Re: [gmx-users] determining restraints for pulling

[abhisek Mondal]

Is it possible to pull (distance pull) along negative of Z axis (for
example, I'm saying Z) ? Do I need to mention -Z in pull code or the
program improvises if I say Z axis distance pull in .mdp ?

On Wed, Apr 5, 2017 at 5:40 PM, Justin Lemkul  wrote:

>
> Please keep the discussion on the mailing list.
>
> On 4/5/17 8:04 AM, abhisek Mondal wrote:
>
>> Hello Justin,
>>
>> Can you provide some direction to this approach I'm using for performing
>> umbrella sampling of a protein-ligand complex ?
>>
>> I had restrained it during the equilibration of the molecule. As advised
>> in the
>> Protein-ligand simulation tutorial. But I'm unsure regarding what kind of
>> treatment I'm supposed to give the complex while targeting for umbrella
>> sampling. Do I need to restrain the ligand during equilibration ?
>>
>> I have solved the crystal structure of the complex and want to determine
>> if I
>> pull out the ligand then how the side chains reorient according to the
>> ligand
>> withdrawal. That's the goal.
>>
>> Some suggestions regarding the issue will be highly appreciated.
>>
>>
> What does your examination of the literature for similar systems suggest
> as an appropriate protocol?
>
> -Justin
>
> Thank you
>>
>> On Wed, Apr 5, 2017 at 3:51 PM, abhisek Mondal > > wrote:
>>
>> I had restrained it during the equilibration of the molecule. As
>> advised in
>> the Protein-ligand simulation tutorial. But I'm unsure regarding what
>> kind
>> of treatment I'm supposed to give the complex while targeting for
>> umbrella
>> sampling. Do I need to restrain the ligand during equilibration ?
>>
>> I have solved the crystal structure of the complex and want to
>> determine if
>> I pull out the ligand then how the side chains reorient according to
>> the
>> ligand withdrawal. That's the goal.
>>
>> On Wed, Apr 5, 2017 at 3:09 PM, Mark Abraham <
>> mark.j.abra...@gmail.com
>> > wrote:
>>
>> Hi,
>>
>> Why are you trying to keep the ligand in place (by restraining
>> it) and pull
>> it out?
>>
>> Mark
>>
>> On Wed, 5 Apr 2017 09:51 abhisek Mondal > > wrote:
>>
>> > Hi,
>> >
>> > I'm trying to pull a ligand from a protein-ligand complex. As
>> per the
>> > ligand-protein tutorial, I have restrained the ligand in
>> topology file and
>> > it looks like:
>> >
>> > ; Include Position restraint file
>> > #ifdef POSRES
>> > #include "posre.itp"
>> > #endif
>> >
>> > ; Include ligand topology
>> > #include "drg.itp"
>> >
>> > ; Include position restraints
>> > #ifdef POSRES_LIG
>> > #include "posre_ACO.itp"
>> > #endif
>> >
>> > ; Include water topology
>> > #include "gromos43a1.ff/spc.itp"
>> >
>> > In the md_pull.mdp, I'm using:
>> >
>> > title   = Umbrella pulling simulation
>> > define  = -DPOSRES
>> > ; Run parameters
>> > integrator  = md;applying leap frog algorithm
>> >
>> > So, is it proper for pulling ligand (ACO) from the protein or
>> I'm doing
>> > something wrong ? I'm really lost here, please help me out.
>> >
>> > Thank you.
>> >
>> >
>> > --
>> > Abhisek Mondal
>> >
>> > *Senior Research Fellow*
>> >
>> > *Structural Biology and Bioinformatics Division*
>> > *CSIR-Indian Institute of Chemical Biology*
>> >
>> > *Kolkata 700032*
>> >
>> > *INDIA*
>> > --
>> > Gromacs Users mailing list
>> >
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>> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List
>> 
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>> > posting!
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>> -users
>> > x-users> or
>> > send a mail to gmx-users-requ...@gromacs.org
>> .
>> >
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[gmx-users] Position restraint on DPPC lipid bilayer

[Sithara Perera]

Hi!,

 I' making a 512 DPPC bi-layer out of 128 bilayer available in
http://www.cgmartini.nl. The force field used is martini.

