Re: [gmx-users] Periodic Molecule's Free Energy Calculation Error

[Jason Zhu]

Dear Alex,

Many thanks for your replies and helping.

I totally agree with your comments about infinite molecules and periodic
boundary condition.

Here in our simulations, the hBN sheet covers the box dimensions (6nm*6nm)
without free edges. By using PBC and "periodic-molecules = yes", we could
calculate the surface energy of hBN sheet without effects of edges.

The parameters of force field we are using are borrowed from the following
papers. We introduced them into the Gromos force field. We are having a new
publication using this modified force field in which all the parameters are
shown explicitly. I could send it to you when it is published online. The
functions and parameters are fitted by the setting of "nrexcl=3" in these
papers. We couldn't make any changes for this. But we could try to use
larger value of "nrexcl" to fit the force field of hBN and include
short-range non-bonded interactions into bonded interactions. Thank you for
your suggestions.

1. Hilder, T. A. et al. Validity of current force fields for simulations on
boron nitride nanotubes. IET Micro & Nano Letters 5, 150-156,
doi:10.1049/mnl.2009.0112 (2010).

2. Kamath, G. & Baker, G. A. Are ionic liquids suitable media for boron
nitride exfoliation and dispersion? Insight via molecular dynamics. RSC
Advances 3, 8197-8202, doi:10.1039/c3ra40488a (2013).

3. Wu, J., Wang, B., Wei, Y., Yang, R. & Dresselhaus, M. Mechanics and
Mechanically Tunable Band Gap in Single-Layer Hexagonal Boron-Nitride.
Materials Research Letters 1, 200-206, doi:10.1080/21663831.2013.824516
(2013).

Best,
Jason


Message: 5
Date: Wed, 12 Jul 2017 19:12:26 -0600
From: Alex 
To: Discussion list for GROMACS users 
Subject: Re: [gmx-users] Periodic Molecule's Free Energy Calculation
Error
Message-ID: <4b927ef2-9a56-6655-8053-d284cf88b...@gmail.com>
Content-Type: text/plain; charset=utf-8; format=flowed


>
> I wonder if the "couple-intramol = yes" is a must. Does it have any
> influence on the output results if we turn off the intra-molecular
> non-bonded interactions of a large infinite molecule?
>
The answer to your question has nothing to do with Gromacs, but with
understanding the difference between crystals and biomolecules (for
which Gromacs was designed).
Also (unrelated), it is a common misconception to believe that PBC makes
something infinite -- the effective size of your system is entirely
determined by the supercell size (proof: consider the ripples in hBN and
determine the lowest wavelength of the ripple that can propagate -- it
is commensurate with the box size). In an infinite system, you can have
an immensely long wave (though not infinite, as shown by Landau a while
back). PBC does not make anything infinite, it is a mathematical way of
avoiding surfaces.
>
> There is no universal force field for HBN, so I am using a modified
> gromos54a7_atb force field, i.e., manually adding the parameters for
> boron and nitrogen to the bonded & nonbonded .itp files.
Oh, I know that there is no force fields for these structures. ;) My
question was about which Gromacs ff you were using to insert your
parameters, and, most importantly, where those parameters came from.

> The parameters are obtained from literature.
>
What literature? All bio-style ff adaptations of solid-state potentials
(e.g. Tersoff-Brenner for hBN) I am aware of make it very clear that
"intramolecular" interactions between atoms sharing up to a fairly
distant covalently bound neighbor are limited to bonds and angles. This
comes from the math involved in developing potentials for crystals.
There was a recent question regarding this very problem here, which was
solved by setting a larger nrexcl value. In your case, you solved it
with turning off intramolecular coupling. In fact, if you set your
nrexcl to something like 4 or 5, you may not even need to turn off the
coupling. But then again, I don't know where the parameters came from.

Alex
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[gmx-users] (no subject)

[Jason Zhu]

Dear Alex,

Many thanks for your replies and helping.

I totally agree with your comments about infinite molecules and periodic
boundary condition.

Here in our simulations, the hBN sheet covers the box dimensions (6nm*6nm)
without free edges. By using PBC and "periodic-molecules = yes", we could
calculate the surface energy of hBN sheet without effects of edges.

The parameters of force field we are using are borrowed from the following
papers. We introduced them into the Gromos force field. We are having a new
publication using this modified force field in which all the parameters are
shown explicitly. I could send it to you when it is published online. The
functions and parameters are fitted by the setting of "nrexcl=3" in these
papers. We couldn't make any changes for this. But we could try to use
larger value of "nrexcl" to fit the force field of hBN and include
short-range non-bonded interactions into bonded interactions. Thank you for
your suggestions.

1. Hilder, T. A. et al. Validity of current force fields for simulations on
boron nitride nanotubes. IET Micro & Nano Letters 5, 150-156,
doi:10.1049/mnl.2009.0112 (2010).

2. Kamath, G. & Baker, G. A. Are ionic liquids suitable media for boron
nitride exfoliation and dispersion? Insight via molecular dynamics. RSC
Advances 3, 8197-8202, doi:10.1039/c3ra40488a (2013).

3. Wu, J., Wang, B., Wei, Y., Yang, R. & Dresselhaus, M. Mechanics and
Mechanically Tunable Band Gap in Single-Layer Hexagonal Boron-Nitride.
Materials Research Letters 1, 200-206, doi:10.1080/21663831.2013.824516
(2013).

Best,
Jason


Message: 5
Date: Wed, 12 Jul 2017 19:12:26 -0600
From: Alex 
To: Discussion list for GROMACS users 
Subject: Re: [gmx-users] Periodic Molecule's Free Energy Calculation
Error
Message-ID: <4b927ef2-9a56-6655-8053-d284cf88b...@gmail.com>
Content-Type: text/plain; charset=utf-8; format=flowed


>
> I wonder if the "couple-intramol = yes" is a must. Does it have any
> influence on the output results if we turn off the intra-molecular
> non-bonded interactions of a large infinite molecule?
>
The answer to your question has nothing to do with Gromacs, but with
understanding the difference between crystals and biomolecules (for
which Gromacs was designed).
Also (unrelated), it is a common misconception to believe that PBC makes
something infinite -- the effective size of your system is entirely
determined by the supercell size (proof: consider the ripples in hBN and
determine the lowest wavelength of the ripple that can propagate -- it
is commensurate with the box size). In an infinite system, you can have
an immensely long wave (though not infinite, as shown by Landau a while
back). PBC does not make anything infinite, it is a mathematical way of
avoiding surfaces.
>
> There is no universal force field for HBN, so I am using a modified
> gromos54a7_atb force field, i.e., manually adding the parameters for
> boron and nitrogen to the bonded & nonbonded .itp files.
Oh, I know that there is no force fields for these structures. ;) My
question was about which Gromacs ff you were using to insert your
parameters, and, most importantly, where those parameters came from.

> The parameters are obtained from literature.
>
What literature? All bio-style ff adaptations of solid-state potentials
(e.g. Tersoff-Brenner for hBN) I am aware of make it very clear that
"intramolecular" interactions between atoms sharing up to a fairly
distant covalently bound neighbor are limited to bonds and angles. This
comes from the math involved in developing potentials for crystals.
There was a recent question regarding this very problem here, which was
solved by setting a larger nrexcl value. In your case, you solved it
with turning off intramolecular coupling. In fact, if you set your
nrexcl to something like 4 or 5, you may not even need to turn off the
coupling. But then again, I don't know where the parameters came from.

Alex
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Re: [gmx-users] Periodic Molecule's Free Energy Calculation Error

[Jason Zhu]

Dear Justin,

Many thanks for your reply and explanation.

Now I understand the difference between "couple-intramol = no"
and "couple-intramol = yes" and their consequences.

According to the manual, it is recommended to use "couple-intramol = yes"
for relatively large molecules. Why is that?

I don't know why "couple-intramol = no" doesn't work on large molecules or
infinite molecules with periodic boundary condition.

Is it because the code of "couple-intramol = no" doesn't consider molecules
longer than box size or for any consideration.

Looking forward to hearing from you. Thank you again.

Best,
Jason

On 7/12/17 9:12 PM, Alex wrote:
>
>>
>> I wonder if the "couple-intramol = yes" is a must. Does it have any
influence
>> on the output results if we turn off the intra-molecular non-bonded
>> interactions of a large infinite molecule?
>>
> The answer to your question has nothing to do with Gromacs, but with
> understanding the difference between crystals and biomolecules (for which
> Gromacs was designed).

There is a functional difference between coupling intramolecular
interactions
and not, which will affect the computed free energy.  With couple-intramol
= no,
you get the correct vacuum state of the solute molecule; with
couple-intramol =
yes, you get perturbed intramolecular interactions.  This has important
consequences for what one is trying to compute.

-Justin

> Also (unrelated), it is a common misconception to believe that PBC makes
> something infinite -- the effective size of your system is entirely
determined
> by the supercell size (proof: consider the ripples in hBN and determine
the
> lowest wavelength of the ripple that can propagate -- it is commensurate
with
> the box size). In an infinite system, you can have an immensely long wave
> (though not infinite, as shown by Landau a while back). PBC does not make
> anything infinite, it is a mathematical way of avoiding surfaces.
>>
>> There is no universal force field for HBN, so I am using a modified
>> gromos54a7_atb force field, i.e., manually adding the parameters for
boron and
>> nitrogen to the bonded & nonbonded .itp files.
> Oh, I know that there is no force fields for these structures. ;) My
question
> was about which Gromacs ff you were using to insert your parameters, and,
most
> importantly, where those parameters came from.
>
>> The parameters are obtained from literature.
>>
> What literature? All bio-style ff adaptations of solid-state potentials
(e.g.
> Tersoff-Brenner for hBN) I am aware of make it very clear that
"intramolecular"
> interactions between atoms sharing up to a fairly distant covalently bound
> neighbor are limited to bonds and angles. This comes from the math
involved in
> developing potentials for crystals. There was a recent question regarding
this
> very problem here, which was solved by setting a larger nrexcl value. In
your
> case, you solved it with turning off intramolecular coupling. In fact, if
you
> set your nrexcl to something like 4 or 5, you may not even need to turn
off the
> coupling. But then again, I don't know where the parameters came from.
>
> Alex

--
==

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
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Re: [gmx-users] Concrete pull code explanation needed

[Du, Yu]

> -Original Messages-
> From: "Justin Lemkul" 
> Sent Time: Thursday, July 13, 2017
> To: gmx-us...@gromacs.org
> Cc: 
> Subject: Re: [gmx-users] Concrete pull code explanation needed
> 
> 
> 
> On 7/11/17 8:23 PM, Du, Yu wrote:
> >> On 7/10/17 11:19 PM, Du, Yu wrote:
> >>> Dear Justin and gmx users,
> >>>
> >>>
> >>> I have gone through mdp-option and Justin A. Lemkul's COM pulling 
> >>> tutorial serveral times.
> >>>
> >>>
> >>> The following is Justin's pull code.
> >>>
> >>>
> >>> ; Pull code
> >>> pull= yes
> >>> pull_ngroups= 2
> >>> pull_ncoords= 1
> >>> pull_group1_name= Chain_B
> >>> pull_group2_name= Chain_A
> >>> pull_coord1_type= umbrella  ; harmonic biasing force
> >>> pull_coord1_geometry= distance  ; simple distance increase
> >>> pull_coord1_groups= 1 2
> >>> pull_coord1_dim = N N Y
> >>> pull_coord1_rate= 0.01  ; 0.01 nm per ps = 10 nm per ns
> >>> pull_coord1_k   = 1000  ; kJ mol^-1 nm^-2
> >>> pull_coord1_start   = yes   ; define initial COM distance > 0
> >>>
> >>>
> >>> My understanding lists as follows,
> >>>
> >>>
> >>> Justin defines two pull groups, with `pull-ngroups = 2`, each of them has 
> >>> a name in the index.ndx generated by `gmx make_ndx -f npt.gro`and their 
> >>> names are defined by `pull_group1_name = Chain_B` and `pull_group2_name = 
> >>> Chain_A`.
> >>>
> >>>
> >>> My question is about the definition of pulling coordination and the 
> >>> orientation of pulling force.
> >>>
> >>>
> >>> 1) I learnt from [gmx-users] Change to umbrella sampling pull code，
> >>> "You need: pull-coord1-groups = 1 2 otherwise the reaction coordinate is 
> >>> undefined, or otherwise defaults to the entire system, I can't remember 
> >>> which. -Justin"
> >>>
> >>>
> >>> I know it's a plot :) in the input.pdb that proteins are placed 
> >>> exquisitely along the z-axis which is the same as the pulling coordinate 
> >>> but it makes pull code confused and here I need a concrete explanation.
> >>> 1.The pull coordinate is the line that connects COM of group1 and group2 
> >>> with `pull_coord1_groups= 1 2`.
> >>> OR 2. The pull coordinate is the z axis with `pull_coord1_dim = N N Y`.
> >>> Which is correct?
> >>>
> >>
> >> The z-component of the vector connecting the COMs of the two groups.
> >>
> >>>
> >>> 2)Then turn to the orientation of pulling forces.
> >>> My understanding is that force1 acts on pull_group1, force2 acts on 
> >>> pull_group2 and the orientation of force 1 and 2 is opposite, both forces 
> >>> have a rate of 10nm per ns.
> >>> Is my understanding and the below schematic draw right?
> >>>
> >>
> >> There is one force.  It acts on the spring connecting the two groups.
> > 
> > 
> > How does the spring connect the two groups? Does the spring link to the COM 
> > of the whole two groups?
> 
> Yes.
> 
> > How does Gromacs define the orientation of the force of pulling? Or by 
> > default is the pulling force just positive along the z axis with 
> > `pull_coord1_geometry = distance` and `pull_coord1_dim = N N Y`?
> > 
> 
> This is not the default, but it is precisely what is specified by those .mdp 
> settings.
> 


Could you please show which line specifies the orientation of the pulling 
force? Is it the positive `pull_coord1_rate`? So `pull_coord1_rate` can be 
either positive or negative?

> >>
> >>>
> >>> Z-axis-0-5--->---positive-orientation--->-25-->
> >>>  
> >>>
> >>>
> >>> The last question is about the umbrella sampling.
> >>> I learnt from [gmx-users] Re: doubt about your Umbrella Sampling tutorial 
> >>> that it's ok to remove the pores of Chain B during the US. But in longer 
> >>> simulation time and in the periodical box, will the COM of Chain B and A 
> >>> be affacted by the boundary? and then affact the calculation of US 
> >>> potential?
> >>>
> >>
> >> The tutorial system won't work if you turn off the restraint.  Eventually 
> >> the
> >> system will rotate and the groups will cross periodic boundaries, which 
> >> will
> >> cause the chosen pull geometry to fail.  So the restraints serve a dual 
> >> purpose:
> >> (1) to mimic the stability of larger amyloid assemblies and (2) to reduce 
> >> the
> >> system size, as several hundred thousand atoms was not feasible for me at 
> >> the time.
> > 
> > 
> > So your point is that during US, we can't remove the Chain B's restrain. 
> > Right?
> 
> *For this specific case* yes.
> 
> > During US, is there any means to study the flexiblity of both groups? (i.e. 
> > there is no restrain on both groups except the umbrella potential between 
> > them and at the same time both groups will not cross periodic boundaries 
> > and will not affact the umbrella potential geometry, which is a necessary 
> > part of my study)
> 
> Normally one 

Re: [gmx-users] mdrun -rerun

[Alex]

You are absolutely right, there seems to be no need to declare the
exclusions. gmx energy produces a much longer list of group combinations
and off we go.

