 
question, where do Zn parameters in Gromacs 54a7 come from ?  Knowing this I 
could try deduce parameters for Fe2+

Thanx 

Serge Crouzy PhD HDR
Groupe de Modélisation et Chimie Théorique
Laboratoire de Chimie et Biologie des Métaux 
Institut de Biosciences et Biotechnologies de Grenoble
CEA Grenoble  UMR  CEA/CNRS/UJF 5249
17, rue des martyrs
38054 Grenoble Cedex 9
Bat. K  pièce 110   
Tel (33)0438782963
Fax (33)0438785487
http://big.cea.fr/drf/big/CBM/GMCT




-Message d'origine-
De : gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] De la part de Hannes 
Loeffler
Envoyé : mardi 10 janvier 2017 17:38
À : gromacs.org_gmx-users@maillist.sys.kth.se
Cc : gmx-us...@gromacs.org
Objet : Re: [gmx-users] Adding FE2+ or FE3+ into the system

What are you planning to do with those parameters?

You could have a look into the Li/Merz parameters (and papers!) available with 
the AmberTools (may not have been converted yet to Gromacs formats and the 
12-6-4 sets would need support in the code).
Generally, you should be wary when using simple ion force fields and check 
carefully how they have been parameterised and what for.
Distinguishing different valencies of the same transition metal atom with only 
vdW/Coulomb parameters will most likely not capture their complex chemistry.


On Tue, 10 Jan 2017 16:24:47 +
CROUZY Serge 119222  wrote:

> I'm interested as well in knowing how to get decent parameters for
> Fe2+
> 
> From gromacs-5.1.2/share/top/gromos54a7.ff/ffnonbonded.itp
> We have Zn2+  (What is a reference for these parameters ?)
> 
> name   bondtype   mass   charge   ptype CA
> ;name  at.num   mass  charge  ptype   c6   c12
> ZN2+   30  0.000  0.000 A  0.0004182025  9.4400656e-09
> 
> From which I deduced
> if LJ = v(rij)=C(12)/r12 - C(6)/r6 = A/r^12 -C/r^6 to be compared to 
> the standard V=4*eps*[(sig/r)^12 - (sig/r)^6] A =4*eps*sig^12
> C=4*eps*sig^6
> sig = (A/C)^1/6
> eps=C^2 / (4 A)
> For Zn sig=0.168112  eps=4.631677 kJ/mol
> 
> But no Fe2+
> 
> Regards
> 
> Serge Crouzy PhD HDR
> Groupe de Modélisation et Chimie Théorique Laboratoire de Chimie et 
> Biologie des Métaux Institut de Biosciences et Biotechnologies de 
> Grenoble CEA Grenoble  UMR  CEA/CNRS/UJF 5249 17, rue des martyrs
> 38054 Grenoble Cedex 9
> Bat. K  pièce 110   
> Tel (33)0438782963
> Fax (33)0438785487
> http://big.cea.fr/drf/big/CBM/GMCT
> 
> 
> 
> -Message d'origine-
> De : gromacs.org_gmx-users-boun...@maillist.sys.kth.se
> [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] De la part
> de liming_52 Envoyé : mardi 10 janvier 2017 16:54 À :
> gmx-us...@gromacs.org Objet : [gmx-users] Adding FE2+ or FE3+ into
> the system
> 
> Dear gromacs users,
> 
> I want to compare the protein in the buffers with FE2+ and FE3+,
> respectively. 
> 
> How can I add FE2+ or FE3+ into the system? What is the command?
> 
> Thanks in advance.
> 
> 
> 
> 
> 
> --
> 
> With my best wishes,
> Ming Li, PhD
> Chinese Academy of Agricultural Sciences, Beijing, China

-- 
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.

Re: [gmx-users] Adding FE2+ or FE3+ into the system

[liming_52]

Thanks  for your apply. Since the protein I simulated could bind FE ions.
I want to compare the affinity difference of FE3+ and FE2+ to the protein. How 
can I solve this problem?
Could you send me the link of the paper you mentioned?





--

With my best wishes,
Ming Li, PhD
Chinese Academy of Agricultural Sciences, Beijing, China



At 2017-01-11 00:37:49, "Hannes Loeffler"  wrote:
>What are you planning to do with those parameters?
>
>You could have a look into the Li/Merz parameters (and papers!)
>available with the AmberTools (may not have been converted yet to
>Gromacs formats and the 12-6-4 sets would need support in the code).
>Generally, you should be wary when using simple ion force fields and
>check carefully how they have been parameterised and what for.
>Distinguishing different valencies of the same transition metal atom
>with only vdW/Coulomb parameters will most likely not capture their
>complex chemistry.
>
>
>On Tue, 10 Jan 2017 16:24:47 +
>CROUZY Serge 119222  wrote:
>
>> I'm interested as well in knowing how to get decent parameters for
>> Fe2+
>> 
>> From gromacs-5.1.2/share/top/gromos54a7.ff/ffnonbonded.itp
>> We have Zn2+  (What is a reference for these parameters ?)
>> 
>> name   bondtype   mass   charge   ptype CA
>> ;name  at.num   mass  charge  ptype   c6   c12
>> ZN2+   30  0.000  0.000 A  0.0004182025  9.4400656e-09
>> 
>> From which I deduced
>> if LJ = v(rij)=C(12)/r12 - C(6)/r6 = A/r^12 -C/r^6
>> to be compared to the standard V=4*eps*[(sig/r)^12 - (sig/r)^6]
>> A =4*eps*sig^12
>> C=4*eps*sig^6
>> sig = (A/C)^1/6
>> eps=C^2 / (4 A)
>> For Zn sig=0.168112  eps=4.631677 kJ/mol
>> 
>> But no Fe2+
>> 
>> Regards
>> 
>> Serge Crouzy PhD HDR
>> Groupe de Modélisation et Chimie Théorique
>> Laboratoire de Chimie et Biologie des Métaux 
>> Institut de Biosciences et Biotechnologies de Grenoble
>> CEA Grenoble  UMR  CEA/CNRS/UJF 5249
>> 17, rue des martyrs
>> 38054 Grenoble Cedex 9
>> Bat. K  pièce 110   
>> Tel (33)0438782963
>> Fax (33)0438785487
>> http://big.cea.fr/drf/big/CBM/GMCT
>> 
>> 
>> 
>> -Message d'origine-
>> De : gromacs.org_gmx-users-boun...@maillist.sys.kth.se
>> [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] De la part
>> de liming_52 Envoyé : mardi 10 janvier 2017 16:54 À :
>> gmx-us...@gromacs.org Objet : [gmx-users] Adding FE2+ or FE3+ into
>> the system
>> 
>> Dear gromacs users,
>> 
>> I want to compare the protein in the buffers with FE2+ and FE3+,
>> respectively. 
>> 
>> How can I add FE2+ or FE3+ into the system? What is the command?
>> 
>> Thanks in advance.
>> 
>> 
>> 
>> 
>> 
>> --
>> 
>> With my best wishes,
>> Ming Li, PhD
>> Chinese Academy of Agricultural Sciences, Beijing, China
>
>-- 
>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.