 But once the energy minimization is done, the bi-layer crashes and
accumulates to  globules.

 So I made an position.itp file using the command


gmx genrestr -f dppc221.gro -n test.ndx -o lipid_posre.itp -fc 1000 1000
1000

And included in the topology file.

Topology file also include

include "martini_v2.0.itp"
#include "martini_v2.0_lipids.itp"  from martini as well.



 But then when the command

gmx grompp -f minim.mdp -c dppc221.gro -p dppc_bilayer.top -o em2.tpr

is given , following error occurs.

Fatal error:
[ file posre.itp, line 29 ]:
Atom index (25) in position_restraints out of bounds (1-24).
This probably means that you have inserted topology section
"position_restraints"
in a part belonging to a different molecule than you intended to.
In that case move the "position_restraints" section to the right molecule.


How can I fix this?
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Re: [gmx-users] Regarding restricting to centre of box, cos theta functions

[Justin Lemkul]

On 4/6/17 4:10 PM, Dilip H N wrote:

Thank you Justin..

For my query on cos theta distribution functions..
How can i calculate cos theta distributions (eg.,cos theta distributions of
hydrogen's of water in first hydration shell layer of amino acid)..??
Is there any command that i need to give like as in rdf  commands
(indexing,etc.,)  ..??



It sounds like you want to be using gmx sorient.

-Justin




   Sent with Mailtrack


On Fri, Apr 7, 2017 at 12:32 AM, Justin Lemkul  wrote:




On 4/6/17 2:58 PM, Dilip H N wrote:


Hello,
I have ran a md simulation of amino acid with solvent molecules with it.
During simulation run, the molecules (amino acid, solvent molecules) move
around the box, but i don't want the amino acid to move around during the
simulation, want to fix it to centre of box..
1] How can i restrict/fix/keep  only the amino acid molecule in/to the
centre of the box during simulation ..? Is it possible..



It's not necessary.  A simulation with periodic boundary conditions is
infinite and therefore there is no center.  If it's inconvenient to
visualize, that has no bearing on the physics.  Don't try to perturb the
system with biasing potentials; just re-center with trjconv when the
simulation is done.

2] How can i calculate the cos theta function in gromacs..??




Put down GROMACS and pick up a high school trigonometry book.  GROMACS
isn't a calculator :)

-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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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] Regarding restricting to centre of box, cos theta functions

[Dilip H N]

Thank you Justin..

For my query on cos theta distribution functions..
How can i calculate cos theta distributions (eg.,cos theta distributions of
hydrogen's of water in first hydration shell layer of amino acid)..??
Is there any command that i need to give like as in rdf  commands
(indexing,etc.,)  ..??



   Sent with Mailtrack


On Fri, Apr 7, 2017 at 12:32 AM, Justin Lemkul  wrote:

>
>
> On 4/6/17 2:58 PM, Dilip H N wrote:
>
>> Hello,
>> I have ran a md simulation of amino acid with solvent molecules with it.
>> During simulation run, the molecules (amino acid, solvent molecules) move
>> around the box, but i don't want the amino acid to move around during the
>> simulation, want to fix it to centre of box..
>> 1] How can i restrict/fix/keep  only the amino acid molecule in/to the
>> centre of the box during simulation ..? Is it possible..
>>
>>
> It's not necessary.  A simulation with periodic boundary conditions is
> infinite and therefore there is no center.  If it's inconvenient to
> visualize, that has no bearing on the physics.  Don't try to perturb the
> system with biasing potentials; just re-center with trjconv when the
> simulation is done.
>
> 2] How can i calculate the cos theta function in gromacs..??
>>
>>
> Put down GROMACS and pick up a high school trigonometry book.  GROMACS
> isn't a calculator :)
>
> -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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>



-- 
With Best Regards,

DILIP.H.N
Ph.D Student
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Re: [gmx-users] Regarding restricting to centre of box, cos theta functions

[Justin Lemkul]

On 4/6/17 2:58 PM, Dilip H N wrote:

Hello,
I have ran a md simulation of amino acid with solvent molecules with it.
During simulation run, the molecules (amino acid, solvent molecules) move
around the box, but i don't want the amino acid to move around during the
simulation, want to fix it to centre of box..
1] How can i restrict/fix/keep  only the amino acid molecule in/to the
centre of the box during simulation ..? Is it possible..