In any case, i changed the cutoff scheme to 'group' and got what I needed
(at least I vaguely feel like I did  :)). Interestingly and possibly
unsurprisingly, mdrun refuses to -rerun on multiple cores in this case,
only -nt 1 works.

Thanks!

Alex

On Thu, Jul 13, 2017 at 3:35 PM, Mark Abraham 
wrote:

> Hi,
>
> Right, sorry. You always had the index group, and I forgot you had to
> declare the energy group. But declaring the groups is all you need to do to
> triger the computation of the short-ranged energy between those groups,
> which is what you originally wanted.
>
> Mark
>
> On Thu, Jul 13, 2017 at 11:27 PM Alex  wrote:
>
> > And they are all exactly as they appear in my topology.
> > However, I think I found the solution:
> >
> > https://www.researchgate.net/post/How_can_I_deal_with_this_
> error_in_gromacs_CNT_in_energygrp-excl_is_not_an_energy_group
> > Except I am not sure how to proceed. if I add:
> >
> > energygrps = BUT DEC CBD
> >
> > grompp throws this: "ERROR 1 [file prod_rerun.mdp]:
> >   Energy group exclusions are not (yet) implemented for the Verlet
> scheme"
> >
> > But the original simulation was performed with Verlet cutoff scheme. Do I
> > change that regardless of this fact?
> >
> > Thanks,
> >
> > Alex
> >
> > On Thu, Jul 13, 2017 at 3:10 PM, Mark Abraham 
> > wrote:
> >
> > > Hi,
> > >
> > > Your input to gmx grompp -c is some other file though, and that's the
> set
> > > of index groups that matter, and the default ones should include those
> > > found by gmx make_ndx.
> > >
> > > Mark
> > >
> > > On Thu, Jul 13, 2017 at 11:06 PM Alex  wrote:
> > >
> > > > Same error in v. 2016.1.
> > > >
> > > > On Thu, Jul 13, 2017 at 2:39 PM, Alex  wrote:
> > > >
> > > > > Here you are, as run on the production tpr:
> > > > >
> > > > > $ gmx make_ndx -f prod.tpr
> > > > > GROMACS:gmx make_ndx, VERSION 5.0.5
> > > > >
> > > > > 
> > > > > 
> > > > >
> > > > > Reading structure file
> > > > > Reading file prod.tpr, VERSION 5.0.5 (single precision)
> > > > > Going to read 0 old index file(s)
> > > > > Analysing residue names:
> > > > > There are:   208  Other residues
> > > > > Analysing residues not classified as Protein/DNA/RNA/Water and
> > > splitting
> > > > > into groups...
> > > > >
> > > > >   0 System  :  6537 atoms
> > > > >   1 Other   :  6537 atoms
> > > > >   2 BUT :84 atoms
> > > > >   3 CBD :53 atoms
> > > > >   4 DEC :  6400 atoms
> > > > >
> > > > >
> > > > > On Thu, Jul 13, 2017 at 2:35 PM, Mark Abraham <
> > > mark.j.abra...@gmail.com>
> > > > > wrote:
> > > > >
> > > > >> What does gmx make_ndx think?
> > > > >>
> > > > >> Mark
> > > > >>
> > > > >> On Thu, Jul 13, 2017 at 10:34 PM Alex 
> wrote:
> > > > >>
> > > > >> > Hi Mark,
> > > > >> > That's the problem: the names are exactly as they appear
> whenever
> > > atom
> > > > >> > group selections are made... Any thoughts?
> > > > >> > My topology is as clean as it gets:
> > > > >> >
> > > > >> > #include "/usr/local/gromacs/share/gromacs/top/oplsaa.ff/
> > > forcefield.
> > > > >> itp"
> > > > >> > #include "but.itp"
> > > > >> > #include "cbd.itp"
> > > > >> > #include "decane.itp"
> > > > >> >
> > > > >> > [ system ]
> > > > >> > ; Name
> > > > >> >
> > > > >> >
> > > > >> > [ molecules ]
> > > > >> > ; Compound#mols
> > > > >> > BUT   7
> > > > >> > CBD   1
> > > > >> > DEC   200
> > > > >> >
> > > > >> > On Thu, Jul 13, 2017 at 2:28 PM, Mark Abraham <
> > > > mark.j.abra...@gmail.com
> > > > >> >
> > > > >> > wrote:
> > > > >> >
> > > > >> > > Hi,
> > > > >> > >
> > > > >> > > As with any index group, you can make them with gmx make_ndx,
> > gmx
> > > > >> select,
> > > > >> > > or your favourite text editor, and feed them to gmx grompp -n.
> > You
> > > > >> > normally
> > > > >> > > get spoiled with automatically generated groups that happen to
> > > match
> > > > >> > > moleculetypes and such. So probably you have SOL already.
> > > > >> > >
> > > > >> > > Mark
> > > > >> > >
> > > > >> > > On Thu, Jul 13, 2017 at 9:55 PM Alex 
> > wrote:
> > > > >> > >
> > > > >> > > > Hi all,
> > > > >> > > >
> > > > >> > > > I have a system that a subsystem of interest (molecules BUT
> > and
> > > > CBD)
> > > > >> > and
> > > > >> > > > the solvent (DEC). I have simulated it and have a
> trajectory.
> > > > >> > > >
> > > > >> > > > I would like to find out the total energy of interaction
> > between
> > > > BUT
> > > > >> > and
> > > > >> > > > CBD as a function of simulated time, so my thought is to do
> > > -rerun
> > > > >> and
> > > > >> > > > exclude the interactions in 

Re: [gmx-users] mdrun -rerun

[Mark Abraham]

Hi,

Right, sorry. You always had the index group, and I forgot you had to
declare the energy group. But declaring the groups is all you need to do to
triger the computation of the short-ranged energy between those groups,
which is what you originally wanted.

Mark

On Thu, Jul 13, 2017 at 11:27 PM Alex  wrote:

> And they are all exactly as they appear in my topology.
> However, I think I found the solution:
>
> https://www.researchgate.net/post/How_can_I_deal_with_this_error_in_gromacs_CNT_in_energygrp-excl_is_not_an_energy_group
> Except I am not sure how to proceed. if I add:
>
> energygrps = BUT DEC CBD
>
> grompp throws this: "ERROR 1 [file prod_rerun.mdp]:
>   Energy group exclusions are not (yet) implemented for the Verlet scheme"
>
> But the original simulation was performed with Verlet cutoff scheme. Do I
> change that regardless of this fact?
>
> Thanks,
>
> Alex
>
> On Thu, Jul 13, 2017 at 3:10 PM, Mark Abraham 
> wrote:
>
> > Hi,
> >
> > Your input to gmx grompp -c is some other file though, and that's the set
> > of index groups that matter, and the default ones should include those
> > found by gmx make_ndx.
> >
> > Mark
> >
> > On Thu, Jul 13, 2017 at 11:06 PM Alex  wrote:
> >
> > > Same error in v. 2016.1.
> > >
> > > On Thu, Jul 13, 2017 at 2:39 PM, Alex  wrote:
> > >
> > > > Here you are, as run on the production tpr:
> > > >
> > > > $ gmx make_ndx -f prod.tpr
> > > > GROMACS:gmx make_ndx, VERSION 5.0.5
> > > >
> > > > 
> > > > 
> > > >
> > > > Reading structure file
> > > > Reading file prod.tpr, VERSION 5.0.5 (single precision)
> > > > Going to read 0 old index file(s)
> > > > Analysing residue names:
> > > > There are:   208  Other residues
> > > > Analysing residues not classified as Protein/DNA/RNA/Water and
> > splitting
> > > > into groups...
> > > >
> > > >   0 System  :  6537 atoms
> > > >   1 Other   :  6537 atoms
> > > >   2 BUT :84 atoms
> > > >   3 CBD :53 atoms
> > > >   4 DEC :  6400 atoms
> > > >
> > > >
> > > > On Thu, Jul 13, 2017 at 2:35 PM, Mark Abraham <
> > mark.j.abra...@gmail.com>
> > > > wrote:
> > > >
> > > >> What does gmx make_ndx think?
> > > >>
> > > >> Mark
> > > >>
> > > >> On Thu, Jul 13, 2017 at 10:34 PM Alex  wrote:
> > > >>
> > > >> > Hi Mark,
> > > >> > That's the problem: the names are exactly as they appear whenever
> > atom
> > > >> > group selections are made... Any thoughts?
> > > >> > My topology is as clean as it gets:
> > > >> >
> > > >> > #include "/usr/local/gromacs/share/gromacs/top/oplsaa.ff/
> > forcefield.
> > > >> itp"
> > > >> > #include "but.itp"
> > > >> > #include "cbd.itp"
> > > >> > #include "decane.itp"
> > > >> >
> > > >> > [ system ]
> > > >> > ; Name
> > > >> >
> > > >> >
> > > >> > [ molecules ]
> > > >> > ; Compound#mols
> > > >> > BUT   7
> > > >> > CBD   1
> > > >> > DEC   200
> > > >> >
> > > >> > On Thu, Jul 13, 2017 at 2:28 PM, Mark Abraham <
> > > mark.j.abra...@gmail.com
> > > >> >
> > > >> > wrote:
> > > >> >
> > > >> > > Hi,
> > > >> > >
> > > >> > > As with any index group, you can make them with gmx make_ndx,
> gmx
> > > >> select,
> > > >> > > or your favourite text editor, and feed them to gmx grompp -n.
> You
> > > >> > normally
> > > >> > > get spoiled with automatically generated groups that happen to
> > match
> > > >> > > moleculetypes and such. So probably you have SOL already.
> > > >> > >
> > > >> > > Mark
> > > >> > >
> > > >> > > On Thu, Jul 13, 2017 at 9:55 PM Alex 
> wrote:
> > > >> > >
> > > >> > > > Hi all,
> > > >> > > >
> > > >> > > > I have a system that a subsystem of interest (molecules BUT
> and
> > > CBD)
> > > >> > and
> > > >> > > > the solvent (DEC). I have simulated it and have a trajectory.
> > > >> > > >
> > > >> > > > I would like to find out the total energy of interaction
> between
> > > BUT
> > > >> > and
> > > >> > > > CBD as a function of simulated time, so my thought is to do
> > -rerun
> > > >> and
> > > >> > > > exclude the interactions in the following group pairs:
> > > >> > > >
> > > >> > > > DEC-DEC
> > > >> > > > BUT-BUT
> > > >> > > > CBD-CBD
> > > >> > > > DEC-BUT
> > > >> > > > DEC-CBD
> > > >> > > >
> > > >> > > > When setting energygrp-excl with the following pairs, I
> > > immediately
> > > >> > get a
> > > >> > > > grompp error saying that DEC isn't an energy group. Since I've
> > > never
> > > >> > done
> > > >> > > > this before, can you please share your wisdom?
> > > >> > > >
> > > >> > > > Thank you,
> > > >> > > >
> > > >> > > > Alex
> > > >> > > > --
> > > >> > > > Gromacs Users mailing list
> > > >> > > >
> > > >> > > > * Please search the archive at
> > > >> > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List
> > > before
> > > >> > > > posting!
> > > >> > > >
> > > 

Re: [gmx-users] mdrun -rerun

[Alex]

And they are all exactly as they appear in my topology.
However, I think I found the solution:
https://www.researchgate.net/post/How_can_I_deal_with_this_error_in_gromacs_CNT_in_energygrp-excl_is_not_an_energy_group
Except I am not sure how to proceed. if I add:

energygrps = BUT DEC CBD

grompp throws this: "ERROR 1 [file prod_rerun.mdp]:
  Energy group exclusions are not (yet) implemented for the Verlet scheme"

But the original simulation was performed with Verlet cutoff scheme. Do I
change that regardless of this fact?

Thanks,

Alex

On Thu, Jul 13, 2017 at 3:10 PM, Mark Abraham 
wrote:

> Hi,
>
> Your input to gmx grompp -c is some other file though, and that's the set
> of index groups that matter, and the default ones should include those
> found by gmx make_ndx.
>
> Mark
>
> On Thu, Jul 13, 2017 at 11:06 PM Alex  wrote:
>
> > Same error in v. 2016.1.
> >
> > On Thu, Jul 13, 2017 at 2:39 PM, Alex  wrote:
> >
> > > Here you are, as run on the production tpr:
> > >
> > > $ gmx make_ndx -f prod.tpr
> > > GROMACS:gmx make_ndx, VERSION 5.0.5
> > >
> > > 
> > > 
> > >
> > > Reading structure file
> > > Reading file prod.tpr, VERSION 5.0.5 (single precision)
> > > Going to read 0 old index file(s)
> > > Analysing residue names:
> > > There are:   208  Other residues
> > > Analysing residues not classified as Protein/DNA/RNA/Water and
> splitting
> > > into groups...
> > >
> > >   0 System  :  6537 atoms
> > >   1 Other   :  6537 atoms
> > >   2 BUT :84 atoms
> > >   3 CBD :53 atoms
> > >   4 DEC :  6400 atoms
> > >
> > >
> > > On Thu, Jul 13, 2017 at 2:35 PM, Mark Abraham <
> mark.j.abra...@gmail.com>
> > > wrote:
> > >
> > >> What does gmx make_ndx think?
> > >>
> > >> Mark
> > >>
> > >> On Thu, Jul 13, 2017 at 10:34 PM Alex  wrote:
> > >>
> > >> > Hi Mark,
> > >> > That's the problem: the names are exactly as they appear whenever
> atom
> > >> > group selections are made... Any thoughts?
> > >> > My topology is as clean as it gets:
> > >> >
> > >> > #include "/usr/local/gromacs/share/gromacs/top/oplsaa.ff/
> forcefield.
> > >> itp"
> > >> > #include "but.itp"
> > >> > #include "cbd.itp"
> > >> > #include "decane.itp"
> > >> >
> > >> > [ system ]
> > >> > ; Name
> > >> >
> > >> >
> > >> > [ molecules ]
> > >> > ; Compound#mols
> > >> > BUT   7
> > >> > CBD   1
> > >> > DEC   200
> > >> >
> > >> > On Thu, Jul 13, 2017 at 2:28 PM, Mark Abraham <
> > mark.j.abra...@gmail.com
> > >> >
> > >> > wrote:
> > >> >
> > >> > > Hi,
> > >> > >
> > >> > > As with any index group, you can make them with gmx make_ndx, gmx
> > >> select,
> > >> > > or your favourite text editor, and feed them to gmx grompp -n. You
> > >> > normally
> > >> > > get spoiled with automatically generated groups that happen to
> match
> > >> > > moleculetypes and such. So probably you have SOL already.
> > >> > >
> > >> > > Mark
> > >> > >
> > >> > > On Thu, Jul 13, 2017 at 9:55 PM Alex  wrote:
> > >> > >
> > >> > > > Hi all,
> > >> > > >
> > >> > > > I have a system that a subsystem of interest (molecules BUT and
> > CBD)
> > >> > and
> > >> > > > the solvent (DEC). I have simulated it and have a trajectory.
> > >> > > >
> > >> > > > I would like to find out the total energy of interaction between
> > BUT
> > >> > and
> > >> > > > CBD as a function of simulated time, so my thought is to do
> -rerun
> > >> and
> > >> > > > exclude the interactions in the following group pairs:
> > >> > > >
> > >> > > > DEC-DEC
> > >> > > > BUT-BUT
> > >> > > > CBD-CBD
> > >> > > > DEC-BUT
> > >> > > > DEC-CBD
> > >> > > >
> > >> > > > When setting energygrp-excl with the following pairs, I
> > immediately
> > >> > get a
> > >> > > > grompp error saying that DEC isn't an energy group. Since I've
> > never
> > >> > done
> > >> > > > this before, can you please share your wisdom?
> > >> > > >
> > >> > > > Thank you,
> > >> > > >
> > >> > > > Alex
> > >> > > > --
> > >> > > > 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] mdrun -rerun

[Mark Abraham]

Hi,

Your input to gmx grompp -c is some other file though, and that's the set
of index groups that matter, and the default ones should include those
found by gmx make_ndx.

