[gmx-users] Protein is Jumping from water Box

[Abid Channa]

Dear Gromacs users,
I have run 40 ns simulation , after 20 ns simulation my protein is continuously 
jumping from water Box. Is there any periodic boundary conditions issue with my 
system or an other error is that . Kindly give your valuable remarks.
Thanks,
Regards, 
Abid Ali Channa,
Junior Research Fellow,
Lab No.  P-133, Computational Chemistry Unit,
 Dr .Panjwani Center for Molecular Medicine and Drug Research (PCMD),
 International Center for Chemical and Biological Sciences  (ICCBS),
 University of Karachi-75270.Karachi-Pakistan.UAN # (92-21) 111-222-292 Ext. 
(309)
 Cell # +923013553051.
http://www.iccs.edu/
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Re: [gmx-users] 5. LINCS warning of QMMM simulation (andrian)

[andrian]

Hi,

thank you for your kindly reply...

system has been successfully minimized, restrained NVT/NPT equilibrated, 
and unrestrained Classical MM before... there is no problem..


*
here is my equilibrated structure (strarting configuration for qmmm)
Grunge ROck MAChoS
   20
1UNL  C1   2.600   2.380   2.439
1UNL C12   2.540   2.521   2.421
1UNL  H3   2.554   2.304   2.376
1UNL  O4   2.587   2.339   2.575
1UNL H15   2.708   2.376   2.422
1UNL C26   2.388   2.522   2.440
1UNL H27   2.554   2.559   2.319
1UNL CL8   2.612   2.651   2.519
1UNL C39   2.327   2.649   2.379
1UNL H3   10   2.363   2.497   2.543
1UNL H4   11   2.354   2.441   2.375
1UNL H5   12   2.287   2.725   2.447
1UNL H6   13   2.241   2.628   2.315
1UNL H7   14   2.400   2.708   2.323
1UNL H8   15   2.565   2.244   2.568
1UNL LA   16   2.464   2.521   2.430
2HOH  O   17   2.592   2.475   2.796
2HOH  H   18   2.684   2.494   2.769
2HOH H1   19   2.589   2.419   2.716
2HOH H2   20   2.560   2.560   2.760
   5.0   5.0   5.0
**
link atom is placed between C1 and C2 atoms, whereas its coordinate was 
calculated by x2 = [(0.153*x1)+ (0.153*x3)]/(0.153+0.153)..


do you have an idea ?

Cheers




On 27/04/16 01:48, Groenhof, Gerrit wrote:

Hi,

Are you able to run a stable MM simulation with that system?

Can you rule out that the system is not strained somewhere?

Where do the starting coordinates come from?

best,

Gerrit


Message: 5
Date: Tue, 26 Apr 2016 22:39:22 +0700
From: andrian 
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: [gmx-users] LINCS warning of QMMM simulation
Message-ID: <571f8baa.30...@gmail.com>
Content-Type: text/plain; charset=utf-8; format=flowed

Dear gromacs users

i was trying to simulate simple QMMM of 2-chlorobutanol versus
protonated water... my simulation was going well until LINCS warning
appeared.

"Step 34, time 0.017 (ps)  LINCS WARNING relative constraint deviation
after LINCS: rms 0.19, max 0.231421 (between atoms 2 and 6) bonds
that rotated more than 30 degrees"

i dont know whats the problem with the system or mdp setting...

any kind of help is really appreciated... thank you

cheers

*
here is my mdp file
title= my_mdp_file
cpp  = /lib/cpp
include  =
define   =

integrator   = md
tinit= 0
dt   = 0.0005
nsteps   = 1000 ; 2ps
nstcomm  = 10
comm_grps= system

nstxout  = 10
nstvout  = 10
nstfout  = 10
nstlog   = 10
nstenergy= 10
nstcalcenergy = 10
nstxtcout= 10
xtc_grps = system
energygrps   = QMatoms MMatoms

nstlist  = 10
ns_type  = grid
pbc  = xyz
rlist= 1

coulombtype  = Reaction-Field
rcoulomb = 1
epsilon_r= 1
epsilon_rf = 50
vdwtype  = cut-off
rvdw = 1
fourierspacing = 0.12
pme-order = 4
ewald-rtol = 1e-5
couple-intramol = no

tcoupl   = v-rescale
tc-grps  = MMatoms QMatoms
tau_t= 0.1 0  ; uncoupled QM atoms
ref_t= 300 300
pcoupl   = Berendsen
pcoupltype   = isotropic
tau_p= 1.0
compressibility  = 4.5e-5
ref_p= 1.0