It's not necessary.  A simulation with periodic boundary conditions is infinite 
and therefore there is no center.  If it's inconvenient to visualize, that has 
no bearing on the physics.  Don't try to perturb the system with biasing 
potentials; just re-center with trjconv when the simulation is done.



2] How can i calculate the cos theta function in gromacs..??



Put down GROMACS and pick up a high school trigonometry book.  GROMACS isn't a 
calculator :)


-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] Regarding restricting to centre of box, cos theta functions

[Dilip H N]

Hello,
I have ran a md simulation of amino acid with solvent molecules with it.
During simulation run, the molecules (amino acid, solvent molecules) move
around the box, but i don't want the amino acid to move around during the
simulation, want to fix it to centre of box..
1] How can i restrict/fix/keep  only the amino acid molecule in/to the
centre of the box during simulation ..? Is it possible..

2] How can i calculate the cos theta function in gromacs..??
-- 
With Best Regards,

DILIP.H.N
Ph.D Student



   Sent with Mailtrack

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[gmx-users] problem to restart the REMD

[YanhuaOuyang]

Hi,
I have run REMD for 80648ps. And I have to restart the REMD because of the 
limited time of super-computing center. However it always failed to restart 
from 80648ps. The errors are as following:

Fatal error in MPI_Allreduce: Message truncated, error stack:
MPI_Allreduce(1339)...: MPI_Allreduce(sbuf=0x7fff4ac3fa90, 
rbuf=0x29af530, count=4, MPI_FLOAT, MPI_SUM, comm=0x8400) fai
led
MPIR_Allreduce_impl(1180).:
MPIR_Allreduce_intra(410).:
MPIR_Bcast_intra(1524): Failure during collective
MPIR_Bcast_intra(1499):
MPIR_Bcast_binomial(147)..:
MPIDI_CH3U_Receive_data_found(129): Message from rank 0 and tag 2 truncated; 
260 bytes received but buffer size is 16

I tried to restart the REMD many times and both use remd0.cpt and 
remd0_prev.cpt. But they all failed and appear error as above.
I don't know how to solve the problem. I don't want to run from beginning since 
I have run such long time(80ns-REMD).
Does anyone know how fix such problem?


Best regards,
Ouyang
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Re: [gmx-users] GROMACS3.3.1 - configure: error: invalid variable name: –-with-fft

[João M . Damas]

Hi Simon,

Assuming you are copying/pasting the command you are running, it seems to
me that the first hyphen of the flag is rather a dash or a minus sign
(weirdly).

Can you rather try: ./configure --with-fft=fftpack

Regards,
João

On Thu, Apr 6, 2017 at 10:12 AM, Simon Kit Sang Chu 
wrote:

> Hi everyone,
>
> Due to some technical issues, I have to install gromacs 3.3.1 in order to
> incorporate my desired forcefield. Following the instructions, I have to
> switch the FFT library to fftpack. However, I run into this error whenever
> I choose the option --with-fft, regardless the library chosen.
>
> ./configure –-with-fft=fftpack
> configure: error: invalid variable name: –-with-fft
>
>
> I checked ./configure and ./configure -h. Indeed, the option is available.
>
> From ./configure,
>
> --with-fft=[fftw3/fftw2/mkl(>=6.0)/fftpack]
>   FFT library to use. fftw3 is default, fftpack
> built
>   in.
>
>
> Would anyone kindly suggest possible solution or items that I could look
> into?
>
> Thank you.
>
> Regards,
> Simon
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-- 
João M. Damas
PhD Student
Protein Modelling Group
ITQB-UNL, Oeiras, Portugal
Tel:+351-214469613
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Re: [gmx-users] Fast energy evaluation

[Peter Kroon]

Hi,

In addition to Erik's tip: once you have a tpr (made once with grompp),
change it for every iteration by writing your new parameters directly to
the tpr file, bypassing grompp entirely. This will require a custom
script and might not be completely trivial though.