Mark

On Thu, Jul 13, 2017 at 11:06 PM Alex  wrote:

> Same error in v. 2016.1.
>
> On Thu, Jul 13, 2017 at 2:39 PM, Alex  wrote:
>
> > Here you are, as run on the production tpr:
> >
> > $ gmx make_ndx -f prod.tpr
> > GROMACS:gmx make_ndx, VERSION 5.0.5
> >
> > 
> > 
> >
> > Reading structure file
> > Reading file prod.tpr, VERSION 5.0.5 (single precision)
> > Going to read 0 old index file(s)
> > Analysing residue names:
> > There are:   208  Other residues
> > Analysing residues not classified as Protein/DNA/RNA/Water and splitting
> > into groups...
> >
> >   0 System  :  6537 atoms
> >   1 Other   :  6537 atoms
> >   2 BUT :84 atoms
> >   3 CBD :53 atoms
> >   4 DEC :  6400 atoms
> >
> >
> > On Thu, Jul 13, 2017 at 2:35 PM, Mark Abraham 
> > wrote:
> >
> >> What does gmx make_ndx think?
> >>
> >> Mark
> >>
> >> On Thu, Jul 13, 2017 at 10:34 PM Alex  wrote:
> >>
> >> > Hi Mark,
> >> > That's the problem: the names are exactly as they appear whenever atom
> >> > group selections are made... Any thoughts?
> >> > My topology is as clean as it gets:
> >> >
> >> > #include "/usr/local/gromacs/share/gromacs/top/oplsaa.ff/forcefield.
> >> itp"
> >> > #include "but.itp"
> >> > #include "cbd.itp"
> >> > #include "decane.itp"
> >> >
> >> > [ system ]
> >> > ; Name
> >> >
> >> >
> >> > [ molecules ]
> >> > ; Compound#mols
> >> > BUT   7
> >> > CBD   1
> >> > DEC   200
> >> >
> >> > On Thu, Jul 13, 2017 at 2:28 PM, Mark Abraham <
> mark.j.abra...@gmail.com
> >> >
> >> > wrote:
> >> >
> >> > > Hi,
> >> > >
> >> > > As with any index group, you can make them with gmx make_ndx, gmx
> >> select,
> >> > > or your favourite text editor, and feed them to gmx grompp -n. You
> >> > normally
> >> > > get spoiled with automatically generated groups that happen to match
> >> > > moleculetypes and such. So probably you have SOL already.
> >> > >
> >> > > Mark
> >> > >
> >> > > On Thu, Jul 13, 2017 at 9:55 PM Alex  wrote:
> >> > >
> >> > > > Hi all,
> >> > > >
> >> > > > I have a system that a subsystem of interest (molecules BUT and
> CBD)
> >> > and
> >> > > > the solvent (DEC). I have simulated it and have a trajectory.
> >> > > >
> >> > > > I would like to find out the total energy of interaction between
> BUT
> >> > and
> >> > > > CBD as a function of simulated time, so my thought is to do -rerun
> >> and
> >> > > > exclude the interactions in the following group pairs:
> >> > > >
> >> > > > DEC-DEC
> >> > > > BUT-BUT
> >> > > > CBD-CBD
> >> > > > DEC-BUT
> >> > > > DEC-CBD
> >> > > >
> >> > > > When setting energygrp-excl with the following pairs, I
> immediately
> >> > get a
> >> > > > grompp error saying that DEC isn't an energy group. Since I've
> never
> >> > done
> >> > > > this before, can you please share your wisdom?
> >> > > >
> >> > > > Thank you,
> >> > > >
> >> > > > Alex
> >> > > > --
> >> > > > 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] mdrun -rerun

[Alex]

Same error in v. 2016.1.

On Thu, Jul 13, 2017 at 2:39 PM, Alex  wrote:

> Here you are, as run on the production tpr:
>
> $ gmx make_ndx -f prod.tpr
> GROMACS:gmx make_ndx, VERSION 5.0.5
>
> 
> 
>
> Reading structure file
> Reading file prod.tpr, VERSION 5.0.5 (single precision)
> Going to read 0 old index file(s)
> Analysing residue names:
> There are:   208  Other residues
> Analysing residues not classified as Protein/DNA/RNA/Water and splitting
> into groups...
>
>   0 System  :  6537 atoms
>   1 Other   :  6537 atoms
>   2 BUT :84 atoms
>   3 CBD :53 atoms
>   4 DEC :  6400 atoms
>
>
> On Thu, Jul 13, 2017 at 2:35 PM, Mark Abraham 
> wrote:
>
>> What does gmx make_ndx think?
>>
>> Mark
>>
>> On Thu, Jul 13, 2017 at 10:34 PM Alex  wrote:
>>
>> > Hi Mark,
>> > That's the problem: the names are exactly as they appear whenever atom
>> > group selections are made... Any thoughts?
>> > My topology is as clean as it gets:
>> >
>> > #include "/usr/local/gromacs/share/gromacs/top/oplsaa.ff/forcefield.
>> itp"
>> > #include "but.itp"
>> > #include "cbd.itp"
>> > #include "decane.itp"
>> >
>> > [ system ]
>> > ; Name
>> >
>> >
>> > [ molecules ]
>> > ; Compound#mols
>> > BUT   7
>> > CBD   1
>> > DEC   200
>> >
>> > On Thu, Jul 13, 2017 at 2:28 PM, Mark Abraham > >
>> > wrote:
>> >
>> > > Hi,
>> > >
>> > > As with any index group, you can make them with gmx make_ndx, gmx
>> select,
>> > > or your favourite text editor, and feed them to gmx grompp -n. You
>> > normally
>> > > get spoiled with automatically generated groups that happen to match
>> > > moleculetypes and such. So probably you have SOL already.
>> > >
>> > > Mark
>> > >
>> > > On Thu, Jul 13, 2017 at 9:55 PM Alex  wrote:
>> > >
>> > > > Hi all,
>> > > >
>> > > > I have a system that a subsystem of interest (molecules BUT and CBD)
>> > and
>> > > > the solvent (DEC). I have simulated it and have a trajectory.
>> > > >
>> > > > I would like to find out the total energy of interaction between BUT
>> > and
>> > > > CBD as a function of simulated time, so my thought is to do -rerun
>> and
>> > > > exclude the interactions in the following group pairs:
>> > > >
>> > > > DEC-DEC
>> > > > BUT-BUT
>> > > > CBD-CBD
>> > > > DEC-BUT
>> > > > DEC-CBD
>> > > >
>> > > > When setting energygrp-excl with the following pairs, I immediately
>> > get a
>> > > > grompp error saying that DEC isn't an energy group. Since I've never
>> > done
>> > > > this before, can you please share your wisdom?
>> > > >
>> > > > Thank you,
>> > > >
>> > > > Alex
>> > > > --
>> > > > 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
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 -rerun

[Alex]

Here you are, as run on the production tpr:

$ gmx make_ndx -f prod.tpr
GROMACS:gmx make_ndx, VERSION 5.0.5




Reading structure file
Reading file prod.tpr, VERSION 5.0.5 (single precision)
Going to read 0 old index file(s)
Analysing residue names:
There are:   208  Other residues
Analysing residues not classified as Protein/DNA/RNA/Water and splitting
into groups...

  0 System  :  6537 atoms
  1 Other   :  6537 atoms
  2 BUT :84 atoms
  3 CBD :53 atoms
  4 DEC :  6400 atoms


On Thu, Jul 13, 2017 at 2:35 PM, Mark Abraham 
wrote:

> What does gmx make_ndx think?
>
> Mark
>
> On Thu, Jul 13, 2017 at 10:34 PM Alex  wrote:
>
> > Hi Mark,
> > That's the problem: the names are exactly as they appear whenever atom
> > group selections are made... Any thoughts?
> > My topology is as clean as it gets:
> >
> > #include "/usr/local/gromacs/share/gromacs/top/oplsaa.ff/forcefield.itp"
> > #include "but.itp"
> > #include "cbd.itp"
> > #include "decane.itp"
> >
> > [ system ]
> > ; Name
> >
> >
> > [ molecules ]
> > ; Compound#mols
> > BUT   7
> > CBD   1
> > DEC   200
> >
> > On Thu, Jul 13, 2017 at 2:28 PM, Mark Abraham 
> > wrote:
> >
> > > Hi,
> > >
> > > As with any index group, you can make them with gmx make_ndx, gmx
> select,
> > > or your favourite text editor, and feed them to gmx grompp -n. You
> > normally
> > > get spoiled with automatically generated groups that happen to match
> > > moleculetypes and such. So probably you have SOL already.
> > >
> > > Mark
> > >
> > > On Thu, Jul 13, 2017 at 9:55 PM Alex  wrote:
> > >
> > > > Hi all,
> > > >
> > > > I have a system that a subsystem of interest (molecules BUT and CBD)
> > and
> > > > the solvent (DEC). I have simulated it and have a trajectory.
> > > >
> > > > I would like to find out the total energy of interaction between BUT
> > and
> > > > CBD as a function of simulated time, so my thought is to do -rerun
> and
> > > > exclude the interactions in the following group pairs:
> > > >
> > > > DEC-DEC
> > > > BUT-BUT
> > > > CBD-CBD
> > > > DEC-BUT
> > > > DEC-CBD
> > > >
> > > > When setting energygrp-excl with the following pairs, I immediately
> > get a
> > > > grompp error saying that DEC isn't an energy group. Since I've never
> > done
> > > > this before, can you please share your wisdom?
> > > >
> > > > Thank you,
> > > >
> > > > Alex
> > > > --
> > > > 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
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Re: [gmx-users] mdrun -rerun

[Mark Abraham]

What does gmx make_ndx think?

Mark

On Thu, Jul 13, 2017 at 10:34 PM Alex  wrote:

> Hi Mark,
> That's the problem: the names are exactly as they appear whenever atom
> group selections are made... Any thoughts?
> My topology is as clean as it gets:
>
> #include "/usr/local/gromacs/share/gromacs/top/oplsaa.ff/forcefield.itp"
> #include "but.itp"
> #include "cbd.itp"
> #include "decane.itp"
>
> [ system ]
> ; Name
>
>
> [ molecules ]
> ; Compound#mols
> BUT   7
> CBD   1
> DEC   200
>
> On Thu, Jul 13, 2017 at 2:28 PM, Mark Abraham 
> wrote:
>
> > Hi,
> >
> > As with any index group, you can make them with gmx make_ndx, gmx select,
> > or your favourite text editor, and feed them to gmx grompp -n. You
> normally
> > get spoiled with automatically generated groups that happen to match
> > moleculetypes and such. So probably you have SOL already.
> >
> > Mark
> >
> > On Thu, Jul 13, 2017 at 9:55 PM Alex  wrote:
> >
> > > Hi all,
> > >
> > > I have a system that a subsystem of interest (molecules BUT and CBD)
> and
> > > the solvent (DEC). I have simulated it and have a trajectory.
> > >
> > > I would like to find out the total energy of interaction between BUT
> and
> > > CBD as a function of simulated time, so my thought is to do -rerun and
> > > exclude the interactions in the following group pairs:
> > >
> > > DEC-DEC
> > > BUT-BUT
> > > CBD-CBD
> > > DEC-BUT
> > > DEC-CBD
> > >
> > > When setting energygrp-excl with the following pairs, I immediately
> get a
> > > grompp error saying that DEC isn't an energy group. Since I've never
> done
> > > this before, can you please share your wisdom?
> > >
> > > Thank you,
> > >
> > > Alex
> > > --
> > > 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!
> >
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> >
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> > send a mail to gmx-users-requ...@gromacs.org.
> >
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Re: [gmx-users] mdrun -rerun

[Alex]

Hi Mark,
That's the problem: the names are exactly as they appear whenever atom
group selections are made... Any thoughts?
My topology is as clean as it gets:

#include "/usr/local/gromacs/share/gromacs/top/oplsaa.ff/forcefield.itp"
#include "but.itp"
#include "cbd.itp"
#include "decane.itp"

[ system ]
; Name


[ molecules ]
; Compound#mols
BUT   7
CBD   1
DEC   200

On Thu, Jul 13, 2017 at 2:28 PM, Mark Abraham 
wrote:

> Hi,
>
> As with any index group, you can make them with gmx make_ndx, gmx select,
> or your favourite text editor, and feed them to gmx grompp -n. You normally
> get spoiled with automatically generated groups that happen to match
> moleculetypes and such. So probably you have SOL already.
>
> Mark
>
> On Thu, Jul 13, 2017 at 9:55 PM Alex  wrote:
>
> > Hi all,
> >
> > I have a system that a subsystem of interest (molecules BUT and CBD) and
> > the solvent (DEC). I have simulated it and have a trajectory.
> >
> > I would like to find out the total energy of interaction between BUT and
> > CBD as a function of simulated time, so my thought is to do -rerun and
> > exclude the interactions in the following group pairs:
> >
> > DEC-DEC
> > BUT-BUT
> > CBD-CBD
> > DEC-BUT
> > DEC-CBD
> >
> > When setting energygrp-excl with the following pairs, I immediately get a
> > grompp error saying that DEC isn't an energy group. Since I've never done
> > this before, can you please share your wisdom?
> >
> > Thank you,
> >
> > Alex
> > --
> > 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.
> >
> --
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>
> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List before posting!
>
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Re: [gmx-users] mdrun -rerun

[Mark Abraham]

Hi,

As with any index group, you can make them with gmx make_ndx, gmx select,
or your favourite text editor, and feed them to gmx grompp -n. You normally
get spoiled with automatically generated groups that happen to match
moleculetypes and such. So probably you have SOL already.

Mark

On Thu, Jul 13, 2017 at 9:55 PM Alex  wrote:

> Hi all,
>
> I have a system that a subsystem of interest (molecules BUT and CBD) and
> the solvent (DEC). I have simulated it and have a trajectory.
>
> I would like to find out the total energy of interaction between BUT and
> CBD as a function of simulated time, so my thought is to do -rerun and
> exclude the interactions in the following group pairs:
>
> DEC-DEC
> BUT-BUT
> CBD-CBD
> DEC-BUT
> DEC-CBD
>
> When setting energygrp-excl with the following pairs, I immediately get a
> grompp error saying that DEC isn't an energy group. Since I've never done
> this before, can you please share your wisdom?
>
> Thank you,
>
> Alex
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
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>
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[gmx-users] mdrun -rerun

[Alex]

Hi all,

I have a system that a subsystem of interest (molecules BUT and CBD) and
the solvent (DEC). I have simulated it and have a trajectory.

I would like to find out the total energy of interaction between BUT and
CBD as a function of simulated time, so my thought is to do -rerun and
exclude the interactions in the following group pairs:

DEC-DEC
BUT-BUT
CBD-CBD
DEC-BUT
DEC-CBD

When setting energygrp-excl with the following pairs, I immediately get a
grompp error saying that DEC isn't an energy group. Since I've never done
this before, can you please share your wisdom?

Thank you,

Alex
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Re: [gmx-users] NPT problem

[Alex]

Also, that tutorial's parameters that are completely wrong for graphene.
For bulk graphene bond types I suggest:

  CJCJ  10.14200   420420.0

For bulk angles:

  CJ CJ CJ  1   120.000659.346

For bulk dihedrals:

  CJ CJ CJ CJ  3 17.30770   0.0 -17.30770   0.0
  0.0   0.0

These are parameters obtained from a Taylor-expanded optimized
Tersoff-Brenner potential. Please count the number of bonds and dihedrals
in your graphene model, as produced by x2top. If the number of dihedrals
divided by the number of bonds gives you a number, say, equal to m, then
multiply the dihedral parameters by that number. And do NOT use bond
constraints -- you are simulating a crystal.