QMMM = yes
QMMM-grps= QMatoms
QMmethod = RHF
QMbasis  = STO-3G
QMMMscheme   = normal
QMcharge = 1
QMmult = 1

gen_vel  = no
gen_temp = 300
gen_seed = 173529

constraints  = all-bonds
constraint_algorithm = LINCS
continuation = no
shake_sor = no
shake_tol= 0.0005
lincs_order  = 4
lincs_iter = 1
lincs_warnangle  = 30
morse= no
*

***
here is my topol.top

; alkohol_GMX.top created by acpype (Rev: 403) on Wed Apr 20 20:48:03 2016

[ defaults ]
; nbfunccomb-rule   gen-pairs   fudgeLJ fudgeQQ
1   2   yes 0.5 0.8333

; Include alkohol_GMX.itp topology
#include "alkohol.acpype/alkohol_GMX.itp"

; Include Position restraint file
#ifdef POSRES_ALKOHOL
#include "posre_alkohol.itp"
#endif

#include 

Re: [gmx-users] mdrun -rerun does not reproduce itself

[Szilárd Páll]

On Tue, Apr 26, 2016 at 10:48 PM, Mark Abraham 
wrote:

> Hi,
>
> Thanks (yet again) for your vigilance!
>
> On Tue, Apr 26, 2016 at 7:44 PM Christopher Neale <
> chris.ne...@alum.utoronto.ca> wrote:
>
> > Dear Users:
> >
> > I find that running gromacs 5.1.2 mdrun -rerun many times gives different
> > energies for some components.
>
>
> Indeed. This is the intended behaviour.
>
> Running floating-point code on different hardware is essentially guaranteed
> to be non-reproducible, because the order of operations will be different.
> In particular, accumulating hundreds of force components happens in a
> different order, and that can cause different round-off effects. You can
> certainly rotate your box 90 degrees and get a different energy. You can
> minimize the size of the effect by running in double precision (which rules
> out GPUs and gives up about half the speed on CPUs). We could re-write the
> code to accumulate in fixed precision (as AMBER now does), which would give
> reproducibility, subject to whatever rounding happens in practice (but this
> is useless except for verification, or permitting certain kinds of
> optimizations). Or you can run with mdrun -reprod, which is intended to
> eliminate all the differences that are possible. (IIRC, that is not
> implemented on GPUs, either.) All these implementations compute different
> approximations to the same numerical result. The open question is what
> quality of approximation is acceptable in practice. Merely implementing
> reproducibility doesn't address the question at all. The answer is unclear
> - one is typically anyway accepting error in
> * whatever choice for the order of force and energy floating-point
> reductions the code uses in practice
> * how likely it is that particle pairs not in the short-range list might
> drift inside the short-range interaction buffer (but this can't happen in
> reruns)
> * how faithfully PME models the full periodic electrostatics (ewald_rtol,
> FFT grid size, and spline interpolation order matter here),
> * the approximate enforcement of holonomic bond constraints (typical both
> for SHAKE and LINCS), and
> * using a model physics with static point partial charges (etc.)
> so the answer has to be empirical - at what point do you start seeing
> relevant differences in observables, and how much additional computer time
> (= reduced sampling) are you prepared to pay to correct that? It does at
> first seem reasonable to require that total energy (or the appropriate
> conserved quantity for the integrator) is in fact conserved over the course
> of the integration, but one still has to decide what tolerance is
> acceptable, and I'm aware of no study that makes a defensible conclusion...
>
> On GPUs I find that its the SR interactions (both LJ and q) that are
> > inconsistent.
>
>
> I believe that's because the scheduling of short-ranged kernels (and thus
> the order of the accumulation) is up to the CUDA runtime (but maybe Szilard
> will correct me).
>

The reason is the use of atomic operations (on floating point values) in
force accumulation of the short-range GPU kernels.

There are well-known ways around it and deterministic accumulation has been
on our todo list, but given other higher priority features and the plans to
rework the kernel infrastructure, it may be some time before this happens
-- unless somebody is keen on pitching in!