Peter


On 06-04-17 13:15, Mark Abraham wrote:
> Hi,
>
> http://www.gromacs.org/Documentation/How-tos/Single-Point_Energy
>
> Mark
>
> On Thu, Apr 6, 2017 at 1:00 PM Erik Marklund 
> wrote:
>
>> Dear Andras,
>>
>> Concatenate all structures into one trajectory and issue gmx mdrun -rerun.
>> That will evaluate the energies for all conformations. You will of course
>> need a tpr file too.
>>
>> Kind regards,
>> Erik
>> __
>> Erik Marklund, PhD, Marie Skłodowska Curie INCA Fellow
>> Department of Chemistry – BMC, Uppsala University
>> +46 (0)18 471 4539 <018-471%2045%2039>
>> erik.markl...@kemi.uu.se
>>
>> On 6 Apr 2017, at 12:39, András Ferenc WACHA > > wrote:
>>
>> Dear Gromacs Users,
>>
>> does someone know a way to quickly evaluate the energy of a few structures?
>>
>> In more detail:
>>
>> I have several conformations of the same peptide, stored in PDB format.
>> In principle, they have the same topology. I want to optimize various
>> force field parameters, which involves the need to calculate the energy
>> multiple times, each time with different bond/angle/dihedral parameters.
>> Currently I use a single-step mdrun (integrator = steep) and
>> "gmx_energy" to extract the energy terms, but the overhead of calling
>> grompp, mdrun and energy in each case for each structure is too much. In
>> charmm you can write a script for this job: is there an equivalent in
>> gromacs without the overheads?
>>
>> Thank you in advance.
>>
>> Best regards,
>>
>> András Wacha
>>
>> --
>> András Ferenc Wacha, PhD
>> research fellow, CREDO instrument responsible
>>
>> Biological Nanochemistry Research Group
>>
>> Institute of Materials and Environmental Chemistry
>> Research Centre for Natural Sciences
>> Hungarian Academy of Sciences (RCNS HAS)
>> Magyar tudósok körútja 2.
>> H-1117 Budapest, Hungary
>> Phone: +36-1-382-6427 <+36%201%20382%206427>
>> Web: http://bionano.ttk.mta.hu,
>> CREDO SAXS instrument: http://credo.ttk.mta.hu
>>
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at
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>> posting!
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>>
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Re: [gmx-users] Fast energy evaluation

[Mark Abraham]

Hi,

http://www.gromacs.org/Documentation/How-tos/Single-Point_Energy

Mark

On Thu, Apr 6, 2017 at 1:00 PM Erik Marklund 
wrote:

> Dear Andras,
>
> Concatenate all structures into one trajectory and issue gmx mdrun -rerun.
> That will evaluate the energies for all conformations. You will of course
> need a tpr file too.
>
> Kind regards,
> Erik
> __
> Erik Marklund, PhD, Marie Skłodowska Curie INCA Fellow
> Department of Chemistry – BMC, Uppsala University
> +46 (0)18 471 4539 <018-471%2045%2039>
> erik.markl...@kemi.uu.se
>
> On 6 Apr 2017, at 12:39, András Ferenc WACHA  > wrote:
>
> Dear Gromacs Users,
>
> does someone know a way to quickly evaluate the energy of a few structures?
>
> In more detail:
>
> I have several conformations of the same peptide, stored in PDB format.
> In principle, they have the same topology. I want to optimize various
> force field parameters, which involves the need to calculate the energy
> multiple times, each time with different bond/angle/dihedral parameters.
> Currently I use a single-step mdrun (integrator = steep) and
> "gmx_energy" to extract the energy terms, but the overhead of calling
> grompp, mdrun and energy in each case for each structure is too much. In
> charmm you can write a script for this job: is there an equivalent in
> gromacs without the overheads?
>
> Thank you in advance.
>
> Best regards,
>
> András Wacha
>
> --
> András Ferenc Wacha, PhD
> research fellow, CREDO instrument responsible
>
> Biological Nanochemistry Research Group
>
> Institute of Materials and Environmental Chemistry
> Research Centre for Natural Sciences
> Hungarian Academy of Sciences (RCNS HAS)
> Magyar tudósok körútja 2.
> H-1117 Budapest, Hungary
> Phone: +36-1-382-6427 <+36%201%20382%206427>
> Web: http://bionano.ttk.mta.hu,
> CREDO SAXS instrument: http://credo.ttk.mta.hu
>
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[gmx-users] Test particle insertion for all atom force field