Re: [gmx-users] Creating a temperature gradient in water

[Mark Abraham]

Hi,

Naturally one can only have a monotonic gradient over half of a periodic
direction of a simulation cell, ie between two themostatted groups. Also,
if you rely on the temperature coupling groups to implement that, then
these are fixed at grompp time, so diffusion will tend to wreck the intent.
One could either use (flat-bottomed?) position restraints to keep the two
groups localized, or periodically stop the simulation and use gmx select to
re-create index groups with the desired spatial locality. Obviously, the
remaining water should not be coupled to a thermostat.

Mark

On Tue, Jan 10, 2017 at 5:44 PM Alex  wrote:

> Erik,
>
> Even with PBC, something like Ibrahim's scenario is possible in principle
> (T_1 in the region at the center of the box, T_2 at the edges). However,
> can this geometry-based thermostatting for fluids be accomplished in GMX?
>
> Alex
>
> On Tue, Jan 10, 2017 at 8:15 AM, Erik Marklund 
> wrote:
>
> > Dear Ibrahim,
> >
> > Do you use pbc? If so, how does that work with your gradient?
> >
> > Kind regards,
> > Erik
> >
> > > On 10 Jan 2017, at 15:00, ibrahim khalil <
> ibrahim.khalil.c...@gmail.com>
> > wrote:
> > >
> > > Dear gromacs users,
> > >
> > > I have a simulation box containing nothing but water (TIP3P). I want to
> > > create a temperature gradient within water (ie. 300K in the left side
> and
> > > 500K in the right side of the simulation box).
> > >
> > > I have successfully applied different temperatures to different groups
> in
> > > my other simulations (for example, different temperatures for water and
> > > proteins).
> > >
> > > How can apply different temperatures within the same group of liquids
> (in
> > > my case, water)?
> > >
> > > Thanks in advance.
> > > --
> > > 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.
> >
> --
> 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.

Re: [gmx-users] Adding FE2+ or FE3+ into the system

[liming_52]

Thanks  for your apply. Since the protein I simulated could bind FE ions.
I want to compare the affinity difference of FE3+ and FE2+ to the protein. How 
can I solve this problem?





--

With my best wishes,
Ming Li, PhD
Chinese Academy of Agricultural Sciences, Beijing, China



At 2017-01-11 00:24:47, "CROUZY Serge 119222"  wrote:
>I'm interested as well in knowing how to get decent parameters for Fe2+
>
>From gromacs-5.1.2/share/top/gromos54a7.ff/ffnonbonded.itp
>We have Zn2+  (What is a reference for these parameters ?)
>
>name   bondtype   mass   charge   ptype CA
>;name  at.num   mass  charge  ptype   c6   c12
>ZN2+   30  0.000  0.000 A  0.0004182025  9.4400656e-09
>
>From which I deduced
>if LJ = v(rij)=C(12)/r12 - C(6)/r6 = A/r^12 -C/r^6
>to be compared to the standard V=4*eps*[(sig/r)^12 - (sig/r)^6]
>A =4*eps*sig^12
>C=4*eps*sig^6
>sig = (A/C)^1/6
>eps=C^2 / (4 A)
>For Zn sig=0.168112  eps=4.631677 kJ/mol
>
>But no Fe2+
>
>Regards
>
>Serge Crouzy PhD HDR
>Groupe de Modélisation et Chimie Théorique
>Laboratoire de Chimie et Biologie des Métaux 
>Institut de Biosciences et Biotechnologies de Grenoble
>CEA Grenoble  UMR  CEA/CNRS/UJF 5249
>17, rue des martyrs
>38054 Grenoble Cedex 9
>Bat. K  pièce 110   
>Tel (33)0438782963
>Fax (33)0438785487
>http://big.cea.fr/drf/big/CBM/GMCT
>
>
>
>-Message d'origine-
>De : gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
>[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] De la part de 
>liming_52
>Envoyé : mardi 10 janvier 2017 16:54
>À : gmx-us...@gromacs.org
>Objet : [gmx-users] Adding FE2+ or FE3+ into the system
>
>Dear gromacs users,
>
>I want to compare the protein in the buffers with FE2+ and FE3+, respectively. 
>
>How can I add FE2+ or FE3+ into the system? What is the command?
>
>Thanks in advance.
>
>
>
>
>
>--
>
>With my best wishes,
>Ming Li, PhD
>Chinese Academy of Agricultural Sciences, Beijing, China
>-- 
>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.
-- 
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] Creating a temperature gradient in water

[Alex]

Erik,

Even with PBC, something like Ibrahim's scenario is possible in principle
(T_1 in the region at the center of the box, T_2 at the edges). However,
can this geometry-based thermostatting for fluids be accomplished in GMX?