Alex

On Thu, Jul 13, 2017 at 10:45 AM,  wrote:

> Hi All GROMACS users,
>
>
>
> I created graphene with nanotube modeler then I created a force field for
> graphene based on OPLS (by using this link and its parameters:
> http://chembytes.wikidot.com/grocnt). I generated the topology file using
> x2top command. I put the graphene inside a box of water (TIP3P) which was
> larger than the graphene dimension with 1000  (kJ/mol nm^2) position
> restraint on all the atoms, and I performed the energy minimization and NVT
> equilibrations (in order to get an optimized structure of the graphene for
> further simulations). The results of both of them were good (energy level
> has reached a negative value with the order of 6 and the temperature has
> converged the preferred value). But, when I run the NPT equilibration, the
> results are not good (the pressure and density fluctuated very much and the
> averaged values are so far from the preferred ones). Also, during the NPT
> run, I received these messages:
>
>
> step 53965: Water molecule starting at atom 127424 can not be settled.
>
> Check for bad contacts and/or reduce the timestep if appropriate.
>
> Wrote pdb files with previous and current coordinates
>
>
>
> step 141454: Water molecule starting at atom 53366 can not be settled.
>
> Check for bad contacts and/or reduce the timestep if appropriate.
>
> Wrote pdb files with previous and current coordinates
>
>
>
> step 141483: Water molecule starting at atom 53366 can not be settled.
>
> Check for bad contacts and/or reduce the timestep if appropriate.
>
> Wrote pdb files with previous and current coordinates
>
>
>
> step 323815: Water molecule starting at atom 30509 can not be settled.
>
> Check for bad contacts and/or reduce the timestep if appropriate.
>
> Wrote pdb files with previous and current coordinates
>
>
>
> step 323816: Water molecule starting at atom 30509 can not be settled.
>
> Check for bad contacts and/or reduce the timestep if appropriate.
>
> Wrote pdb files with previous and current coordinates
>
>
>
> step 323818: Water molecule starting at atom 30509 can not be settled.
>
> Check for bad contacts and/or reduce the timestep if appropriate.
>
> Wrote pdb files with previous and current coordinates
>
>
>
> step 355712: Water molecule starting at atom 121748 can not be settled.
>
> Check for bad contacts and/or reduce the timestep if appropriate.
>
> Wrote pdb files with previous and current coordinates
>
>
>
> step 355714: Water molecule starting at atom 121748 can not be settled.
>
> Check for bad contacts and/or reduce the timestep if appropriate.
>
> Wrote pdb files with previous and current coordinates
>
>
>
> step 355716: Water molecule starting at atom 121748 can not be settled.
>
> Check for bad contacts and/or reduce the timestep if appropriate.
>
> Wrote pdb files with previous and current coordinates
>
>
>
> step 355718: Water molecule starting at atom 121748 can not be settled.
>
> Check for bad contacts and/or reduce the timestep if appropriate.
>
> Wrote pdb files with previous and current coordinates
>
>
>
> step 469414: Water molecule starting at atom 101579 can not be settled.
>
> Check for bad contacts and/or reduce the timestep if appropriate.
>
> Wrote pdb files with previous and current coordinates
>
>
>
> step 469416: Water molecule starting at atom 101579 can not be settled.
>
> Check for bad contacts and/or reduce the timestep if appropriate.
>
> Wrote pdb files with previous and current coordinates
>
>
>
> step 469418: Water molecule starting at atom 101579 can not be settled.
>
> Check for bad contacts and/or reduce the timestep if appropriate.
>
> Wrote pdb files with previous and current coordinates
>
>
>
> step 469420: Water molecule starting at atom 101579 can not be settled.
>
> Check for bad contacts and/or reduce the timestep if appropriate.
>
> Wrote pdb files with previous and current coordinates
>
>
>
> , and a pdb file was saved after each step.
> In addition, something interesting is that I performed another run with
> all of the previous parameters, except I did not put position restraint on
> the graphene, and the results of NPT were good and acceptable, and I did
> not get those messages.
>
>
> Can you 

Re: [gmx-users] NPT problem

[Alex]

It is very unclear what you mean by "the results were good" and then "the
results were not good." Your graphene setup is bad and it propagated to
everything else. Please do not start solvating your graphene sample prior
to making sure that your model is reasonable.
To diagnose what's wrong with your model there isn't enough info. For one,
it is unclear if you followed the tutorial correctly. Second, it is unclear
if your x2top command was issued on graphene coordinates with the same box
size as the solvated box, especially if one resulted in proper PBC and the
other did not. Third, you need to turn off all constraints/restraints and
first equilibrate graphene in vacuum (EM followed by considerably long NPT
at something like 10K) and make absolutely sure that PBC is properly set
in-plane, etc, that SP2 bond lengths in graphene are what they are supposed
to be. Fourth, do you understand what that CNT tutorial is doing, or are
you blindly following it?
This stuff requires effort. Noone can help otherwise.

Alex


On Thu, Jul 13, 2017 at 10:45 AM,  wrote:

> Hi All GROMACS users,
>
>
>
> I created graphene with nanotube modeler then I created a force field for
> graphene based on OPLS (by using this link and its parameters:
> http://chembytes.wikidot.com/grocnt). I generated the topology file using
> x2top command. I put the graphene inside a box of water (TIP3P) which was
> larger than the graphene dimension with 1000  (kJ/mol nm^2) position
> restraint on all the atoms, and I performed the energy minimization and NVT
> equilibrations (in order to get an optimized structure of the graphene for
> further simulations). The results of both of them were good (energy level
> has reached a negative value with the order of 6 and the temperature has
> converged the preferred value). But, when I run the NPT equilibration, the
> results are not good (the pressure and density fluctuated very much and the
> averaged values are so far from the preferred ones). Also, during the NPT
> run, I received these messages:
>
>
> step 53965: Water molecule starting at atom 127424 can not be settled.
>
> Check for bad contacts and/or reduce the timestep if appropriate.
>
> Wrote pdb files with previous and current coordinates
>
>
>
> step 141454: Water molecule starting at atom 53366 can not be settled.
>
> Check for bad contacts and/or reduce the timestep if appropriate.
>
> Wrote pdb files with previous and current coordinates
>
>
>
> step 141483: Water molecule starting at atom 53366 can not be settled.
>
> Check for bad contacts and/or reduce the timestep if appropriate.
>
> Wrote pdb files with previous and current coordinates
>
>
>
> step 323815: Water molecule starting at atom 30509 can not be settled.
>
> Check for bad contacts and/or reduce the timestep if appropriate.
>
> Wrote pdb files with previous and current coordinates
>
>
>
> step 323816: Water molecule starting at atom 30509 can not be settled.
>
> Check for bad contacts and/or reduce the timestep if appropriate.
>
> Wrote pdb files with previous and current coordinates
>
>
>
> step 323818: Water molecule starting at atom 30509 can not be settled.
>
> Check for bad contacts and/or reduce the timestep if appropriate.
>
> Wrote pdb files with previous and current coordinates
>
>
>
> step 355712: Water molecule starting at atom 121748 can not be settled.
>
> Check for bad contacts and/or reduce the timestep if appropriate.
>
> Wrote pdb files with previous and current coordinates
>
>
>
> step 355714: Water molecule starting at atom 121748 can not be settled.
>
> Check for bad contacts and/or reduce the timestep if appropriate.
>
> Wrote pdb files with previous and current coordinates
>
>
>
> step 355716: Water molecule starting at atom 121748 can not be settled.
>
> Check for bad contacts and/or reduce the timestep if appropriate.
>
> Wrote pdb files with previous and current coordinates
>
>
>
> step 355718: Water molecule starting at atom 121748 can not be settled.
>
> Check for bad contacts and/or reduce the timestep if appropriate.
>
> Wrote pdb files with previous and current coordinates
>
>
>
> step 469414: Water molecule starting at atom 101579 can not be settled.
>
> Check for bad contacts and/or reduce the timestep if appropriate.
>
> Wrote pdb files with previous and current coordinates
>
>
>
> step 469416: Water molecule starting at atom 101579 can not be settled.
>
> Check for bad contacts and/or reduce the timestep if appropriate.
>
> Wrote pdb files with previous and current coordinates
>
>
>
> step 469418: Water molecule starting at atom 101579 can not be settled.
>
> Check for bad contacts and/or reduce the timestep if appropriate.
>
> Wrote pdb files with previous and current coordinates
>
>
>
> step 469420: Water molecule starting at atom 101579 can not be settled.
>
> Check for bad contacts and/or reduce the timestep if appropriate.
>
> Wrote pdb files with previous and current coordinates
>
>
>
> , and a pdb file was saved 

Re: [gmx-users] non-zero Coul-SR interaction between metal ion in the system with only one metal (GMX 5.0.7)

[Mark Abraham]

Hi,

The default short-ranged scheme changed in 5.0, and it works differently. I
forget the details because both of these versions are long out of date.
What do you get with 2016?

Mark

On Thu, Jul 13, 2017 at 5:50 PM qiaobf  wrote:

> Dear All,
>
> I just got one problem with the energy printed by the g_energy. Could
> anyone help me with it? Thanks!
>
> In the test system, there is ONLY ONE trivalent metal (Me) and 2240
> modified TIP3P waters. After one MD step, I print the energies using
> g_energy. The results are:
>
> ** GROMACS 5.0.7 
>
> *Coul-SR:Me-Me  -521.008 * -- 0  0  (kJ/mol)
> LJ-SR:Me-Me   0 -- 0  0
> (kJ/mol)
> Coul-SR:Me-SOL -78.5025 --30.1404 -60.2807
> (kJ/mol)
> LJ-SR:Me-SOL195.268--104.218 -208.437
> (kJ/mol)
> Coul-SR:SOL-SOL 1958.38 -- 452.82 -905.64  (kJ/mol)
> LJ-SR:SOL-SOL   91953.5   --1966.23 -3932.45
> (kJ/mol)
>
> *
>
> The weird thing is the Coul-SR: Me-Me is not zero, instead it is negative!
>
> Once I change the atomic charge of the trivalent metal from +3 to 0,
> this Coul-SR: Me-Me becomes zero.
>
> I also rerun the simulation using GROAMCS 4.5.5. The Coul-SR is zero
> (see below). But there exist some difference between the other energies
> between 5.0.7 and 4.5.5.
>
> ** GROMACS 4.5.5 **
>
> Coul-SR:Me-Me 0-- 0  0  (kJ/mol)
> LJ-SR:Me-Me 0-- 0  0  (kJ/mol)
> Coul-SR:Me-SOL -57.4723  --  0  0 (kJ/mol)
> LJ-SR:Me-SOL94.4865 --  0 0  (kJ/mol)
> Coul-SR:SOL-SOL 1771.36  --  0  0 (kJ/mol)
> LJ-SR:SOL-SOL   89843.4--  0 0  (kJ/mol)
>
> **
>
>
> The topology and md.mdp files are listed below:
>
> * system.top *
>
> #include "charmm36-nov2016.ff/forcefield.itp"
>
> [ atomtypes ]
> ;type at.num  mass charge ptype   sigma, nm  epsilon, kJ/mol
>   Me  1 1.000   0.0 A  3.385415e-01   2.092000e-01
>
> ;-- metal---
> [ moleculetype ]
> ; molname   nrexcl
>   Metal1
>
> [ atoms ]
> ; idat type   res.nr  residu.name at.name  cg.nr  charge
> 1   Me1   Me  Me   1   3.0
>
> #include "charmm36-nov2016.ff/tip3p.itp"
>
> [ system ]
> ; Name
> metal ion in water
>
> [ molecules ]
> ; Compound#mols
>   Metal 1
>   SOL 2240
> *
>
> ** md.mdp**
>
> ; Run control
> integrator   = md
> tinit= 0
> dt   = 0.001
> nsteps   = 1; 10ps
> nstcomm  = 10
>
> ; Output control
> nstenergy= 50
> energygrps   = ME SOL
>
>
> ; Neighborsearching and short-range nonbonded interactions
> nstlist  = 10
> ns_type  = grid
> pbc  = xyz
> rlist= 1.2
> ; Electrostatics
> coulombtype  = cutoff
> rcoulomb = 1.2
> ; van der Waals
> vdwtype  = cutoff
> rvdw-switch  = 1.0
> rvdw = 1.2
> ; Apply long range dispersion corrections for Energy and Pressure
> DispCorr  = EnerPres
> ; Spacing for the PME/PPPM FFT grid
> fourierspacing   = 0.12
> ; EWALD/PME/PPPM parameters
> pme_order= 4
> ewald_rtol   = 1e-06
> epsilon_surface  = 0
>
> ; Temperature coupling
> ; tcoupl is implicitly handled by the sd integrator
> tc_grps  = system
> tau_t= 1.0
> ref_t= 298.15
>
> ; Pressure coupling is off for NVT
> Pcoupl   = No
>
> ***
>
>
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
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>
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>
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Re: [gmx-users] xtc trajectory only

[Mark Abraham]

Hi,

Don't choose to write to the "output trajectory" then :-) See
http://manual.gromacs.org/documentation/2016.3/user-guide/mdp-options.html#output-control

Mark

On Thu, Jul 13, 2017 at 6:35 PM Atila Petrosian 
wrote:

> Dear Gromacs users,
>
> I am using the following mdp options:
>
> integrator   = md
> dt   = 0.03
> nsteps   = 500
> nstcomm  = 100
> nstxout  = 5000
> nstvout  = 5000
> nstfout  = 0
> nstlog   = 5000
> nstenergy= 5000
> nstxout-compressed   = 5000
> compressed-x-precision   = 100
>
> ---
>
> These parameters resulted in both of xtc and trr trajectory files?
>
> I want to have just xtc trajectory file.
>
> What parameters in mdp file should I change?
>
> Best,
> Atila
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Re: [gmx-users] Non-periodic COM Pulling

[Daniel Kozuch]

Justin,

It was my understanding that direction-periodic would not allow for the NPT
ensemble (which I would like to use if possible, and why I did not use it
in the first place). Is there a way around this?

Thanks,
Dan

On Thu, Jul 13, 2017 at 8:58 AM, Justin Lemkul  wrote:

>
>
> On 7/12/17 3:05 PM, Daniel Kozuch wrote:
> > Hello,
> >
> > Is it possible to do non-periodic COM pulling using the distance function
> > in GMX 5.14 (i.e. where the distance between the two groups is calculated
> > ignoring pbc)?
> >
>
> No, but this is what direction-periodic is for.
>
> -Justin
>
> > In the tutorials/online the solution seems to be to simply use a box
> twice
> > the size of the largest pulling distance, but that would be very
> > computationally expensive for me.
> >
> > Best,
> > Dan
> >
>
> --
> ==
>
> 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
>
> ==
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Re: [gmx-users] Help on MD performance, GPU has less load than CPU.