[Badmos, Sakiru]

Hi everyone,

  I want to calculate excess chemical potential for some 
molecules in water. I found a tutorial on this but it was on methane (united 
atom). The insertion of the test particle requires that it is included as the 
last atom in the .gro file with coordinate 0.000 0.000 0.000. This works for 
United atom. How do I do this for molecule like CO2 with three atoms?

 Thank you as you help.

Sakiru.

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Re: [gmx-users] Fast energy evaluation

[Erik Marklund]

Dear Andras,

Concatenate all structures into one trajectory and issue gmx mdrun -rerun. That 
will evaluate the energies for all conformations. You will of course need a tpr 
file too.

Kind regards,
Erik
__
Erik Marklund, PhD, Marie Skłodowska Curie INCA Fellow
Department of Chemistry – BMC, Uppsala University
+46 (0)18 471 4539
erik.markl...@kemi.uu.se

On 6 Apr 2017, at 12:39, András Ferenc WACHA 
> wrote:

Dear Gromacs Users,

does someone know a way to quickly evaluate the energy of a few structures?

In more detail:

I have several conformations of the same peptide, stored in PDB format.
In principle, they have the same topology. I want to optimize various
force field parameters, which involves the need to calculate the energy
multiple times, each time with different bond/angle/dihedral parameters.
Currently I use a single-step mdrun (integrator = steep) and
"gmx_energy" to extract the energy terms, but the overhead of calling
grompp, mdrun and energy in each case for each structure is too much. In
charmm you can write a script for this job: is there an equivalent in
gromacs without the overheads?

Thank you in advance.

Best regards,

András Wacha

--
András Ferenc Wacha, PhD
research fellow, CREDO instrument responsible

Biological Nanochemistry Research Group

Institute of Materials and Environmental Chemistry
Research Centre for Natural Sciences
Hungarian Academy of Sciences (RCNS HAS)
Magyar tudósok körútja 2.
H-1117 Budapest, Hungary
Phone: +36-1-382-6427
Web: http://bionano.ttk.mta.hu,
CREDO SAXS instrument: http://credo.ttk.mta.hu

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[gmx-users] Fast energy evaluation

[András Ferenc WACHA]

Dear Gromacs Users,

does someone know a way to quickly evaluate the energy of a few structures?

In more detail:

I have several conformations of the same peptide, stored in PDB format.
In principle, they have the same topology. I want to optimize various
force field parameters, which involves the need to calculate the energy
multiple times, each time with different bond/angle/dihedral parameters.
Currently I use a single-step mdrun (integrator = steep) and
"gmx_energy" to extract the energy terms, but the overhead of calling
grompp, mdrun and energy in each case for each structure is too much. In
charmm you can write a script for this job: is there an equivalent in
gromacs without the overheads?

Thank you in advance.

Best regards,

András Wacha

-- 
András Ferenc Wacha, PhD
research fellow, CREDO instrument responsible

Biological Nanochemistry Research Group

Institute of Materials and Environmental Chemistry
Research Centre for Natural Sciences
Hungarian Academy of Sciences (RCNS HAS)
Magyar tudósok körútja 2.
H-1117 Budapest, Hungary
Phone: +36-1-382-6427
Web: http://bionano.ttk.mta.hu, 
CREDO SAXS instrument: http://credo.ttk.mta.hu



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Re: [gmx-users] Force Fields Keeping sp3 Nitrogen Groups Planar?

[David van der Spoel]

On 05/04/17 16:09, Phillip Rauscher wrote:

Thanks so much for the reply Mark!  For my own curiosity, is there a way
that people generally deal with neutral sp3 Nitogens?  They're chiral
centers on simulation time scales, but on macroscopic scales pyramidal
inversion eliminates that.
If we take ammonia NH3 as the simplest example, there is no reason why 
it could not invert. You would model this without any dihedral, just 
bond and angle potentials. If the three HNH angles are less than 120 the 
structure will be pyrimidal. Whether this yields a faithful 
representation of the inversion energy barrier is another matter, most 
likely the simulated barrier will be too high.