Alex

On Tue, Jan 10, 2017 at 8:15 AM, Erik Marklund 
wrote:

> Dear Ibrahim,
>
> Do you use pbc? If so, how does that work with your gradient?
>
> Kind regards,
> Erik
>
> > On 10 Jan 2017, at 15:00, ibrahim khalil 
> wrote:
> >
> > Dear gromacs users,
> >
> > I have a simulation box containing nothing but water (TIP3P). I want to
> > create a temperature gradient within water (ie. 300K in the left side and
> > 500K in the right side of the simulation box).
> >
> > I have successfully applied different temperatures to different groups in
> > my other simulations (for example, different temperatures for water and
> > proteins).
> >
> > How can apply different temperatures within the same group of liquids (in
> > my case, water)?
> >
> > Thanks in advance.
> > --
> > 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.
>
-- 
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] Adding FE2+ or FE3+ into the system

[Hannes Loeffler]

What are you planning to do with those parameters?

You could have a look into the Li/Merz parameters (and papers!)
available with the AmberTools (may not have been converted yet to
Gromacs formats and the 12-6-4 sets would need support in the code).
Generally, you should be wary when using simple ion force fields and
check carefully how they have been parameterised and what for.
Distinguishing different valencies of the same transition metal atom
with only vdW/Coulomb parameters will most likely not capture their
complex chemistry.


On Tue, 10 Jan 2017 16:24:47 +
CROUZY Serge 119222  wrote:

> I'm interested as well in knowing how to get decent parameters for
> Fe2+
> 
> From gromacs-5.1.2/share/top/gromos54a7.ff/ffnonbonded.itp
> We have Zn2+  (What is a reference for these parameters ?)
> 
> name   bondtype   mass   charge   ptype CA
> ;name  at.num   mass  charge  ptype   c6   c12
> ZN2+   30  0.000  0.000 A  0.0004182025  9.4400656e-09
> 
> From which I deduced
> if LJ = v(rij)=C(12)/r12 - C(6)/r6 = A/r^12 -C/r^6
> to be compared to the standard V=4*eps*[(sig/r)^12 - (sig/r)^6]
> A =4*eps*sig^12
> C=4*eps*sig^6
> sig = (A/C)^1/6
> eps=C^2 / (4 A)
> For Zn sig=0.168112  eps=4.631677 kJ/mol
> 
> But no Fe2+
> 
> Regards
> 
> Serge Crouzy PhD HDR
> Groupe de Modélisation et Chimie Théorique
> Laboratoire de Chimie et Biologie des Métaux 
> Institut de Biosciences et Biotechnologies de Grenoble
> CEA Grenoble  UMR  CEA/CNRS/UJF 5249
> 17, rue des martyrs
> 38054 Grenoble Cedex 9
> Bat. K  pièce 110   
> Tel (33)0438782963
> Fax (33)0438785487
> http://big.cea.fr/drf/big/CBM/GMCT
> 
> 
> 
> -Message d'origine-
> De : gromacs.org_gmx-users-boun...@maillist.sys.kth.se
> [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] De la part
> de liming_52 Envoyé : mardi 10 janvier 2017 16:54 À :
> gmx-us...@gromacs.org Objet : [gmx-users] Adding FE2+ or FE3+ into
> the system
> 
> Dear gromacs users,
> 
> I want to compare the protein in the buffers with FE2+ and FE3+,
> respectively. 
> 
> How can I add FE2+ or FE3+ into the system? What is the command?
> 
> Thanks in advance.
> 
> 
> 
> 
> 
> --
> 
> With my best wishes,
> Ming Li, PhD
> Chinese Academy of Agricultural Sciences, Beijing, China

-- 
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] Adding FE2+ or FE3+ into the system

[CROUZY Serge 119222]

I'm interested as well in knowing how to get decent parameters for Fe2+

>From gromacs-5.1.2/share/top/gromos54a7.ff/ffnonbonded.itp
We have Zn2+  (What is a reference for these parameters ?)

name   bondtype   mass   charge   ptype CA
;name  at.num   mass  charge  ptype   c6   c12
ZN2+   30  0.000  0.000 A  0.0004182025  9.4400656e-09

>From which I deduced
if LJ = v(rij)=C(12)/r12 - C(6)/r6 = A/r^12 -C/r^6
to be compared to the standard V=4*eps*[(sig/r)^12 - (sig/r)^6]
A =4*eps*sig^12
C=4*eps*sig^6
sig = (A/C)^1/6
eps=C^2 / (4 A)
For Zn sig=0.168112  eps=4.631677 kJ/mol

But no Fe2+

Regards

Serge Crouzy PhD HDR
Groupe de Modélisation et Chimie Théorique
Laboratoire de Chimie et Biologie des Métaux 
Institut de Biosciences et Biotechnologies de Grenoble
CEA Grenoble  UMR  CEA/CNRS/UJF 5249
17, rue des martyrs
38054 Grenoble Cedex 9
Bat. K  pièce 110   
Tel (33)0438782963
Fax (33)0438785487
http://big.cea.fr/drf/big/CBM/GMCT



-Message d'origine-
De : gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] De la part de 
liming_52
Envoyé : mardi 10 janvier 2017 16:54
À : gmx-us...@gromacs.org
Objet : [gmx-users] Adding FE2+ or FE3+ into the system

Dear gromacs users,

I want to compare the protein in the buffers with FE2+ and FE3+, respectively. 

How can I add FE2+ or FE3+ into the system? What is the command?

Thanks in advance.





--

With my best wishes,
Ming Li, PhD
Chinese Academy of Agricultural Sciences, Beijing, China
-- 
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] Adding FE2+ or FE3+ into the system

[liming_52]

Dear gromacs users,

I want to compare the protein in the buffers with FE2+ and FE3+, respectively. 

How can I add FE2+ or FE3+ into the system? What is the command?

Thanks in advance.





--

With my best wishes,
Ming Li, PhD
Chinese Academy of Agricultural Sciences, Beijing, China
-- 
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] Creating a temperature gradient in water

[Erik Marklund]

Dear Ibrahim,

Do you use pbc? If so, how does that work with your gradient?