[Mark Abraham]

So the state of the art in the whole field is to just blindly copy .mdp
settings from webpages rather than review the literature of related work?
Nice. :-D

Mark

On Thu, Jul 13, 2017 at 7:18 PM Téletchéa Stéphane <
stephane.teletc...@univ-nantes.fr> wrote:

> Le 12/07/2017 à 18:15, Mark Abraham a écrit :
> > Hi,
> >
> > Sure. But who has data that shows that e.g. a free-energy calculation
> with
> > the defaults produces lower quality observables than you get with the
> > defaults?
> >
> > Mark
>
> Hi,
>
> As defaults are defaults ... who knows :-) To get number in front of
> these assumptions is hard, and probably nobody wants to do this on a
> large scale ... But I'm too close to holidays to argue on this point by
> now!
>
> Stéphane
>
> --
> Assistant Professor in BioInformatics, UFIP, UMR 6286 CNRS, Team Protein
> Design In Silico
> UFR Sciences et Techniques, 2, rue de la Houssinière, Bât. 25, 44322
> Nantes cedex 03, France
> Tél : +33 251 125 636 / Fax : +33 251 125 632
> http://www.ufip.univ-nantes.fr/ - http://www.steletch.org
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Re: [gmx-users] Help on MD performance, GPU has less load than CPU.

[Téletchéa Stéphane]

Le 12/07/2017 à 18:15, Mark Abraham a écrit :

Hi,

Sure. But who has data that shows that e.g. a free-energy calculation with
the defaults produces lower quality observables than you get with the
defaults?

Mark


Hi,

As defaults are defaults ... who knows :-) To get number in front of 
these assumptions is hard, and probably nobody wants to do this on a 
large scale ... But I'm too close to holidays to argue on this point by now!


Stéphane

--
Assistant Professor in BioInformatics, UFIP, UMR 6286 CNRS, Team Protein 
Design In Silico
UFR Sciences et Techniques, 2, rue de la Houssinière, Bât. 25, 44322 
Nantes cedex 03, France

Tél : +33 251 125 636 / Fax : +33 251 125 632
http://www.ufip.univ-nantes.fr/ - http://www.steletch.org
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[gmx-users] NPT problem

[‪Mohammad Roostaie‬ ‪]

Hi All GROMACS users,


 
I created graphene with nanotube modeler then I created a force field for 
graphene based on OPLS (by using this link and its parameters: 
http://chembytes.wikidot.com/grocnt). I generated the topology file using x2top 
command. I put the graphene inside a box of water (TIP3P) which was larger than 
the graphene dimension with 1000  (kJ/mol nm^2) position restraint on all the 
atoms, and I performed the energy minimization and NVT equilibrations (in order 
to get an optimized structure of the graphene for further simulations). The 
results of both of them were good (energy level has reached a negative value 
with the order of 6 and the temperature has converged the preferred value). 
But, when I run the NPT equilibration, the results are not good (the pressure 
and density fluctuated very much and the averaged values are so far from the 
preferred ones). Also, during the NPT run, I received these messages:


step 53965: Water molecule starting at atom 127424 can not be settled.

Check for bad contacts and/or reduce the timestep if appropriate.

Wrote pdb files with previous and current coordinates


 
step 141454: Water molecule starting at atom 53366 can not be settled.

Check for bad contacts and/or reduce the timestep if appropriate.

Wrote pdb files with previous and current coordinates


 
step 141483: Water molecule starting at atom 53366 can not be settled.

Check for bad contacts and/or reduce the timestep if appropriate.

Wrote pdb files with previous and current coordinates


 
step 323815: Water molecule starting at atom 30509 can not be settled.

Check for bad contacts and/or reduce the timestep if appropriate.

Wrote pdb files with previous and current coordinates


 
step 323816: Water molecule starting at atom 30509 can not be settled.

Check for bad contacts and/or reduce the timestep if appropriate.

Wrote pdb files with previous and current coordinates


 
step 323818: Water molecule starting at atom 30509 can not be settled.

Check for bad contacts and/or reduce the timestep if appropriate.

Wrote pdb files with previous and current coordinates


 
step 355712: Water molecule starting at atom 121748 can not be settled.

Check for bad contacts and/or reduce the timestep if appropriate.

Wrote pdb files with previous and current coordinates


 
step 355714: Water molecule starting at atom 121748 can not be settled.

Check for bad contacts and/or reduce the timestep if appropriate.

Wrote pdb files with previous and current coordinates


 
step 355716: Water molecule starting at atom 121748 can not be settled.

Check for bad contacts and/or reduce the timestep if appropriate.

Wrote pdb files with previous and current coordinates


 
step 355718: Water molecule starting at atom 121748 can not be settled.

Check for bad contacts and/or reduce the timestep if appropriate.

Wrote pdb files with previous and current coordinates


 
step 469414: Water molecule starting at atom 101579 can not be settled.

Check for bad contacts and/or reduce the timestep if appropriate.

Wrote pdb files with previous and current coordinates


 
step 469416: Water molecule starting at atom 101579 can not be settled.

Check for bad contacts and/or reduce the timestep if appropriate.

Wrote pdb files with previous and current coordinates


 
step 469418: Water molecule starting at atom 101579 can not be settled.

Check for bad contacts and/or reduce the timestep if appropriate.

Wrote pdb files with previous and current coordinates


 
step 469420: Water molecule starting at atom 101579 can not be settled.

Check for bad contacts and/or reduce the timestep if appropriate.

Wrote pdb files with previous and current coordinates


 
, and a pdb file was saved after each step.
In addition, something interesting is that I performed another run with all of 
the previous parameters, except I did not put position restraint on the 
graphene, and the results of NPT were good and acceptable, and I did not get 
those messages.


Can you please help me figure this problem out? Since I should put the position 
restrain on the graphene. I really would appreciate any help.


If you need further information please let me know.
Kind regards,Mohammad
 

 
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[gmx-users] xtc trajectory only

[Atila Petrosian]

Dear Gromacs users,

I am using the following mdp options:

integrator   = md
dt   = 0.03
nsteps   = 500
nstcomm  = 100
nstxout  = 5000
nstvout  = 5000
nstfout  = 0
nstlog   = 5000
nstenergy= 5000
nstxout-compressed   = 5000
compressed-x-precision   = 100

---

These parameters resulted in both of xtc and trr trajectory files?

I want to have just xtc trajectory file.

What parameters in mdp file should I change?

Best,
Atila
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Re: [gmx-users] frozen ligand for free energy calculations

[Ahmet Yildirim]

OK, thanks. Which of the following option do you suggest me under
intermolecular interactions?
1) function type 6, 1 and 1 for [ bonds ], [ angles ] and [ dihedrals ]
respectively
2) function type 6, 1 and 1 for [ bonds ], [ angle_restraints ] and[
dihedral_restraints ] respectively
3) function type 10, 1 and 1 for [ distance_restraints ], [
angle_restraints ] and [ dihedral_restraints ] respectively



On 13 July 2017 at 17:21, Justin Lemkul  wrote:

>
>
> On 7/13/17 9:59 AM, Ahmet Yildirim wrote:
>
>> Dear users,
>>
>> I come across with an issue when I try to do free energy calculations. The
>> issue is about the roto-translational motions of the ligand in the
>> decoupled state. I mean the ligand doesn't stay stable in the binding
>> pocket as in the coupled state.
>> It seems that the restraints that are applied on the atoms of the protein
>> and ligand under [ intermolecular_interactions ] part (an example of it is
>> below) in the compex top file aren't sufficient to keep the ligand from
>> repositioning/rotation with respect to the protein in the decoupled state.
>> Even one, two and three sets of restraints couldn't solve the issue.
>>
>> [ intermolecular_interactions ]
>> [ bonds ]
>> ; ai  ajtype   bA   kA   bBkB
>>629 3 6  0.5970.0  0.597 4184.0
>>
>> [ angles ]
>> ; ai  ajaktype   thA  fcA  thBfcB
>>281   629 3 1   37.50.0   37.5  41.84
>>629 321 1  121.50.0  121.5  41.84
>>
>> [ dihedrals ]
>> ; ai aj akaltypethA fcA   thB   fcB
>>249   281   629 3 2 -147.40.0 -147.4  41.84
>>281   629 321 2  -60.50.0  -60.5  41.84
>>629 32116 2 -153.90.0 -153.9  41.84
>>
>>
> Here, with function type 2, you're specifying improper dihedrals.  This
> isn't going to be what you want.  You probably want to be using a series of
> dihedral restraints, not actual dihedrals.
>
> 
>
> I would try to freeze the ligand in the decoupled state in the canonical
>> ensemle with the above restrains under [ intermolecular_interactions ] but
>> I am not sure whether that makes sense or not? Justin says (
>> https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users
>> /2013-August/083647.html):
>>
>> "...Anything that is frozen, by definition, never has its position
>> updated.  Under the influence of
>> pressure coupling, other particles around the frozen group can have their
>> positions scaled and thus collide with the frozen group, which has
>> remained
>> in
>> its original location". I think I can use the frozen ligand in both
>> coupled
>> and decoupled state? And I should take into consideration the effect of
>> the
>> frozen ligand on the free energy calculation, right?
>>
>>
> By doing this, you're negating any conformational sampling of the ligand,
> therefore its entropy is wrong, and if the protein drifts and the ligand
> stays put (because it's frozen) that's a fairly useless state.  The
> appropriate strategy is a system of intermolecular interactions, but they
> need to be properly defined.  As well, the choice of atoms can be
> significant, e.g. dx.doi.org/10.1021/ci300505n and references therein.
>
> -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
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-- 
Ahmet Yildirim
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[gmx-users] non-zero Coul-SR interaction between metal ion in the system with only one metal (GMX 5.0.7)

[qiaobf]

Dear All,

I just got one problem with the energy printed by the g_energy. Could 
anyone help me with it? Thanks!


In the test system, there is ONLY ONE trivalent metal (Me) and 2240 
modified TIP3P waters. After one MD step, I print the energies using 
g_energy. The results are:


** GROMACS 5.0.7 

*Coul-SR:Me-Me  -521.008 * -- 0  0  (kJ/mol)
LJ-SR:Me-Me   0 -- 0  0  
(kJ/mol)

Coul-SR:Me-SOL -78.5025 --30.1404 -60.2807  (kJ/mol)
LJ-SR:Me-SOL195.268--104.218 -208.437  
(kJ/mol)

Coul-SR:SOL-SOL 1958.38 -- 452.82 -905.64  (kJ/mol)
LJ-SR:SOL-SOL   91953.5   --1966.23 -3932.45  
(kJ/mol)


*

The weird thing is the Coul-SR: Me-Me is not zero, instead it is negative!

Once I change the atomic charge of the trivalent metal from +3 to 0, 
this Coul-SR: Me-Me becomes zero.


I also rerun the simulation using GROAMCS 4.5.5. The Coul-SR is zero 
(see below). But there exist some difference between the other energies 
between 5.0.7 and 4.5.5.


** GROMACS 4.5.5 **

Coul-SR:Me-Me 0-- 0  0  (kJ/mol)
LJ-SR:Me-Me 0-- 0  0  (kJ/mol)
Coul-SR:Me-SOL -57.4723  --  0  0 (kJ/mol)
LJ-SR:Me-SOL94.4865 --  0 0  (kJ/mol)
Coul-SR:SOL-SOL 1771.36  --  0  0 (kJ/mol)
LJ-SR:SOL-SOL   89843.4--  0 0  (kJ/mol)

**


The topology and md.mdp files are listed below:

* system.top *

#include "charmm36-nov2016.ff/forcefield.itp"

[ atomtypes ]
;type at.num  mass charge ptype   sigma, nm  epsilon, kJ/mol
 Me  1 1.000   0.0 A  3.385415e-01   2.092000e-01

;-- metal---
[ moleculetype ]
; molname   nrexcl
 Metal1

[ atoms ]
; idat type   res.nr  residu.name at.name  cg.nr  charge
1   Me1   Me  Me   1   3.0

#include "charmm36-nov2016.ff/tip3p.itp"

[ system ]
; Name
metal ion in water

[ molecules ]
; Compound#mols
 Metal 1
 SOL 2240
*

** md.mdp**

; Run control
integrator   = md
tinit= 0
dt   = 0.001
nsteps   = 1; 10ps
nstcomm  = 10

; Output control
nstenergy= 50
energygrps   = ME SOL


; Neighborsearching and short-range nonbonded interactions
nstlist  = 10
ns_type  = grid
pbc  = xyz
rlist= 1.2
; Electrostatics
coulombtype  = cutoff
rcoulomb = 1.2
; van der Waals
vdwtype  = cutoff
rvdw-switch  = 1.0
rvdw = 1.2
; Apply long range dispersion corrections for Energy and Pressure
DispCorr  = EnerPres
; Spacing for the PME/PPPM FFT grid
fourierspacing   = 0.12
; EWALD/PME/PPPM parameters
pme_order= 4
ewald_rtol   = 1e-06
epsilon_surface  = 0

; Temperature coupling
; tcoupl is implicitly handled by the sd integrator
tc_grps  = system
tau_t= 1.0
ref_t= 298.15

; Pressure coupling is off for NVT
Pcoupl   = No

***



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[gmx-users] Equilibration

[‪farial tavakoli‬ ‪]

Hi Justin
Thank you so much for your reply about minimize ligand in vacuoaccording to 
:http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System
 I minimized my protein and ligand alone to fix the problem (  LINCS warning, ( 
one or more water molecules can not to be settled . check for bad contacts or 
reduce time step))I checked my protein in desired solvent as i noticed in the 
previous mail, and it was stable. i minimized my ligand too in vacuo with the 
.mdp file which you advised me, it was minimized well and monitored by pymol, 
its configuration was ok.
In addition, I reduced the time step from 0,002 to 0.001 , but got the same 
error in 2 steps.then, reduced the temperature to 100 k , but the same error 
displayed again. 
Actually, I cant understand some advices and causes in this site. like:
I dont understand  some of causes and advices in this site, include:1) you are 
doing particle insertion in free energy calculations without using soft core2) 
your position restraints are to coordinates too different from those present in 
the system3) Make sure the forces don't get that large
How can i make sure the forces dont get that large? I dont know what these 3 
causes are.
 I have not recognized where the problem is and fixed it yet. It is wasting my 
time a lot. My protein and ligand were intact . so what is its problem?would 
you please help me? and introduce me an appropriate reference to be expert in 
GROMACS?
Thanks in advanceFarial

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Re: [gmx-users] Ramping down the restraint on molecules

[Justin Lemkul]

On 7/13/17 10:37 AM, Lakshman Ji Verma wrote:

Dear all,

I want to ramp down the restraint on the two molecules from 1000k to 0 on
some time interval so that restraint is removed gradually. My colleagues
said that it can be done with single md parameter file in LAMMPS and NAMD.
Can this be done using a single .mdp file in Gromacs too?  Or I will have


No.


to prepare different .mdp and restraint file for each step.


Yes.

-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

==
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[gmx-users] Ramping down the restraint on molecules

[Lakshman Ji Verma]

Dear all,

I want to ramp down the restraint on the two molecules from 1000k to 0 on
some time interval so that restraint is removed gradually. My colleagues
said that it can be done with single md parameter file in LAMMPS and NAMD.
Can this be done using a single .mdp file in Gromacs too?  Or I will have
to prepare different .mdp and restraint file for each step.
Thanks

Regards
Lakshman
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Re: [gmx-users] Benchmarks v5.0

[Szilárd Páll]

Hi,

One of the systems is The Prace test case A
(http://www.prace-ri.eu/ueabs/), though the setup offered there is
only the vsites-enabled version.

Cheers,
--
Szilárd


On Wed, Jul 12, 2017 at 10:34 AM,   wrote:
> Hi there,
>   where can I find the benchmark input files for the 2 cases reported in this 
> paper (ion channel and ethanol-water system)?
>
> http://www.gromacs.org/@api/deki/files/240/=gromacs-5.0-benchmarks.pdf
>
> Many thanks.
> Jony
>
> Dr Jony Castagna
> Sci-Tech Daresbury
> Keckwick Lane
> Daresbury
> Warrington
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Re: [gmx-users] frozen ligand for free energy calculations

[Justin Lemkul]

On 7/13/17 9:59 AM, Ahmet Yildirim wrote:

Dear users,

I come across with an issue when I try to do free energy calculations. The
issue is about the roto-translational motions of the ligand in the
decoupled state. I mean the ligand doesn't stay stable in the binding
pocket as in the coupled state.
It seems that the restraints that are applied on the atoms of the protein
and ligand under [ intermolecular_interactions ] part (an example of it is
below) in the compex top file aren't sufficient to keep the ligand from
repositioning/rotation with respect to the protein in the decoupled state.
Even one, two and three sets of restraints couldn't solve the issue.