On Wed, Apr 5, 2017 at 1:16 AM, Mark Abraham 
wrote:


Hi,

Amide nitrogen atoms are trigonal planar because the group is planar.
There's no free rotation about the n-c bond, and the lone pair forms a
hybrid orbital with the carbonyl.

Mark

On Tue, 4 Apr 2017 18:05 Phillip Rauscher  wrote:


It occurs to me that an example would be helpful.  Here is an excerpt

from

the OPLS aminoacids.rtp file detailing alanine:


























*[ ALA ] [ atoms ]  Nopls_238   -0.500 1 Hopls_241
0.300 1 CAopls_224B   0.140 1 HAopls_140
0.060 1 CBopls_135   -0.180 2HB1opls_140
0.060 2HB2opls_1400.060 2HB3opls_140
0.060 2  Copls_2350.500 3 Oopls_236
-0.500 3 [ bonds ] N H NCACAHACACB
CA CCB   HB1CB   HB2CB   HB3 C O-C N [
impropers ]-CCA N Himproper_Z_N_X_Y CA+N
C Oimproper_O_C_X_Y *

We can see that the Nitrogen is bound to atoms H, CA, and -C (on the
previous residue).  In the [impropers] section, an improper dihedral is
defined for these four atoms (with the nitrogen in both of the dihedral
planes).  If we look at the definition of that improper in the OPLS
ffbonded.itp file, we see the following:













*[ dihedraltypes ]; Improper OPLS dihedrals to keep groups planar.; (OPLS
doesnt use impropers for chiral atoms).; Since these functions are

periodic

of the form 1-cos(2*x), they are actually; implemented as proper

dihedrals

[1+cos(2*x+180)] for the moment, ; to keep things compatible.; The

defines

are used in ffoplsaa.rtp or directly in your .top file; Z -N?-X -Y
improper torsion#define improper_Z_N_X_Y180.0  4.18400   2*
Given the functional form and the parameters used, this potential has
minima at 0 and 180 degrees, thus keeping all four atoms (centered at the
nitrogen) in the same plane.

On Tue, Apr 4, 2017 at 10:38 AM, Phillip Rauscher <

pmrausc...@uchicago.edu



wrote:


Hello all,

I've noticed that in some of the force fields (in the aminoacid.rtp
files), an improper dihedral is applied to the nitrogens in the peptide
bond (and sometimes other amine groups as well), which are all sp3
hybridized with one lone pair.  Interestingly, the dihedral potential
parameters serve to keep the groups trigonal planar, rather than
tetrahedral.  More specifically, I've seen this in OPLS, Amber03, and
Charmm27 - enough to indicate that it's not a mistake (besides the fact
that it's applied to ALL amino acids!)  The functional form of the

improper

potential varies between force fields, but the lowest energy angle is
always 0 or 180 indicating planar structure.

Why is this done?  I've done some digging through the GROMACS

publications

as well as those for the force fields and can't seem to find any

reference

to this practice?  Is it an attempt to "average out" nitrogen

inversions?

Is it just to eliminate a chiral center?

Thanks for your help!

-Phil Rauscher

--
Phil Rauscher
Graduate Student
de Pablo and Rowan Research Groups
Institute for Molecular Engineering
University of Chicago





--
Phil Rauscher
Graduate Student
de Pablo and Rowan Research Groups
Institute for Molecular Engineering
University of Chicago
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Head of Department, Cell & Molecular Biology, Uppsala University.
Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
http://www.icm.uu.se
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Gromacs Users 

[gmx-users] Position restraint on DPPC lipid bilayer

[Sithara Perera]

Hi!,

I'm really new to Gromacs and I' making a 512 DPPC bi-layer out of 128
bilayer available in http://www.cgmartini.nl. The force field used is
martini.

 But once the energy minimization is done, the bi layers crashes.