Kind regards,
Erik

> On 10 Jan 2017, at 15:00, ibrahim khalil  
> wrote:
> 
> Dear gromacs users,
> 
> I have a simulation box containing nothing but water (TIP3P). I want to
> create a temperature gradient within water (ie. 300K in the left side and
> 500K in the right side of the simulation box).
> 
> I have successfully applied different temperatures to different groups in
> my other simulations (for example, different temperatures for water and
> proteins).
> 
> How can apply different temperatures within the same group of liquids (in
> my case, water)?
> 
> Thanks in advance.
> -- 
> 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] Creating a temperature gradient in water

[ibrahim khalil]

Dear gromacs users,

I have a simulation box containing nothing but water (TIP3P). I want to
create a temperature gradient within water (ie. 300K in the left side and
500K in the right side of the simulation box).

I have successfully applied different temperatures to different groups in
my other simulations (for example, different temperatures for water and
proteins).

How can apply different temperatures within the same group of liquids (in
my case, water)?

Thanks in advance.
-- 
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] Adding detergent to simulation box - SOLVED

[Yasser Almeida Hernández]

I solved the problem adding NG, water and ions in that order.

Cheers

Yasser


On 10.01.2017 13:25, Yasser Almeida Hernández wrote:

Hello all,

I am trying to build a system containing a membrane protein, water, 
ions and NG detergent (beta-nonylglucoside). A conflict arise when I 
try to add NG and ions. If I build the system containing the protein, 
water and ions, and then add NG (with -ci and -nmol options of genbox 
command), none NG molecule is added. On the other hand if I build the 
solvated box with the protein and NG, and then add the ions, the NG 
molecules are destroyed/disordered and clustered in the box edges.


Any thoughts?

Thanks in advance

Yasser



--
Yasser Almeida Hernández
PhD student
Institute of Biochemistry and Molecular Biology
Department of Chemistry
University of Hamburg
Martin-Luther-King-Platz 6
20146 Hamburg
Germany
+49 40 42838 2845
yasser.almeida.hernan...@chemie.uni-hamburg.de
office: Grindelallee 117, room 250c

--
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] Regarding g_energy of heterogenous systems

[Peter Stern]

It is given in well-define units: Kilojoules per mole.  A mole contains an 
Avogadro's number worth of molecules: ~6.022 X 10**23.
What would dividing by the total number of molecules gives you?

Peter

-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of 
Apramita Chand
Sent: Tuesday, January 10, 2017 8:53 AM
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: [gmx-users] Regarding g_energy of heterogenous systems

Dear All,
In the calculation of various energy terms (Coulombic/LJ) for interaction 
energies between Protein-Solvent systems , do we need to specify -nmol as total 
number of molecules of protein and solvent molecules?
If the -nmol option is not specified, the energy value which comes as output as 
, for instance :
LJ-SR -Protein-SOL -   -52.9383 kJ/mol
Should it be divided by total number of molecules(protein+sol) to arrive at the 
value?
Please advise.

yours sincerely,
Apramita Chand
--
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] Adding detergent to simulation box

[Yasser Almeida Hernández]

Hello all,

I am trying to build a system containing a membrane protein, water, ions 
and NG detergent (beta-nonylglucoside). A conflict arise when I try to 
add NG and ions. If I build the system containing the protein, water and 
ions, and then add NG (with -ci and -nmol options of genbox command), 
none NG molecule is added. On the other hand if I build the solvated box 
with the protein and NG, and then add the ions, the NG molecules are 
destroyed/disordered and clustered in the box edges.


Any thoughts?

Thanks in advance

Yasser

--
Yasser Almeida Hernández
PhD student
Institute of Biochemistry and Molecular Biology
Department of Chemistry
University of Hamburg
Martin-Luther-King-Platz 6
20146 Hamburg
Germany
+49 40 42838 2845
yasser.almeida.hernan...@chemie.uni-hamburg.de
office: Grindelallee 117, room 250c

--
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] mdrun initialises, fails to run, no error message

[Natalie Tatum]

Hi Mark,

Excellent, thanks for the helpful guidance!

Natalie





On 10 January 2017 at 10:12, Mark Abraham  wrote:

> Hi,
>
> Yes. Or if you are running two quite similar simulations of the same
> length, use gmx_mpi mdrun -multidir first second and leave the details to
> mdrun (it'll use everything it can, and the default is what you want).
> Check the performance against the above run for sanity.
>
> Mark
>
> On Tue, Jan 10, 2017 at 10:59 AM Natalie Tatum 
> wrote:
>
> > Hi Mark,
> >
> > So using one GPU, with say 6 of 12 logical cores, something like this
> would
> > be more appropriate?
> >
> > gmx mdrun -gpu_id 0 -nt 6 -pin on
> >
> > Adding an offset for any second process?
> >
> >
> > Natalie
> >
> > On 9 January 2017 at 15:18, Mark Abraham 
> wrote:
> >
> > > Hi,
> > >
> > > That's still likely disastrous for performance. Mdrun uses all the
> cores
> > of
> > > the CPU that you permit, as well as the GPU, and running two mdrun on
> the
> > > same cores risks a super-linear slowdown. See suggested examples at
> > > http://manual.gromacs.org/documentation/2016.1/user-
> > > guide/mdrun-performance.html#examples-for-mdrun-on-one-node
> > >
> > > Mark
> > >
> > > On Mon, 9 Jan 2017 16:12 Natalie Tatum 
> wrote:
> > >
> > > > Dear Justin,
> > > >
> > > > Thanks for the advice - after a clean up, a reboot, and some careful
> > > > application of commands, everything seems to be running nicely again.
> > > > Switching the call to below (instead of using -deffnm) is working.
> > > >
> > > > gmx mdrun -s md.tpr -gpu_id 1 &
> > > >
> > > > Many thanks,
> > > >
> > > > Natalie
> > > >
> > > >
> > > >
> > > >
> > > > On 4 January 2017 at 01:02, Justin Lemkul  wrote:
> > > >
> > > > >
> > > > >
> > > > > On 1/3/17 10:43 AM, Natalie Tatum wrote:
> > > > >
> > > > >> Dear all,
> > > > >>
> > > > >> I'm hoping you can shed light on (a) what my mdrun problem is and
> > (b)
> > > > >> where
> > > > >> to start fixing it.
> > > > >>
> > > > >> I'm simulating different mutants of a protein dimer on DNA, for 10
> > ns
> > > > >> a-piece. I have successfully run this protocol on the wild-type
> > > protein,
> > > > >> on
> > > > >> two single residue mutants, and on a double mutant. I came to run
> > the
> > > > same
> > > > >> on a fourth, single site mutant. I have followed the same
> protocols
> > > and
> > > > >> utilised the same MDP settings throughout. All were subject to
> 5000
> > > > steps
> > > > >> of steepest-descent energy minimisation, then 200 ps of
> > equilibration
> > > in
> > > > >> the NVT ensemble, then the same in the NPT. For this particular
> > mutant
> > > > >> there were no issues apparent going into production MD.
> Therefore, I
> > > > don't
> > > > >> think it's an issue of my MDP setup or system...
> > > > >>
> > > > >> So I have two compatible (OpenCL 1.2) AMD Radeon HD Firepro D300
> > GPUs,
> > > > and
> > > > >> I have one mutant (run/process) assigned to each.
> > > > >>
> > > > >> For this mutant I call mdrun with:
> > > > >>
> > > > >> gmx mdrun -deffnm md -gpu_id 1 &
> > > > >>
> > > > >> Whereas the other is on -gpu_id 0, and walk away. This worked
> > > > successfully
> > > > >> in the week prior for two other systems. It's New Year, then I
> come
> > > back
> > > > >> to
> > > > >> what should be completed simulations this morning to get my hands
> > > dirty
> > > > in
> > > > >> analysis.
> > > > >>
> > > > >> Run on gpu 0 has completed successfully, all is grand.
> > > > >>
> > > > >> Mutant on gpu 1 has not. Attempts to resume/restart fail (on
> either
> > > GPU,
> > > > >> or
> > > > >> both, or calling neither explicitly). All output looks like this:
> > > > >>
> > > > >> GROMACS:  gmx mdrun, VERSION 5.1.3
> > > > >>
> > > > >> Executable:   /usr/local/gromacs/bin/gmx
> > > > >>
> > > > >> Data prefix:  /usr/local/gromacs
> > > > >>
> > > > >> Command line:
> > > > >>
> > > > >>
> > > > >>
> > > > >>   gmx mdrun -deffnm md
> > > > >>
> > > > >>
> > > > > From the .log, it appears your command was not what you think it
> was.
> > > Is
> > > > > it possible that the job failed because mdrun tried to consume all
> > > > > available hardware and got hung up?
> > > > >
> > > > >
> > > > >>
> > > > >> GROMACS version:VERSION 5.1.3
> > > > >>
> > > > >> Precision:  single
> > > > >>
> > > > >> Memory model:   64 bit
> > > > >>
> > > > >> MPI library:thread_mpi
> > > > >>
> > > > >> OpenMP support: disabled
> > > > >>
> > > > >> GPU support:enabled
> > > > >>
> > > > >> OpenCL support: enabled
> > > > >>
> > > > >> invsqrt routine:gmx_software_invsqrt(x)
> > > > >>
> > > > >> SIMD instructions:  AVX_256
> > > > >>
> > > > >> FFT library:fftw-3.3.4-sse2
> > > > >>
> > > > >> RDTSCP usage:   enabled
> > > > >>
> > > > >> C++11 compilation:  disabled
> > > > >>
> > > > >> TNG support:enabled
> > > 

Re: [gmx-users] mdrun initialises, fails to run, no error message

[Mark Abraham]

Hi,

Yes. Or if you are running two quite similar simulations of the same
length, use gmx_mpi mdrun -multidir first second and leave the details to
mdrun (it'll use everything it can, and the default is what you want).
Check the performance against the above run for sanity.

Mark

On Tue, Jan 10, 2017 at 10:59 AM Natalie Tatum 
wrote:

> Hi Mark,
>
> So using one GPU, with say 6 of 12 logical cores, something like this would
> be more appropriate?
>
> gmx mdrun -gpu_id 0 -nt 6 -pin on
>
> Adding an offset for any second process?
>
>
> Natalie
>
> On 9 January 2017 at 15:18, Mark Abraham  wrote:
>
> > Hi,
> >
> > That's still likely disastrous for performance. Mdrun uses all the cores
> of
> > the CPU that you permit, as well as the GPU, and running two mdrun on the
> > same cores risks a super-linear slowdown. See suggested examples at
> > http://manual.gromacs.org/documentation/2016.1/user-
> > guide/mdrun-performance.html#examples-for-mdrun-on-one-node
> >
> > Mark
> >
> > On Mon, 9 Jan 2017 16:12 Natalie Tatum  wrote:
> >
> > > Dear Justin,
> > >
> > > Thanks for the advice - after a clean up, a reboot, and some careful
> > > application of commands, everything seems to be running nicely again.
> > > Switching the call to below (instead of using -deffnm) is working.
> > >
> > > gmx mdrun -s md.tpr -gpu_id 1 &
> > >
> > > Many thanks,
> > >
> > > Natalie
> > >
> > >
> > >
> > >
> > > On 4 January 2017 at 01:02, Justin Lemkul  wrote:
> > >
> > > >
> > > >
> > > > On 1/3/17 10:43 AM, Natalie Tatum wrote:
> > > >
> > > >> Dear all,
> > > >>
> > > >> I'm hoping you can shed light on (a) what my mdrun problem is and
> (b)
> > > >> where
> > > >> to start fixing it.
> > > >>
> > > >> I'm simulating different mutants of a protein dimer on DNA, for 10
> ns
> > > >> a-piece. I have successfully run this protocol on the wild-type
> > protein,
> > > >> on
> > > >> two single residue mutants, and on a double mutant. I came to run
> the
> > > same
> > > >> on a fourth, single site mutant. I have followed the same protocols
> > and
> > > >> utilised the same MDP settings throughout. All were subject to 5000
> > > steps
> > > >> of steepest-descent energy minimisation, then 200 ps of
> equilibration
> > in
> > > >> the NVT ensemble, then the same in the NPT. For this particular
> mutant
> > > >> there were no issues apparent going into production MD. Therefore, I
> > > don't
> > > >> think it's an issue of my MDP setup or system...
> > > >>
> > > >> So I have two compatible (OpenCL 1.2) AMD Radeon HD Firepro D300
> GPUs,
> > > and
> > > >> I have one mutant (run/process) assigned to each.
> > > >>
> > > >> For this mutant I call mdrun with:
> > > >>
> > > >> gmx mdrun -deffnm md -gpu_id 1 &
> > > >>
> > > >> Whereas the other is on -gpu_id 0, and walk away. This worked
> > > successfully
> > > >> in the week prior for two other systems. It's New Year, then I come
> > back
> > > >> to
> > > >> what should be completed simulations this morning to get my hands
> > dirty
> > > in
> > > >> analysis.
> > > >>
> > > >> Run on gpu 0 has completed successfully, all is grand.
> > > >>
> > > >> Mutant on gpu 1 has not. Attempts to resume/restart fail (on either
> > GPU,
> > > >> or
> > > >> both, or calling neither explicitly). All output looks like this:
> > > >>
> > > >> GROMACS:  gmx mdrun, VERSION 5.1.3
> > > >>
> > > >> Executable:   /usr/local/gromacs/bin/gmx
> > > >>
> > > >> Data prefix:  /usr/local/gromacs
> > > >>
> > > >> Command line:
> > > >>
> > > >>
> > > >>
> > > >>   gmx mdrun -deffnm md
> > > >>
> > > >>
> > > > From the .log, it appears your command was not what you think it was.
> > Is
> > > > it possible that the job failed because mdrun tried to consume all
> > > > available hardware and got hung up?
> > > >
> > > >
> > > >>
> > > >> GROMACS version:VERSION 5.1.3
> > > >>
> > > >> Precision:  single
> > > >>
> > > >> Memory model:   64 bit
> > > >>
> > > >> MPI library:thread_mpi
> > > >>
> > > >> OpenMP support: disabled
> > > >>
> > > >> GPU support:enabled
> > > >>
> > > >> OpenCL support: enabled
> > > >>
> > > >> invsqrt routine:gmx_software_invsqrt(x)
> > > >>
> > > >> SIMD instructions:  AVX_256
> > > >>
> > > >> FFT library:fftw-3.3.4-sse2
> > > >>
> > > >> RDTSCP usage:   enabled
> > > >>
> > > >> C++11 compilation:  disabled
> > > >>
> > > >> TNG support:enabled
> > > >>
> > > >> Tracing support:disabled
> > > >>
> > > >> Built on:   Mon  1 Aug 2016 17:20:18 BST
> > > >>
> > > >> Built by:   natalie@t 
> > > >> hemachineIuse.here.there [CMAKE]
> > > >>
> > > >>
> > > >> Build OS/arch:  Darwin 15.5.0 x86_64
> > > >>
> > > >> Build CPU vendor:   GenuineIntel
> > > >>
> > > >> Build CPU brand:Intel(R) Xeon(R) CPU E5-1650 v2 @ 3.50GHz
> > > >>
> > > >> Build CPU family:   6   Model: 62   

Re: [gmx-users] mdrun initialises, fails to run, no error message

[Natalie Tatum]

Hi Mark,

So using one GPU, with say 6 of 12 logical cores, something like this would
be more appropriate?

gmx mdrun -gpu_id 0 -nt 6 -pin on

Adding an offset for any second process?


Natalie

On 9 January 2017 at 15:18, Mark Abraham  wrote:

> Hi,
>
> That's still likely disastrous for performance. Mdrun uses all the cores of
> the CPU that you permit, as well as the GPU, and running two mdrun on the
> same cores risks a super-linear slowdown. See suggested examples at
> http://manual.gromacs.org/documentation/2016.1/user-
> guide/mdrun-performance.html#examples-for-mdrun-on-one-node
>
> Mark
>
> On Mon, 9 Jan 2017 16:12 Natalie Tatum  wrote:
>
> > Dear Justin,
> >
> > Thanks for the advice - after a clean up, a reboot, and some careful
> > application of commands, everything seems to be running nicely again.
> > Switching the call to below (instead of using -deffnm) is working.
> >
> > gmx mdrun -s md.tpr -gpu_id 1 &
> >
> > Many thanks,
> >
> > Natalie
> >
> >
> >
> >
> > On 4 January 2017 at 01:02, Justin Lemkul  wrote:
> >
> > >
> > >
> > > On 1/3/17 10:43 AM, Natalie Tatum wrote:
> > >
> > >> Dear all,
> > >>
> > >> I'm hoping you can shed light on (a) what my mdrun problem is and (b)
> > >> where
> > >> to start fixing it.
> > >>
> > >> I'm simulating different mutants of a protein dimer on DNA, for 10 ns
> > >> a-piece. I have successfully run this protocol on the wild-type
> protein,
> > >> on
> > >> two single residue mutants, and on a double mutant. I came to run the
> > same
> > >> on a fourth, single site mutant. I have followed the same protocols
> and
> > >> utilised the same MDP settings throughout. All were subject to 5000
> > steps
> > >> of steepest-descent energy minimisation, then 200 ps of equilibration
> in
> > >> the NVT ensemble, then the same in the NPT. For this particular mutant
> > >> there were no issues apparent going into production MD. Therefore, I
> > don't
> > >> think it's an issue of my MDP setup or system...
> > >>
> > >> So I have two compatible (OpenCL 1.2) AMD Radeon HD Firepro D300 GPUs,
> > and
> > >> I have one mutant (run/process) assigned to each.
> > >>
> > >> For this mutant I call mdrun with:
> > >>
> > >> gmx mdrun -deffnm md -gpu_id 1 &
> > >>
> > >> Whereas the other is on -gpu_id 0, and walk away. This worked
> > successfully
> > >> in the week prior for two other systems. It's New Year, then I come
> back
> > >> to
> > >> what should be completed simulations this morning to get my hands
> dirty
> > in
> > >> analysis.
> > >>
> > >> Run on gpu 0 has completed successfully, all is grand.
> > >>
> > >> Mutant on gpu 1 has not. Attempts to resume/restart fail (on either
> GPU,
> > >> or
> > >> both, or calling neither explicitly). All output looks like this:
> > >>
> > >> GROMACS:  gmx mdrun, VERSION 5.1.3
> > >>
> > >> Executable:   /usr/local/gromacs/bin/gmx
> > >>
> > >> Data prefix:  /usr/local/gromacs
> > >>
> > >> Command line:
> > >>
> > >>
> > >>
> > >>   gmx mdrun -deffnm md
> > >>
> > >>
> > > From the .log, it appears your command was not what you think it was.
> Is
> > > it possible that the job failed because mdrun tried to consume all
> > > available hardware and got hung up?
> > >
> > >
> > >>
> > >> GROMACS version:VERSION 5.1.3
> > >>
> > >> Precision:  single
> > >>
> > >> Memory model:   64 bit
> > >>
> > >> MPI library:thread_mpi
> > >>
> > >> OpenMP support: disabled
> > >>
> > >> GPU support:enabled
> > >>
> > >> OpenCL support: enabled
> > >>
> > >> invsqrt routine:gmx_software_invsqrt(x)
> > >>
> > >> SIMD instructions:  AVX_256
> > >>
> > >> FFT library:fftw-3.3.4-sse2
> > >>
> > >> RDTSCP usage:   enabled
> > >>
> > >> C++11 compilation:  disabled
> > >>
> > >> TNG support:enabled
> > >>
> > >> Tracing support:disabled
> > >>
> > >> Built on:   Mon  1 Aug 2016 17:20:18 BST
> > >>
> > >> Built by:   natalie@t 
> > >> hemachineIuse.here.there [CMAKE]
> > >>
> > >>
> > >> Build OS/arch:  Darwin 15.5.0 x86_64
> > >>
> > >> Build CPU vendor:   GenuineIntel
> > >>
> > >> Build CPU brand:Intel(R) Xeon(R) CPU E5-1650 v2 @ 3.50GHz
> > >>
> > >> Build CPU family:   6   Model: 62   Stepping: 4
> > >>
> > >> Build CPU features: aes apic avx clfsh cmov cx8 cx16 f16c htt lahf_lm
> > mmx
> > >> msr nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdrnd rdtscp
> sse2
> > >> sse3 sse4.1 sse4.2 ssse3 tdt x2apic
> > >>
> > >> C compiler: /Applications/Xcode.app/Conte
> > >> nts/Developer/Toolchains/
> > >> XcodeDefault.xctoolchain/usr/bin/cc Clang 7.3.0.7030031
> > >>
> > >> C compiler flags:-mavx-Wall -Wno-unused -Wunused-value
> > >> -Wunused-parameter -Wno-unknown-pragmas  -O3 -DNDEBUG
> > >>
> > >> C++ compiler:   /Applications/Xcode.app/Conte
> > >> nts/Developer/Toolchains/
> > >> XcodeDefault.xctoolchain/usr/bin/c++ Clang 

[gmx-users] Adding a new(modefied) fatty acid to charm 36 force field.

[Tushar Ranjan Moharana]

Hi All,
I want to understand the interaction of a fatty acid to various amino acid
side chain while it forms a covalent link with the hydroxyle group of the
serine. For that I wanted to add covalently linked serine-fatty acid as a
different amino acid so the pdb2gmx can generate the topology. For the
above reason I made the required complex in pdb format and converted to
mol2 format and generated .itp file from swissparam server. My plan was to
copy the [ atom ]  and [ bond ] section of the .itp to aminoacid.rtp under
the new amino acid with suitable modifications and add it to
residuetype.dat with type protein.

While trying the above, I did the same thing with only serine
(unmodefied).  The [ atom ] and [ bond ] section of the .itp generated by
swissparam looks completly different from that of serine mentioned in
aminoacid.rtp. This is giving me a fishy smell about what I am doing.
Kindly enlighten me about my mistakes and the correct protocol to do the
same. Following are the entry of  the [ atom ] and [ bond ] section of the
aminoacid.rtp and .itp that I have generated.

aminoacid.rtp entry

[ SER ]
 [ atoms ]
N NH1 -0.47 0
HN H 0.31 1
CA CT1 0.07 2
HA HB 0.09 3
CB CT2 0.05 4
HB1 HA 0.09 5
HB2 HA 0.09 6
OG OH1 -0.66 7
HG1 H 0.43 8
C C 0.51 9
O O -0.51 10
 [ bonds ]
CB CA
OG CB
N HN
N CA
C CA
C +N
CA HA
CB HB1
CB HB2
OG HG1
O C
 [ impropers ]
N -C CA HN
C CA +N O
 [ cmap ]
-C N CA C +N


Modifiedserine.itp entry


[ atoms ]
; nr type resnr resid atom cgnr charge mass
   1 CR   1 MSER CA  1  0.3310  12.0110
   2 C=O  1 MSER C   2  0.6590  12.0110
   3 O=C  1 MSER O   3 -0.5700  15.9994
   4 CR   1 MSER CB  4  0.2800  12.0110
   5 NR   1 MSER N01 5 -0.9900  14.0067
   6 OR   1 MSER O01 6 -0.6500  15.9994
   7 OR   1 MSER O02 7 -0.6800  15.9994
   8 HOCO 1 MSER H01 8  0.5000   1.0079
   9 HNR  1 MSER H02 9  0.3600   1.0079
  10 HCMM 1 MSER H0310  0.   1.0079
  11 HCMM 1 MSER H0411  0.   1.0079
  12 HCMM 1 MSER H0512  0.   1.0079
  13 HNR  1 MSER H0613  0.3600   1.0079
  14 HOR  1 MSER H0714  0.4000   1.0079