[ intermolecular_interactions ]
[ bonds ]
; ai  ajtype   bA   kA   bBkB
   629 3 6  0.5970.0  0.597 4184.0

[ angles ]
; ai  ajaktype   thA  fcA  thBfcB
   281   629 3 1   37.50.0   37.5  41.84
   629 321 1  121.50.0  121.5  41.84

[ dihedrals ]
; ai aj akaltypethA fcA   thB   fcB
   249   281   629 3 2 -147.40.0 -147.4  41.84
   281   629 321 2  -60.50.0  -60.5  41.84
   629 32116 2 -153.90.0 -153.9  41.84



Here, with function type 2, you're specifying improper dihedrals.  This isn't 
going to be what you want.  You probably want to be using a series of dihedral 
restraints, not actual dihedrals.





I would try to freeze the ligand in the decoupled state in the canonical
ensemle with the above restrains under [ intermolecular_interactions ] but
I am not sure whether that makes sense or not? Justin says (
https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2013-August/083647.html):

"...Anything that is frozen, by definition, never has its position
updated.  Under the influence of
pressure coupling, other particles around the frozen group can have their
positions scaled and thus collide with the frozen group, which has remained
in
its original location". I think I can use the frozen ligand in both coupled
and decoupled state? And I should take into consideration the effect of the
frozen ligand on the free energy calculation, right?



By doing this, you're negating any conformational sampling of the ligand, 
therefore its entropy is wrong, and if the protein drifts and the ligand stays 
put (because it's frozen) that's a fairly useless state.  The appropriate 
strategy is a system of intermolecular interactions, but they need to be 
properly defined.  As well, the choice of atoms can be significant, e.g. 
dx.doi.org/10.1021/ci300505n and references therein.


-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

==
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Re: [gmx-users] 4-letter residues

[João Henriques]

Absolutely spot on Justin! I just discovered it by myself 30 seconds ago.

Thanks!
João

On Thu, Jul 13, 2017 at 4:17 PM, Justin Lemkul  wrote:

>
>
> On 7/13/17 10:16 AM, João Henriques wrote:
>
>> Dear all,
>>
>> I have a protein with a phosphorylated threonine and the corresponding
>> residue name in my FF of interest is THP1. 4-letter residues and PDB files
>> are a recipe for disaster, but somehow pdb2gmx detects the residue's name
>> and number perfectly. What happens next is somewhat odd (at least to me).
>> It now ends in a fatal error regarding OXT atoms. This should not occur
>> and, in fact, the problem disappears as soon as I use the same exact PDB
>> but with a regular non-phosphorylated threonine residue instead. The OXT
>> atoms are still there. Anyone has any idea of what's going on? Should I
>> edit the FF to use a three letter name instead of THP1?
>>
>>
> You probably forgot to add THP1 as a Protein residue in residuetypes.dat,
> so pdb2gmx is inserting an incorrect chain termination before it.
>
> -Justin
>
>
> I'm using gmx 5.1.4.
>>
>> This is the THP1 residue in my PDB:
>>
>> ATOM   1171  N   THP1A 160  14.798   3.634  55.810  1.00 28.16
>>N
>> ATOM   1172  CA  THP1A 160  13.457   3.397  56.297  1.00 32.05
>>C
>> ATOM   1173  CB  THP1A 160  13.440   2.416  57.453  1.00 31.31
>>C
>> ATOM   1174  CG2 THP1A 160  12.002   2.135  57.857  1.00 28.13
>>C
>> ATOM   1175  OG1 THP1A 160  14.038   1.189  57.027  1.00 35.99
>>O
>> ATOM   1176  P   THP1A 160  15.501   0.748  57.510  1.00 37.49
>>P
>> ATOM   1177  O1P THP1A 160  15.810  -0.350  56.582  1.00 38.61
>>O
>> ATOM   1178  O2P THP1A 160  16.325   1.972  57.300  1.00 35.09
>>O
>> ATOM   1179  OT  THP1A 160  15.173   0.306  58.890  1.00 40.70
>>O
>> ATOM   1180  C   THP1A 160  12.747   4.659  56.712  1.00 39.18
>>C
>> ATOM   1181  O   THP1A 160  13.202   5.412  57.567  1.00 38.80
>>O
>>
>> This is the error:
>>
>> Fatal error:
>> Atom OXT in residue LEU 298 was not found in rtp entry LEU with 19 atoms
>> while sorting atoms.
>>
>> Thank you in advance,
>> Best regards,
>> João
>>
>>
> --
> ==
>
> 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
>
> ==
> --
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Re: [gmx-users] gmx select

[Justin Lemkul]

On 7/13/17 10:01 AM, Pandya, Akash wrote:

So I tried with both opening and closing. It seems to select all the molecules 
in my box which is not what I want. I only want certain glycine molecules that 
are closest to the protein. May you please suggest another way is which I could 
achieve this. The command I used is below:

gmx select -f output.xtc -s output.gro -select '"Close to protein" resname Glycine and 
within 0.5 of group "Protein"' -pdbatoms selected -ofpdb



"resname Glycine" surely will return nothing.  You need to use valid residue 
names as found in the .gro file.  The format of .gro permits residue names up to 
5 characters, so clearly "Glycine" is never going to match anything.


-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

==
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Re: [gmx-users] 4-letter residues

[Justin Lemkul]

On 7/13/17 10:16 AM, João Henriques wrote:

Dear all,

I have a protein with a phosphorylated threonine and the corresponding
residue name in my FF of interest is THP1. 4-letter residues and PDB files
are a recipe for disaster, but somehow pdb2gmx detects the residue's name
and number perfectly. What happens next is somewhat odd (at least to me).
It now ends in a fatal error regarding OXT atoms. This should not occur
and, in fact, the problem disappears as soon as I use the same exact PDB
but with a regular non-phosphorylated threonine residue instead. The OXT
atoms are still there. Anyone has any idea of what's going on? Should I
edit the FF to use a three letter name instead of THP1?



You probably forgot to add THP1 as a Protein residue in residuetypes.dat, so 
pdb2gmx is inserting an incorrect chain termination before it.


-Justin


I'm using gmx 5.1.4.

This is the THP1 residue in my PDB:

ATOM   1171  N   THP1A 160  14.798   3.634  55.810  1.00 28.16
   N
ATOM   1172  CA  THP1A 160  13.457   3.397  56.297  1.00 32.05
   C
ATOM   1173  CB  THP1A 160  13.440   2.416  57.453  1.00 31.31
   C
ATOM   1174  CG2 THP1A 160  12.002   2.135  57.857  1.00 28.13
   C
ATOM   1175  OG1 THP1A 160  14.038   1.189  57.027  1.00 35.99
   O
ATOM   1176  P   THP1A 160  15.501   0.748  57.510  1.00 37.49
   P
ATOM   1177  O1P THP1A 160  15.810  -0.350  56.582  1.00 38.61
   O
ATOM   1178  O2P THP1A 160  16.325   1.972  57.300  1.00 35.09
   O
ATOM   1179  OT  THP1A 160  15.173   0.306  58.890  1.00 40.70
   O
ATOM   1180  C   THP1A 160  12.747   4.659  56.712  1.00 39.18
   C
ATOM   1181  O   THP1A 160  13.202   5.412  57.567  1.00 38.80
   O

This is the error:

Fatal error:
Atom OXT in residue LEU 298 was not found in rtp entry LEU with 19 atoms
while sorting atoms.

Thank you in advance,
Best regards,
João



--
==

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

==
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[gmx-users] 4-letter residues

[João Henriques]

Dear all,

I have a protein with a phosphorylated threonine and the corresponding
residue name in my FF of interest is THP1. 4-letter residues and PDB files
are a recipe for disaster, but somehow pdb2gmx detects the residue's name
and number perfectly. What happens next is somewhat odd (at least to me).
It now ends in a fatal error regarding OXT atoms. This should not occur
and, in fact, the problem disappears as soon as I use the same exact PDB
but with a regular non-phosphorylated threonine residue instead. The OXT
atoms are still there. Anyone has any idea of what's going on? Should I
edit the FF to use a three letter name instead of THP1?

I'm using gmx 5.1.4.

This is the THP1 residue in my PDB:

ATOM   1171  N   THP1A 160  14.798   3.634  55.810  1.00 28.16
  N
ATOM   1172  CA  THP1A 160  13.457   3.397  56.297  1.00 32.05
  C
ATOM   1173  CB  THP1A 160  13.440   2.416  57.453  1.00 31.31
  C
ATOM   1174  CG2 THP1A 160  12.002   2.135  57.857  1.00 28.13
  C
ATOM   1175  OG1 THP1A 160  14.038   1.189  57.027  1.00 35.99
  O
ATOM   1176  P   THP1A 160  15.501   0.748  57.510  1.00 37.49
  P
ATOM   1177  O1P THP1A 160  15.810  -0.350  56.582  1.00 38.61
  O
ATOM   1178  O2P THP1A 160  16.325   1.972  57.300  1.00 35.09
  O
ATOM   1179  OT  THP1A 160  15.173   0.306  58.890  1.00 40.70
  O
ATOM   1180  C   THP1A 160  12.747   4.659  56.712  1.00 39.18
  C
ATOM   1181  O   THP1A 160  13.202   5.412  57.567  1.00 38.80
  O

This is the error:

Fatal error:
Atom OXT in residue LEU 298 was not found in rtp entry LEU with 19 atoms
while sorting atoms.

Thank you in advance,
Best regards,
João
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Re: [gmx-users] gmx select

[Pandya, Akash]

So I tried with both opening and closing. It seems to select all the molecules 
in my box which is not what I want. I only want certain glycine molecules that 
are closest to the protein. May you please suggest another way is which I could 
achieve this. The command I used is below:

gmx select -f output.xtc -s output.gro -select '"Close to protein" resname 
Glycine and within 0.5 of group "Protein"' -pdbatoms selected -ofpdb 

Akash


-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 Justin 
Lemkul
Sent: 13 July 2017 14:01
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] gmx select



On 7/13/17 3:38 AM, Pandya, Akash wrote:
> gmx select -f output.gro -select "Close to protein" resname Glyci and within 
> 0.5 of group "Protein"'
> 

I suspect Mark is right, this is an invalid command, because you have a closing 
' without an opening ' in your -select argument.  This should fail with a 
generic error message that the selection can't be parsed.  I am also curious 
about "resname Glyci" because if that's the case, then you must have hacked 
some force field files, because everyone calls glycine "GLY" per standard 
nomenclature.

-Justin

> -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 Mark Abraham
> Sent: 13 July 2017 00:04
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] gmx select
> 
> Hi,
> 
> Can you please copy, paste and post your actual commands. I don't think your 
> use of quote marks would have led to a valid shell command. The whole 
> selection text will need to be inside some quotes.
> 
> Mark
> 
> On Wed, 12 Jul 2017 23:47 Pandya, Akash  wrote:
> 
>> I have used the same name in my coordinate file. For Glycine it is 
>> spelt as Glyci, so the word has been cut off. I know this is correct 
>> because I use the same name in VMD.
>>
>> -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 Mark 
>> Abraham
>> Sent: 12 July 2017 22:42
>> To: gmx-us...@gromacs.org
>> Subject: Re: [gmx-users] gmx select
>>
>> Hi,
>>
>> What are the residue names in your coordinate file? Glyci probably 
>> doesn't fit
>>
>> Mark
>>
>> On Wed, Jul 12, 2017 at 10:36 PM Pandya, Akash 
>> 
>> wrote:
>>
>>> Hi all,
>>>
>>>
>>> I am trying to select all the glycine molecules with 0.5nm of my protein.
>>> I tried both of these commands I got from the gromacs website:
>>>
>>> gmx select -f output.gro -select "Close to protein" resname Glyci 
>>> and within 0.5 of group "Protein"' -ofpdb
>>>
>>> gmx select -f output.xtc -s output.tpr (my converted input file) 
>>> -select "Close to protein" resname Glyci and within 0.5 of group 
>>> "Protein"' -ofpdb
>>>
>>>
>>> Nothing comes up when I enter them. Please could someone help me 
>>> with
>> this?
>>>
>>>
>>> Akash
>>> --
>>> Gromacs Users mailing list
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>>> * Please search the archive at
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>>> posting!
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>>>
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--
==

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 

[gmx-users] frozen ligand for free energy calculations

[Ahmet Yildirim]

Dear users,

I come across with an issue when I try to do free energy calculations. The
issue is about the roto-translational motions of the ligand in the
decoupled state. I mean the ligand doesn't stay stable in the binding
pocket as in the coupled state.
It seems that the restraints that are applied on the atoms of the protein
and ligand under [ intermolecular_interactions ] part (an example of it is
below) in the compex top file aren't sufficient to keep the ligand from
repositioning/rotation with respect to the protein in the decoupled state.
Even one, two and three sets of restraints couldn't solve the issue.

[ intermolecular_interactions ]
[ bonds ]
; ai  ajtype   bA   kA   bBkB
  629 3 6  0.5970.0  0.597 4184.0

[ angles ]
; ai  ajaktype   thA  fcA  thBfcB
  281   629 3 1   37.50.0   37.5  41.84
  629 321 1  121.50.0  121.5  41.84

[ dihedrals ]
; ai aj akaltypethA fcA   thB   fcB
  249   281   629 3 2 -147.40.0 -147.4  41.84
  281   629 321 2  -60.50.0  -60.5  41.84
  629 32116 2 -153.90.0 -153.9  41.84

The mdp file used for production run with GROMACS2016.2 is here.