 So I made an position.itp file using the command


gmx genrestr -f dppc221.gro -n test.ndx -o lipid_posre.itp -fc 1000 1000
1000

And included in the topology file. Topology file also include

include "martini_v2.0.itp"
#include "martini_v2.0_lipids.itp"  from martini.



 But then when the command

gmx grompp -f minim.mdp -c dppc221.gro -p dppc_bilayer.top -o em2.tpr

is given , following error occurs.

Fatal error:
[ file posre.itp, line 29 ]:
Atom index (25) in position_restraints out of bounds (1-24).
This probably means that you have inserted topology section
"position_restraints"
in a part belonging to a different molecule than you intended to.
In that case move the "position_restraints" section to the right molecule.


How can I fix this?


Thank You,
Sithara
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Re: [gmx-users] g-C3N4 GROMOS parameters

[Lamm Gro]

Dear Morten ,

Greetings .
I exactly have the same question !
Did you find a way about doing simulation on g-C3N4 by GROMACS ?
I will be grateful if you can let me know about that.

Regards,
Saeed.


On Tue, Dec 6, 2016 at 1:13 AM, Morten  wrote:

> Hi,
>
>
> anyone got an idea of the best way to parameterize a g-C3N4 structure for
> the GROMOS force field? I am not sure if PRODRG will be useful as it is
> difficult to find properties to parameterize after. Any applicable
> literature is welcome :)
>
>
> Best regards
>
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[gmx-users] GROMACS3.3.1 - configure: error: invalid variable name: –-with-fft

[Simon Kit Sang Chu]

Hi everyone,

Due to some technical issues, I have to install gromacs 3.3.1 in order to
incorporate my desired forcefield. Following the instructions, I have to
switch the FFT library to fftpack. However, I run into this error whenever
I choose the option --with-fft, regardless the library chosen.

./configure –-with-fft=fftpack
configure: error: invalid variable name: –-with-fft


I checked ./configure and ./configure -h. Indeed, the option is available.

From ./configure,

--with-fft=[fftw3/fftw2/mkl(>=6.0)/fftpack]
  FFT library to use. fftw3 is default, fftpack
built
  in.


Would anyone kindly suggest possible solution or items that I could look
into?

Thank you.

Regards,
Simon
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Re: [gmx-users] PROTEIN FOLDING

[Vytautas Rakeviius]

Yes, you can open all structural output files with VMD. Or Chimera (tools MD so 
on).
 

On Thursday, April 6, 2017 9:56 AM, Neha Gupta  
wrote:
 

 Hi gromacs users,


I have run 2ns simulation of protein ligand complex using NVT ensemble
(after equilibration).


I want to know whether there is a structural/conformational change in the
protein especially in the active site where, the ligand forms hydrogen
bonds with the protein during simulation.


Can we visualize it? Is it possible?

Please let me know.


Thanks,
Neha
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[gmx-users] Building box arround given membrane with gmx solvate. As small as possible.

[Vytautas Rakeviius]

Hello,
I want to build box around my membrane with gmx solvate or sth. Ofc. I do not 
want water in side gap between membrane and box.
I do like this:
gmx editconf -f gap_processed.gro -o gap_newbox.gro -c -bt cubicI expect -d 0 
so everything packed in box as tightly as possible, but still after "gmx 
solvate" I see some water between box and membrane side.Maybe this is normal? 
Maybe I should do small run to let water flow away? Or maybe my command is 
wrong and I should make tight box in other way?
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[gmx-users] Free energy calculation .cpt file problem

[Anjali Patel]

Hello all:

I am following tutorial of Free energy calculation. But in first
equilibration i am not getting .cpt file.  Am i missing some step? Any
suggestions for that


With regards
Anjali Patel
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[gmx-users] PROTEIN FOLDING

[Neha Gupta]

Hi gromacs users,


I have run 2ns simulation of protein ligand complex using NVT ensemble
(after equilibration).


I want to know whether there is a structural/conformational change in the
protein especially in the active site where, the ligand forms hydrogen
bonds with the protein during simulation.


Can we visualize it? Is it possible?

Please let me know.


Thanks,
Neha
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Re: [gmx-users] gmx convert-tpr problem

[Mark Abraham]

Hi,

Yep.