[ bonds ]
; ai aj fu b0 kb, b0 kb
  8   6 1 0.09810  445818.6  0.09810  445818.6
 11   4 1 0.10930  287014.9  0.10930  287014.9
  9   5 1 0.10190  390836.6  0.10190  390836.6
  6   2 1 0.13550  349343.9  0.13550  349343.9
 14   7 1 0.09720  469365.3  0.09720  469365.3
  4  12 1 0.10930  287014.9  0.10930  287014.9
  4   7 1 0.14180  303937.5  0.14180  303937.5
  4   1 1 0.15080  256422.3  0.15080  256422.3
  2   3 1 0.12220  779866.6  0.12220  779866.6
  2   1 1 0.14920  252327.8  0.14920  252327.8
  5  13 1 0.10190  390836.6  0.10190  390836.6
  5   1 1 0.14510  306165.0  0.14510  306165.0
  1  10 1 0.10930  287014.9  0.10930  287014.9

-- 
Tushar Ranjan Moharana
B. Tech, NIT Warangal
Ph D Student, CCMB
-- 
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] Topology parameters for ligand

[tasneem kausar]

Thank You for your reply

The system under my study has positive charge. There are 3 positive charges
on the protein and one on drug molecule. How these charges will be handled.


On Mon, Jan 9, 2017 at 6:37 PM, Justin Lemkul  wrote:

>
>
> On 1/9/17 2:31 AM, tasneem kausar wrote:
>
>> I got it.
>>
>> I have looked at the input files for the T4-lysozyme tutorial available at
>> alchemistry.org. They have defined state A and state B. I am using
>> GROMACS-5.1.4 for these calculation. So as mentioned in gromacs manual
>> decoupling parameters are taken from the mdp options, like by defining
>> [lambda-moltype] in mdp file. As I know from the tutorials and manual the
>> solvation free energy of the ligand can calculated.
>>
>> From the alchemistry.org input files, the topology parameters of ligand
>> are
>> inserted in protein topology named as complex.top.
>>
>> If I follow the same protocol without defining the state B of the ligand
>> in
>> topology, how the ligand molecule will be decoulped in complex.
>>
>>
> An explicit B-state is necessary for a relative free energy calculation,
> in which one molecule is transformed into another.
>
> For any absolute free energy calculation (solvation, binding, etc) then
> you do not need to define a B-state, and just couple the physical
> parameters to lambda to turn them on/off.
>
> -Justin
>
>
>
>>
>> On Sun, Jan 8, 2017 at 10:21 PM, Justin Lemkul  wrote:
>>
>>
>>>
>>> On 1/7/17 10:29 PM, tasneem kausar wrote:
>>>
>>> Thank you for your reply

 In last section of your tutorial you have suggested some changes to made
 in
 mdp file. That can be used for solvation free energies.
 For free energy calculation of protein drug complex, is it only lambda
 restraint to be defined?


 Along with a complex system of [intermolecular_interactions] that
>>> preserve
>>> the relative orientation of the ligand.  This is a very complex
>>> calculation
>>> in practice.  See examples on alchemistry.org and in the literature in
>>> works by Roux, Im, Karplus, etc.  My tutorial is not very useful for such
>>> calculations; it is extremely basic relative to what is needed to carry
>>> out
>>> a binding free energy calculation.  I only mentioned it there because so
>>> many people asked about it and I wanted to clear up any confusion.
>>>
>>> -Justin
>>>
>>>
>>> On 8 Jan 2017 01:45, "Justin Lemkul"  wrote:
>>>



> On 1/7/17 6:05 AM, tasneem kausar wrote:
>
> Dear all
>
>>
>> I am following Justin's tutorial methane in water for free energy
>> calculation. I am using Gromacs-5.1.4. The charges of methane in
>> topology
>> are set to zero. So following the same protocol, is it relevant to set
>> the
>> charges at zero in topology of the drug. I am confused because in
>> tutorial
>> of Sander (ethanol in water) charges are present in the topology file.
>>
>> Please tell me the difference in both the tutorials and how can I
>> apply
>> it
>> to drug that I want to study.
>>
>>
>> The charges in my tutorial are set to zero because the stated goal of
>>
> that
> tutorial is to reproduce *only the LJ portion of the hydration free
> energy*
> to match a published paper.  This creates a very simple, robust system.
> If
> you want to calculate a real, meaningful hydration or binding free
> energy,
> charge transformation is required.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==
> --
> 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.
>
>
> --
>>> ==
>>>
>>> Justin A. Lemkul, Ph.D.
>>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>>
>>> Department of Pharmaceutical Sciences
>>> School of Pharmacy
>>> Health Sciences Facility II, Room 629
>>> University of Maryland, Baltimore
>>> 20 Penn St.
>>> Baltimore, MD 21201
>>>
>>> jalem...@outerbanks.umaryland.edu | (410) 706-7441
>>> http://mackerell.umaryland.edu/~jalemkul
>>>
>>> 

Re: [gmx-users] REg MD results

[Parul Raj Srivastava]

Dear Sir,

On analysing each chain separately,though the rmsd is stable but the rmsf
is not beginning from the origin and suddenly rising from the centre of
falling off towards the end.

Regards,
Parul Raj Srivastava,
M.Tech.Computational Biology,
Anna University,Chennai-600025

On Sun, Jan 8, 2017 at 1:44 AM, Justin Lemkul  wrote:

>
>
> On 1/7/17 5:14 AM, Parul Raj Srivastava wrote:
>
>> I have given an MD run for a quaternary protein structure by taking 2
>> chains at a time for the MD run.The rmsf graph so obtained is showing
>> erratic behaviour,please find attached graph.Is this result justified or
>> incorrect??
>>
>>
> The list does not accept attachments.  If you want to share an image,
> upload it to a file-sharing service and provide a link.
>
> Often it is just easier to create index groups for each chain and analyze
> them separately.  This eliminates most confusion associated with
> residue-specific analyses like RMSF.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==
> --
> 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.