; RUN CONTROL
;
integrator   = sd; leap-frog integrator
nsteps   = 2000
dt   = 0.001 ; 2 fs
comm-mode= Linear; remove center of mass translation
nstcomm  = 100   ; frequency for center of mass motion removal
comm-grps= System

; OUTPUT CONTROL
;
nstxout   = 2  ; save coordinates to .trr every
100 ps
nstvout   = 2  ; don't save velocities to .trr
nstfout   = 0  ; don't save forces to .trr
nstxout-compressed= 2  ; xtc compressed trajectory
output every 2 ps
compressed-x-precision= 1000   ; precision with which to write
to the compressed trajectory file
nstlog= 2  ; update log file every 2 ps
nstenergy = 2  ; save energies every 2 ps
nstcalcenergy = 100; calculate energies every 100
steps
energygrps= Protein ligand

; BONDS
;
constraint_algorithm   = lincs; holonomic constraints
constraints= h-bonds  ; hydrogens only are constrained
lincs_iter = 2; accuracy of LINCS (1 is default)
lincs_order= 12; also related to accuracy (4 is default)
lincs-warnangle= 30   ; maximum angle that a bond can rotate
before LINCS will complain (30 is default)
continuation   = yes   ; formerly known as
'unconstrained-start' - useful for exact continuations and reruns

; NEIGHBOR SEARCHING
;
cutoff-scheme= verlet  ; 'group' is default in 4.6 - from GMX5 on
'Verlet' is default
ns-type  = grid   ; search neighboring grid cells
nstlist  = 10 ; 20 fs (default is 10)
pbc  = xyz; 3D PBC

; ELECTROSTATICS & EWALD
;
coulombtype  = PME  ; Particle Mesh Ewald for long-range
electrostatics
rcoulomb = 1.2  ; short-range electrostatic cutoff (in nm)
ewald_geometry   = 3d   ; Ewald sum is performed in all three dimensions
pme-order= 6; interpolation order for PME (default is 4)
fourierspacing   = 0.12 ; grid spacing for FFT
ewald-rtol   = 1e-6 ; relative strength of the Ewald-shifted direct
potential at rcoulomb

; VAN DER WAALS
;
vdwtype = Cut-off
vdw_modifier= Potential-switch
rvdw= 1.1  ; short-range van der Waals cutoff (in nm)
rvdw-switch = 1.0  ; where to start switching the LJ force
DispCorr= EnerPres ; apply long range dispersion corrections
for Energy and Pressure
; TEMPERATURE COUPLING (SD ==> Langevin dynamics)
;
tc_grps=  Protein_ligand Water_and_ions
tau_t  =  1.0 1.0
ref_t  =  300 300

; PRESSURE COUPLING
;
pcoupl   = no
pcoupltype   = isotropic  ; uniform scaling of box vectors
tau_p= 1.0; time constant (ps)
ref_p= 1.0; reference pressure (bar)
compressibility  = 4.5e-05; isothermal compressibility of water
(bar^-1)

; VELOCITY GENERATION
;
gen_vel  = no  ; Velocity generation is on (if gen_vel is 'yes',
continuation 

[gmx-users] Crash in minimization that involves dummy atoms

[Davide Bonanni]

Hi gromacs users,

I'm doing a relative free energy calculation of a ligand-protein complex.
I'm transforming a hydrogen atom into methyl. I have generated input
topology with FESetup. When I try to run minimization I get that error:

"""
Energy minimization has stopped, but the forces have not converged to the
Requested precision Fmax It stopped because the algorithm tried to make a
new step whose size was too
Small, or there was no change in the energy since last step. Either way, we
Regard the minimization as converged to within the available machine
Precision, given your starting configuration and EM parameters.

Double precision normally gives you more accuracy, but this is often not
Needed for preparing to run molecular dynamics.
You may need to increase your constraint accuracy, or turn
Off constraints altogether (set constraints = none in mdp file)

Steepest Descents converged to machine precision in 50 steps,
But did not reach the requested Fmax <100.
Potential Energy = 1.1698845e + 07
Maximum force = 7.4549694e + 05 is atom 5745
Norm of force = 3.5688174e + 03
"""
As you can see the Potential Energy is too high and if a look at the system
I got is completely messed up. Exactly the same complex with the same
parameters but a different perturbation (H -> Cl) gave me no problems. So
the minimization crash should be related to the presence of dummy atoms.
I read some discussion about the same topic but I was not able to find a
solution. Everything looks good to me, I do not see anything wrong in the
file .gro or .top.

I have tried also to run the same minimization on T4 lysozyme tutorial
input (https://ccpforge.cse.rl.ac.uk/gf/project/ccpbiosim/wiki/?
pagename=T4+lysozyme), and when there are dummy atom involved I obtain the
same problem.
Probably I'm missing something in the .mdp or there is some error I can not
see.

I tried to modify constraint but nothing changed.

Any kind of suggestion is really appreciated, thank you in advance.

Cheers,

Davide Bonanni


This is the first part of ligand's topology:
"""
[ moleculetype ]
LIG 3

[ atoms ]
;   nr  type resno resnm atomcgnr  chargemass typeB
chargeB   massB
  1   c1   LIG   C1   10.667751 12.0100   c
 0.667700 12.0100
  2  cc   1   LIG   C2   2   -0.469349 12.0100  cc
-0.471400 12.0100
  3  ca   1   LIG   C3   30.034751 12.0100  ca
 0.039700 12.0100
  4  ca   1   LIG   C4   4   -0.083249 12.0100  ca
-0.032600 12.0100
  5   c1   LIG   C5   50.742351 12.0100   c
 0.742300 12.0100
  6  ca   1   LIG   C6   60.121651 12.0100  ca
 0.122600 12.0100
  7  ca   1   LIG   C7   70.029951 12.0100  ca
 0.029400 12.0100
  8  ca   1   LIG   C8   80.029951 12.0100  ca
 0.029400 12.0100
  9  ca   1   LIG   C9   90.134451 12.0100  ca
 0.134400 12.0100
 10  ca  1   LIG  C10  100.134451 12.0100  ca
 0.134400 12.0100
 11  cp  1   LIG  C11  11   -0.137949 12.0100  cp
-0.139000 12.0100
 12  cp  1   LIG  C12  12   -0.012949 12.0100  cp
-0.013000 12.0100
 13  ca  1   LIG  C13  13   -0.108449 12.0100  ca
-0.109000 12.0100
 14  ca  1   LIG  C14  14   -0.108449 12.0100  ca
-0.109000 12.0100
 15  ca  1   LIG  C15  15   -0.136949 12.0100  ca
-0.137000 12.0100
 16  ca  1   LIG  C16  16   -0.136949 12.0100  ca
-0.137000 12.0100
 17  ca  1   LIG  C17  17   -0.134949 12.0100  ca
-0.135000 12.0100
 18  ca  1   LIG  C18  18   -0.155949 12.0100  ca
-0.158000 12.0100
 19  ca  1   LIG  C19  19   -0.122949 12.0100  ca
-0.122000 12.0100
 20  ca  1   LIG  C20  20   -0.226949 12.0100  ca
-0.223000 12.0100
 21   f1   LIG  F21  21   -0.109349 19.   f
-0.109400 19.
 22   f1   LIG  F22  22   -0.130849 19.   f
-0.131400 19.
 23   f1   LIG  F23  23   -0.130849 19.   f
-0.131400 19.
 24   f1   LIG  F24  24   -0.109349 19.   f
-0.109400 19.
 25  nc  1   LIG  N25  25   -0.632449 14.0100  nc
-0.632500 14.0100
 26  na  1   LIG  N26  260.281751 14.0100  na
 0.281700 14.0100
 27   n   1   LIG  N27  27   -0.465049 14.0100   n
-0.464100 14.0100
 28   o   1   LIG  O28  28   -0.704049 16.   o
-0.705100 16.
 29   o   1   LIG  O29  29   -0.651049 16.   o
-0.652100 16.
 30  h4  1   LIG  H30  300.158051  1.0080  c3
-0.035800 12.0100
 31  ha  1   LIG  H31  310.141051  1.0080  ha
 0.141000  1.0080
 32  ha  1   LIG  H32  320.141051  1.0080  ha
 

Re: [gmx-users] Acetonitrile with CHARMM ff

[Justin Lemkul]

On 7/13/17 9:16 AM, Sonia Milena Aguilera Segura wrote:

Message: 2
Date: Thu, 13 Jul 2017 08:56:14 -0400
From: Justin Lemkul 
To: Discussion list for GROMACS users 
Subject: Re: [gmx-users] umbrella sampling
Message-ID: <995aa507-8875-8c41-674b-84eded63e...@vt.edu>
Content-Type: text/plain; charset=utf-8; format=flowed




Dear Justin,

I increased the size of the simulation box to 4 nm. Indeed, the values of
pressure improved (averages around -1 bar or 1.5, 2 bar, or so). However,
the T keeps being overestimated (302 K). During NVT I got the right value,
so I decided to run the 200 ns NPT equilibration with Berendsen barostat
instead of P-R. I got the right T value, around 298.3 and a pressure of
1.5 more or less. Then I launched a continuation test with 200 ps MD with
P-R (I couldn't use the -e option because it gives me the error Could not
find energy term named 'Box-Vel-XX', moreover, I didn't use P-R before so
I guess I shouldn't expect stored values for it?. But I am using -t ).
Despite I got low pressure averages around 0.5 bar, the temperature raised
again to 301-302. This happens very early in the simulation, which seems
to indicate that for sd integrator/thermostat and P-R barostat there is
something going on. I am getting practically the same density in between
simulation, so I guess I can say t

  ha

   t in term of P, the system has been equilibrated. However, what can I do
   to get the right T for this system? If I was able to get the right T
   with Berendsen barostat, I don't understand what's wrong when I change
   to P-R.



Sounds buggy.  What version of GROMACS are you using?  There were temperature
issues with the Langevin integrator in previous versions, but those should
have
been long since solved.


I am using version 5.1.2. I checked the release notes for version 5.1.3 and 5.1.4 
and the only thing related with sd integrator (none) or P-R barostat is this one 
'Fixed Parrinello-Rahman with nstpcouple > 1'. Can this be the cause?



I don't know.  Upgrade to 2016.3 and try again.

-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

==
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Re: [gmx-users] Acetonitrile with CHARMM ff

[Sonia Milena Aguilera Segura]

- Original Message -
> From: "gromacs org gmx-users-request" 
> 
> To: "gromacs org gmx-users" 
> Sent: Thursday, July 13, 2017 2:58:39 PM
> Subject: gromacs.org_gmx-users Digest, Vol 159, Issue 66
> 
> Send gromacs.org_gmx-users mailing list submissions to
>   gromacs.org_gmx-users@maillist.sys.kth.se
> 
> To subscribe or unsubscribe via the World Wide Web, visit
>   https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> or, via email, send a message with subject or body 'help' to
>   gromacs.org_gmx-users-requ...@maillist.sys.kth.se
> 
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> 
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of gromacs.org_gmx-users digest..."
> 
> 
> Today's Topics:
> 
>1. Error in simulating graphene (B S Bhushan)
>2. Re: umbrella sampling (Justin Lemkul)
>3. Re: Concrete pull code explanation needed (Justin Lemkul)
>4. Re: ACETONITRILE with CHARM ff (Justin Lemkul)
>5. Re: Non-periodic COM Pulling (Justin Lemkul)
> 
> 
> --
> 
> Message: 1
> Date: Thu, 13 Jul 2017 15:33:16 +0530
> From: B S Bhushan 
> To: gromacs.org_gmx-users@maillist.sys.kth.se
> Subject: [gmx-users] Error in simulating graphene
> Message-ID:
>   
> Content-Type: text/plain; charset="UTF-8"
> 
> Dear Experts,
> 
> I am new to gromacs. I want to simulate electric double layer capacitance
> at graphene - liquid electrolyte interface. so far, I have practiced the
> tutorials from bevanlab page "Lysozyme in water" "biphasic systems". Next,
> I was trying to simulate the CNT/graphene tutorials available at thirdparty
> web pages. However I am getting errors while trying to generate topology
> file using *x2top* module.
> 
> When following the tutorial given at
> http://chembytes.wikidot.com/grocnt#toc
> I am getting the error,
> "*Inconsistency in user input:*
> *Could not find force field 'cnt_oplsaa' in current directory, install tree
> or*
> *GMXLIB path*."
> 
> 
> When following the tutorial given at
> http://machine-phase.blogspot.in/2009/04/single-wall-carbon-
> nanotubes-in-403.html
> I am getting the error,
> "*Fatal error:*
> *Could only find a forcefield type for 0 out of 168 atoms.*"
> 
> 
> Please suggest.
> Thank you so much for your time and knowledge.
> 
> 
> 
> 
> Awaiting suggestions,
> B S Bhushan
> Research Scholar,
> ABV - Indian Institute of Information Technology and Management, Gwalior,
> India.
> 
> 
> --
> 
> Message: 2
> Date: Thu, 13 Jul 2017 08:56:14 -0400
> From: Justin Lemkul 
> To: Discussion list for GROMACS users 
> Subject: Re: [gmx-users] umbrella sampling
> Message-ID: <995aa507-8875-8c41-674b-84eded63e...@vt.edu>
> Content-Type: text/plain; charset=utf-8; format=flowed

> > 
> > Dear Justin,
> > 
> > I increased the size of the simulation box to 4 nm. Indeed, the values of
> > pressure improved (averages around -1 bar or 1.5, 2 bar, or so). However,
> > the T keeps being overestimated (302 K). During NVT I got the right value,
> > so I decided to run the 200 ns NPT equilibration with Berendsen barostat
> > instead of P-R. I got the right T value, around 298.3 and a pressure of
> > 1.5 more or less. Then I launched a continuation test with 200 ps MD with
> > P-R (I couldn't use the -e option because it gives me the error Could not
> > find energy term named 'Box-Vel-XX', moreover, I didn't use P-R before so
> > I guess I shouldn't expect stored values for it?. But I am using -t ).
> > Despite I got low pressure averages around 0.5 bar, the temperature raised
> > again to 301-302. This happens very early in the simulation, which seems
> > to indicate that for sd integrator/thermostat and P-R barostat there is
> > something going on. I am getting practically the same density in between
> > simulation, so I guess I can say t
>  ha
> >   t in term of P, the system has been equilibrated. However, what can I do
> >   to get the right T for this system? If I was able to get the right T
> >   with Berendsen barostat, I don't understand what's wrong when I change
> >   to P-R.
> > 
> 
> Sounds buggy.  What version of GROMACS are you using?  There were temperature
> issues with the Langevin integrator in previous versions, but those should
> have
> been long since solved.

I am using version 5.1.2. I checked the release notes for version 5.1.3 and 
5.1.4 and the only thing related with sd integrator (none) or P-R barostat is 
this one 'Fixed Parrinello-Rahman with nstpcouple > 1'. Can this be the cause? 

Thank you.
> 
> -Justin
> 
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Re: [gmx-users] gmx select

[Justin Lemkul]

On 7/13/17 3:38 AM, Pandya, Akash wrote:

gmx select -f output.gro -select "Close to protein" resname Glyci and within 0.5 of group 
"Protein"'



I suspect Mark is right, this is an invalid command, because you have a closing 
' without an opening ' in your -select argument.  This should fail with a 
generic error message that the selection can't be parsed.  I am also curious 
about "resname Glyci" because if that's the case, then you must have hacked some 
force field files, because everyone calls glycine "GLY" per standard nomenclature.


-Justin


-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 Mark 
Abraham
Sent: 13 July 2017 00:04
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] gmx select

Hi,

Can you please copy, paste and post your actual commands. I don't think your 
use of quote marks would have led to a valid shell command. The whole selection 
text will need to be inside some quotes.

Mark

On Wed, 12 Jul 2017 23:47 Pandya, Akash  wrote:


I have used the same name in my coordinate file. For Glycine it is
spelt as Glyci, so the word has been cut off. I know this is correct
because I use the same name in VMD.

-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 Mark
Abraham
Sent: 12 July 2017 22:42
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] gmx select

Hi,

What are the residue names in your coordinate file? Glyci probably
doesn't fit

Mark

On Wed, Jul 12, 2017 at 10:36 PM Pandya, Akash

wrote:


Hi all,


I am trying to select all the glycine molecules with 0.5nm of my protein.
I tried both of these commands I got from the gromacs website:

gmx select -f output.gro -select "Close to protein" resname Glyci
and within 0.5 of group "Protein"' -ofpdb

gmx select -f output.xtc -s output.tpr (my converted input file)
-select "Close to protein" resname Glyci and within 0.5 of group
"Protein"' -ofpdb


Nothing comes up when I enter them. Please could someone help me
with

this?



Akash
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--
==

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

==
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Re: [gmx-users] Error in simulating graphene

[Justin Lemkul]

On 7/13/17 5:49 AM, B S Bhushan wrote:

Dear Experts,

I am new to gromacs. I want to simulate electric double layer capacitance
at graphene - liquid electrolyte interface. so far, I have practiced the
tutorials from bevanlab page "Lysozyme in water" "biphasic systems". Next,
I was trying to simulate the CNT/graphene tutorials available at thirdparty
web pages. How ever I am getting errors while trying to generate topology
file using *x2top* module.