If you want to end up with a series of numbered parts, then mdrun -noappend
is useful.

Mark

On Thu, 6 Apr 2017 02:43 Gregory Man Kai Poon  wrote:

> Hi Mark,
>
> To clarify, I should be calling mdrun like:
>
> gmx mdrun -s new.tpr -cpi old.cpt -deffnm old
>
> ?
>
> I apologize ahead if this sounds obvious.
>
> Kind regards,
> Gregory
>
> G
>
> et Outlook for Android
>
>
> From: Mark Abraham
> Sent: Wednesday, April 5, 19:25
> Subject: Re: [gmx-users] gmx convert-tpr problem
> To: Discussion list for GROMACS users
>
> Hi, As the messages suggest, if you would like to change the output names,
> you can't append. If you would like to append, don't change the output
> names. The old output files are there, but you've told mdrun to expect them
> to have different names, and to append to them, but used a checkpoint file
> that has different names. It doesn't know whether the error was in you
> using the wrong checkpoint file, or a mismatching output name, or that
> there are missing files, or that you don't want appending. Mark On Thu, 6
> Apr 2017 00:43 Gregory Man Kai Poon wrote: > Hello all: > > > I am having
> problems extending my runs using convert-tpr in GROMACS > 2016.1. In the
> latest instance, for example, I have a 100-ns run that I > want to extend
> to 200 ns. I used the convert-tpr command to get my new > .tpr file: > > >
> gmx convert-tpr -s md_0_100.tpr -until 200 -o md_100_200.tpr > > > With
> the new .tpr file in hand, I start mdrun: > > > gmx mdrun -s md_100_200.tpr
> -cpi md_0_100.cpt -v -deffnm
>  md_0_200 > > > At this point I get this error: > > > GROMACS: gmx mdrun,
> version 2016.1 > Executable: /usr/local/gromacs/bin/gmx > Data prefix:
> /usr/local/gromacs > Working dir: /media/i5/EXTREME 64/AGC_GTG2 > Command
> line: > gmx mdrun -s md_100_200.tpr -cpi md_0_100.cpt -v -deffnm md_100_200
> > > Output file appending has been requested, > but some output files
> listed in the checkpoint file md_0_100.cpt > are not present or not named
> as the output files by the current program: > Expect output files present:
> > > Expected output files not present or named differently: > md_0_100.log
> > md_0_100.xtc > md_0_100.trr > md_0_100.edr > >
> --- > Program: gmx
> mdrun, version 2016.1 > Source file:
> src/gromacs/mdrunutility/handlerestart.cpp (line 177) > > Fatal error: >
> File appending requested, but 4 of the 4 output files are not present or >
> are > named differently. For safety reasons, GROMACS-2016 and later only
> allows > file > appendi
>  ng to be used when all files have the same names as they had in the >
> original run. Checkpointing is merely intended for plain continuation of >
> runs. > For safety reasons you must specify all file names (e.g. with
> -deffnm), and > all these files must match the names used in the run prior
> to checkpointing > since we will append to them by default. If the files
> are not available, > you > can add the -noappend flag to mdrun and write
> separate new parts. For mere > concatenation of files, you should use the
> gmx trjcat tool instead. > > For more information and tips for
> troubleshooting, please check the GROMACS > website at
> https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.gromacs.org%2FDocumentation%2FErrors=02%7C01%7Cgpoon%40gsu.edu%7Ccd5f1661e0be4bfea85608d47c7b0a58%7C515ad73d8d5e4169895c9789dc742a70%7C0%7C0%7C636270315275689367=wud%2BY7HyhMxHQhwPzSzJ836fq8vKy%2FUj9BjZ0EMscBY%3D=0
> > ---
>  > > > I checked, double-checked, triple-checked that all the files the
> error is > referring to is in the working directory. In fact, all the files
> (the > md_0_100.* files from the previous run) as well as md_100_200.tpr
> are in > the same folder (the working directory), in which the mdrun
> command is > invoked. Any suggestions would be appreciated. > > > Kind
> regards, > > Gregory > > -- > Gromacs Users mailing list > > * Please
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