When following the tutorial given at
http://chembytes.wikidot.com/grocnt#toc
I am getting the error,
"*Inconsistency in user input:*
*Could not find force field 'cnt_oplsaa' in current directory, install tree
or*
*GMXLIB path*."



This means the force field isn't anywhere the the program can find it.



When following the tutorial given at
http://machine-phase.blogspot.in/2009/04/single-wall-carbon-nanotubes-in-403.html
I am getting the error,
"*Fatal error:*
*Could only find a forcefield type for 0 out of 168 atoms.*"



The .n2t file is constructed incorrectly such that no topology assignments can 
be made.


-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

==
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Re: [gmx-users] Periodic Molecule's Free Energy Calculation Error

[Justin Lemkul]

On 7/12/17 9:12 PM, Alex wrote:




I wonder if the "couple-intramol = yes" is a must. Does it have any influence 
on the output results if we turn off the intra-molecular non-bonded 
interactions of a large infinite molecule?


The answer to your question has nothing to do with Gromacs, but with 
understanding the difference between crystals and biomolecules (for which 
Gromacs was designed).


There is a functional difference between coupling intramolecular interactions 
and not, which will affect the computed free energy.  With couple-intramol = no, 
you get the correct vacuum state of the solute molecule; with couple-intramol = 
yes, you get perturbed intramolecular interactions.  This has important 
consequences for what one is trying to compute.


-Justin

Also (unrelated), it is a common misconception to believe that PBC makes 
something infinite -- the effective size of your system is entirely determined 
by the supercell size (proof: consider the ripples in hBN and determine the 
lowest wavelength of the ripple that can propagate -- it is commensurate with 
the box size). In an infinite system, you can have an immensely long wave 
(though not infinite, as shown by Landau a while back). PBC does not make 
anything infinite, it is a mathematical way of avoiding surfaces.


There is no universal force field for HBN, so I am using a modified 
gromos54a7_atb force field, i.e., manually adding the parameters for boron and 
nitrogen to the bonded & nonbonded .itp files.
Oh, I know that there is no force fields for these structures. ;) My question 
was about which Gromacs ff you were using to insert your parameters, and, most 
importantly, where those parameters came from.



The parameters are obtained from literature.

What literature? All bio-style ff adaptations of solid-state potentials (e.g. 
Tersoff-Brenner for hBN) I am aware of make it very clear that "intramolecular" 
interactions between atoms sharing up to a fairly distant covalently bound 
neighbor are limited to bonds and angles. This comes from the math involved in 
developing potentials for crystals. There was a recent question regarding this 
very problem here, which was solved by setting a larger nrexcl value. In your 
case, you solved it with turning off intramolecular coupling. In fact, if you 
set your nrexcl to something like 4 or 5, you may not even need to turn off the 
coupling. But then again, I don't know where the parameters came from.


Alex


--
==

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

==
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Re: [gmx-users] Non-periodic COM Pulling

[Justin Lemkul]

On 7/12/17 3:05 PM, Daniel Kozuch wrote:

Hello,

Is it possible to do non-periodic COM pulling using the distance function
in GMX 5.14 (i.e. where the distance between the two groups is calculated
ignoring pbc)?



No, but this is what direction-periodic is for.

-Justin


In the tutorials/online the solution seems to be to simply use a box twice
the size of the largest pulling distance, but that would be very
computationally expensive for me.

Best,
Dan



--
==

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

==
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Re: [gmx-users] ACETONITRILE with CHARM ff

[Justin Lemkul]

On 7/12/17 8:56 AM, Sonia Milena Aguilera Segura wrote:





Message: 3
Date: Tue, 11 Jul 2017 12:57:05 -0400
From: Justin Lemkul 

Moreover, I observed that this time I got lower values for P during the NPT
equilibration, but still is too far from 1 bar.  I really don't understand
why for the NVT simulation I get a T around 298, but as soon as I turn on
the pcoupl, the T rises to 300-301 K and the P gets average values of 7
and 4 bar (vs 8 and 14 for the previous simulations). Then at the end of
the 1-ns MD the temperature remains around 301 and the P is -1 and 2.7
bar. Considering the parameters I am using, is there anything I can change
to make the P coupling better? I am running a 3 nm box with 308 molecules.
This is the full mdp file:



http://www.gromacs.org/Documentation/Terminology/Pressure

Your box is very small and will be subject to large fluctuations.


Dear Justin,

I increased the size of the simulation box to 4 nm. Indeed, the values of 
pressure improved (averages around -1 bar or 1.5, 2 bar, or so). However, the T 
keeps being overestimated (302 K). During NVT I got the right value, so I 
decided to run the 200 ns NPT equilibration with Berendsen barostat instead of 
P-R. I got the right T value, around 298.3 and a pressure of 1.5 more or less. 
Then I launched a continuation test with 200 ps MD with P-R (I couldn't use the 
-e option because it gives me the error Could not find energy term named 
'Box-Vel-XX', moreover, I didn't use P-R before so I guess I shouldn't expect 
stored values for it?. But I am using -t ). Despite I got low pressure averages 
around 0.5 bar, the temperature raised again to 301-302. This happens very 
early in the simulation, which seems to indicate that for sd 
integrator/thermostat and P-R barostat there is something going on. I am 
getting practically the same density in between simulation, so I guess I can 
say t

ha

  t in term of P, the system has been equilibrated. However, what can I do to 
get the right T for this system? If I was able to get the right T with 
Berendsen barostat, I don't understand what's wrong when I change to P-R.



Sounds buggy.  What version of GROMACS are you using?  There were temperature 
issues with the Langevin integrator in previous versions, but those should have 
been long since solved.


-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

==
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Re: [gmx-users] Concrete pull code explanation needed

[Justin Lemkul]

On 7/11/17 8:23 PM, Du, Yu wrote:

On 7/10/17 11:19 PM, Du, Yu wrote:

Dear Justin and gmx users,


I have gone through mdp-option and Justin A. Lemkul's COM pulling tutorial 
serveral times.


The following is Justin's pull code.


; Pull code
pull= yes
pull_ngroups= 2
pull_ncoords= 1
pull_group1_name= Chain_B
pull_group2_name= Chain_A
pull_coord1_type= umbrella  ; harmonic biasing force
pull_coord1_geometry= distance  ; simple distance increase
pull_coord1_groups= 1 2
pull_coord1_dim = N N Y
pull_coord1_rate= 0.01  ; 0.01 nm per ps = 10 nm per ns
pull_coord1_k   = 1000  ; kJ mol^-1 nm^-2
pull_coord1_start   = yes   ; define initial COM distance > 0


My understanding lists as follows,


Justin defines two pull groups, with `pull-ngroups = 2`, each of them has a 
name in the index.ndx generated by `gmx make_ndx -f npt.gro`and their names are 
defined by `pull_group1_name = Chain_B` and `pull_group2_name = Chain_A`.


My question is about the definition of pulling coordination and the orientation 
of pulling force.


1) I learnt from [gmx-users] Change to umbrella sampling pull code，
"You need: pull-coord1-groups = 1 2 otherwise the reaction coordinate is undefined, 
or otherwise defaults to the entire system, I can't remember which. -Justin"


I know it's a plot :) in the input.pdb that proteins are placed exquisitely 
along the z-axis which is the same as the pulling coordinate but it makes pull 
code confused and here I need a concrete explanation.
1.The pull coordinate is the line that connects COM of group1 and group2 with 
`pull_coord1_groups= 1 2`.
OR 2. The pull coordinate is the z axis with `pull_coord1_dim = N N Y`.
Which is correct?



The z-component of the vector connecting the COMs of the two groups.



2)Then turn to the orientation of pulling forces.
My understanding is that force1 acts on pull_group1, force2 acts on pull_group2 
and the orientation of force 1 and 2 is opposite, both forces have a rate of 
10nm per ns.
Is my understanding and the below schematic draw right?



There is one force.  It acts on the spring connecting the two groups.



How does the spring connect the two groups? Does the spring link to the COM of 
the whole two groups?


Yes.


How does Gromacs define the orientation of the force of pulling? Or by default 
is the pulling force just positive along the z axis with `pull_coord1_geometry 
= distance` and `pull_coord1_dim = N N Y`?



This is not the default, but it is precisely what is specified by those .mdp 
settings.






Z-axis-0-5--->---positive-orientation--->-25-->
 


The last question is about the umbrella sampling.
I learnt from [gmx-users] Re: doubt about your Umbrella Sampling tutorial that 
it's ok to remove the pores of Chain B during the US. But in longer simulation 
time and in the periodical box, will the COM of Chain B and A be affacted by 
the boundary? and then affact the calculation of US potential?



The tutorial system won't work if you turn off the restraint.  Eventually the
system will rotate and the groups will cross periodic boundaries, which will
cause the chosen pull geometry to fail.  So the restraints serve a dual purpose:
(1) to mimic the stability of larger amyloid assemblies and (2) to reduce the
system size, as several hundred thousand atoms was not feasible for me at the 
time.



So your point is that during US, we can't remove the Chain B's restrain. Right?


*For this specific case* yes.


During US, is there any means to study the flexiblity of both groups? (i.e. 
there is no restrain on both groups except the umbrella potential between them 
and at the same time both groups will not cross periodic boundaries and will 
not affact the umbrella potential geometry, which is a necessary part of my 
study)


Normally one should not apply any position restraints, except in niche cases 
like mine.


-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

==
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Re: [gmx-users] umbrella sampling

[Justin Lemkul]

On 7/11/17 5:29 PM, Ben Tam wrote:

Hi Justin,

Thanks for answering. I have tried sending the histogram however it is too big 
of a file. But the histogram shows a lot of overlapping and multiple peaks. All 
of the value in profile.xvg  showing nan. What can that mean?




Most likely a sampling problem.  But as I cannot see your histograms, I can't 
guess any further at specifically what's going on.


-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

==
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[gmx-users] Error in simulating graphene

[B S Bhushan]

Dear Experts,

I am new to gromacs. I want to simulate electric double layer capacitance
at graphene - liquid electrolyte interface. so far, I have practiced the
tutorials from bevanlab page "Lysozyme in water" "biphasic systems". Next,
I was trying to simulate the CNT/graphene tutorials available at thirdparty
web pages. However I am getting errors while trying to generate topology
file using *x2top* module.

When following the tutorial given at
http://chembytes.wikidot.com/grocnt#toc
I am getting the error,
"*Inconsistency in user input:*
*Could not find force field 'cnt_oplsaa' in current directory, install tree
or*
*GMXLIB path*."


When following the tutorial given at
http://machine-phase.blogspot.in/2009/04/single-wall-carbon-
nanotubes-in-403.html
I am getting the error,
"*Fatal error:*
*Could only find a forcefield type for 0 out of 168 atoms.*"


Please suggest.
Thank you so much for your time and knowledge.




Awaiting suggestions,
B S Bhushan
Research Scholar,
ABV - Indian Institute of Information Technology and Management, Gwalior,
India.
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[gmx-users] Error in simulating graphene

[B S Bhushan]

Dear Experts,

I am new to gromacs. I want to simulate electric double layer capacitance
at graphene - liquid electrolyte interface. so far, I have practiced the
tutorials from bevanlab page "Lysozyme in water" "biphasic systems". Next,
I was trying to simulate the CNT/graphene tutorials available at thirdparty
web pages. How ever I am getting errors while trying to generate topology
file using *x2top* module.

When following the tutorial given at
http://chembytes.wikidot.com/grocnt#toc
I am getting the error,
"*Inconsistency in user input:*
*Could not find force field 'cnt_oplsaa' in current directory, install tree
or*
*GMXLIB path*."


When following the tutorial given at
http://machine-phase.blogspot.in/2009/04/single-wall-carbon-nanotubes-in-403.html
I am getting the error,
"*Fatal error:*
*Could only find a forcefield type for 0 out of 168 atoms.*"


Please suggest.
Thank you so much for your time and knowledge.




Awaiting suggestions,
B S Bhushan
Research Scholar,
ABV - Indian Institute of Information Technology and Management, Gwalior,
India.
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Re: [gmx-users] gmx select

[Pandya, Akash]

gmx select -f output.gro -select "Close to protein" resname Glyci and within 
0.5 of group "Protein"'

-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 Mark 
Abraham
Sent: 13 July 2017 00:04
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] gmx select

Hi,

Can you please copy, paste and post your actual commands. I don't think your 
use of quote marks would have led to a valid shell command. The whole selection 
text will need to be inside some quotes.

Mark

On Wed, 12 Jul 2017 23:47 Pandya, Akash  wrote:

> I have used the same name in my coordinate file. For Glycine it is 
> spelt as Glyci, so the word has been cut off. I know this is correct 
> because I use the same name in VMD.
>
> -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 Mark 
> Abraham
> Sent: 12 July 2017 22:42
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] gmx select
>
> Hi,
>
> What are the residue names in your coordinate file? Glyci probably 
> doesn't fit
>
> Mark
>
> On Wed, Jul 12, 2017 at 10:36 PM Pandya, Akash 
> 
> wrote:
>
> > Hi all,
> >
> >
> > I am trying to select all the glycine molecules with 0.5nm of my protein.
> > I tried both of these commands I got from the gromacs website:
> >
> > gmx select -f output.gro -select "Close to protein" resname Glyci 
> > and within 0.5 of group "Protein"' -ofpdb
> >
> > gmx select -f output.xtc -s output.tpr (my converted input file) 
> > -select "Close to protein" resname Glyci and within 0.5 of group 
> > "Protein"' -ofpdb
> >
> >
> > Nothing comes up when I enter them. Please could someone help me 
> > with
> this?
> >
> >
> > Akash
> > --
> > Gromacs Users mailing list
> >
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> > posting!
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> > or send a mail to gmx-users-requ...@gromacs.org.
> >
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Re: [gmx-users] problem: gromacs run on gpu

[Mark Abraham]

Hi,

Probably you have some strange character after "on" if you edited the file
on Windows or pasted the line from elsewhere

Mark

On Thu, 13 Jul 2017 07:22 Alex  wrote:

> Can you try to open the script in vi, delete the mdrun line and then
> manually retype it?
>
>
> On 7/12/2017 11:03 PM, leila karami wrote:
> > Dear Gromacs users,
> >
> > I am doing md simulation on Gromacs 5.1.3. on GPU in Rocks cluster
> system using
> > command:
> >
> > gmx_mpi mdrun -nb gpu -v -deffnm gpu -ntomp 16 -gpu_id 0 -pin on
> >
> > All things are ok.
> >
> > When I use this command in a script to do md simulation by queuing
> system:
> >
> >
> -
> > #!/bin/bash
> > #$ -S /bin/bash
> > #$ -q gpu.q
> > #$ -cwd
> > #$ -N cell_1
> > #$ -e error_1.dat
> > #$ -o output_1.dat
> > echo "Job started at date"
> > gmx_mpi mdrun -nb gpu -v -deffnm gpu -ntomp 16 -gpu_id 0 -pin on
> > echo "Job Ended at date"
> >
> -
> >
> > I encountered with following error:
> >
> > Program: gmx mdrun, VERSION 5.1.3
> > Source file: src/gromacs/commandline/cmdlineparser.cpp (line 234)
> > Function:void gmx::CommandLineParser::parse(int*, char**)
> >
> > Error in user input:
> > Invalid command-line options
> >In command-line option -pin
> >  Invalid value: on
> >
> > For more information and tips for troubleshooting, please check the
> GROMACS
> > website at http://www.gromacs.org/Documentation/Errors
> > ---
> > Halting program gmx mdrun
> >
> --
> > MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
> > with errorcode 1.
> >
> > NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
> > You may or may not see output from other processes, depending on
> > exactly when Open MPI kills them.
> >
> >
> ---
> >
> > How to resolve this error?
> > Any help will be highly appreciated
>
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