Cheers,
--
Szilárd



>
> On CPU only, I find that its the Coul. recip. that is inconsistent.
>
>
> That is likely caused by FFTW's auto-tuning deciding on a different codelet
> because whatever machine activity happens alongside mdrun was higher or
> lower each run. This is suppressed by mdrun -reprod.
>
>
> > On CPU only with NPME=1 I find consistency but I am surprised still by
> how
> > much the coulombic SR depends on the approach (see differences in average
> > value between the 3 approaches). Note that the issue here is not that the
> > rerun energies differ from the runtime energies, but that mdrun rerun is
> > not entirely reproducible compared to itself.
>
>
> It's expected, normal, and intended. If there's a problem someone can show,
> then we can discuss it. :-)
>
> Also note that differences in the Coul. SR but not the LJ SR  changes are
> > reflected in the last column, which is the total potential energy...
> > strange, and possibly off-topic to this post, but I note it in case some
> of
> > these differences might just be output related.
>
>
> Single-precision floating-point arithmetic is only accurate to about one
> part in 10^-7, so the round-off accumulated in the component (Coul. SR) of
> largest magnitude tends to dominate the round-off in the total.
>
>
> > There's also the difference between rows 5 and 6, where none of the
> > potential energy components changes, but the total does ch
> >  ange.
> >
>
> I can't think of a reason for that one.
>
>
> >
> > ### [GPU TEST] Note the differences down column 8 (LJ SR) and column 9 (q

Re: [gmx-users] 5. LINCS warning of QMMM simulation (andrian)

[andrian]

Hi,

thank you for your kindly reply...

system has been successfully minimized, restrained NVT/NPT equilibrated, 
and unrestrained Classical MM before... there is no problem..


*
here is my equilibrated structure (strarting configuration for qmmm)
Grunge ROck MAChoS
   20
1UNL  C1   2.600   2.380   2.439
1UNL C12   2.540   2.521   2.421
1UNL  H3   2.554   2.304   2.376
1UNL  O4   2.587   2.339   2.575
1UNL H15   2.708   2.376   2.422
1UNL C26   2.388   2.522   2.440
1UNL H27   2.554   2.559   2.319
1UNL CL8   2.612   2.651   2.519
1UNL C39   2.327   2.649   2.379
1UNL H3   10   2.363   2.497   2.543
1UNL H4   11   2.354   2.441   2.375
1UNL H5   12   2.287   2.725   2.447
1UNL H6   13   2.241   2.628   2.315
1UNL H7   14   2.400   2.708   2.323
1UNL H8   15   2.565   2.244   2.568
1UNL LA   16   2.464   2.521   2.430
2HOH  O   17   2.592   2.475   2.796
2HOH  H   18   2.684   2.494   2.769
2HOH H1   19   2.589   2.419   2.716
2HOH H2   20   2.560   2.560   2.760
   5.0   5.0   5.0
**
link atom is placed between C1 and C2 atoms, whereas its coordinate was 
calculated by x2 = [(0.153*x1)+ (0.153*x3)]/(0.153+0.153)..


do you have an idea ?

Cheers



On 27/04/16 01:48, Groenhof, Gerrit wrote:

Hi,

Are you able to run a stable MM simulation with that system?

Can you rule out that the system is not strained somewhere?

Where do the starting coordinates come from?

best,

Gerrit


Message: 5
Date: Tue, 26 Apr 2016 22:39:22 +0700
From: andrian 
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: [gmx-users] LINCS warning of QMMM simulation
Message-ID: <571f8baa.30...@gmail.com>
Content-Type: text/plain; charset=utf-8; format=flowed

Dear gromacs users

i was trying to simulate simple QMMM of 2-chlorobutanol versus
protonated water... my simulation was going well until LINCS warning
appeared.

"Step 34, time 0.017 (ps)  LINCS WARNING relative constraint deviation
after LINCS: rms 0.19, max 0.231421 (between atoms 2 and 6) bonds
that rotated more than 30 degrees"

i dont know whats the problem with the system or mdp setting...

any kind of help is really appreciated... thank you

cheers

*
here is my mdp file
title= my_mdp_file
cpp  = /lib/cpp
include  =
define   =

integrator   = md
tinit= 0
dt   = 0.0005
nsteps   = 1000 ; 2ps
nstcomm  = 10
comm_grps= system

nstxout  = 10
nstvout  = 10
nstfout  = 10
nstlog   = 10
nstenergy= 10
nstcalcenergy = 10
nstxtcout= 10
xtc_grps = system
energygrps   = QMatoms MMatoms

nstlist  = 10
ns_type  = grid
pbc  = xyz
rlist= 1

coulombtype  = Reaction-Field
rcoulomb = 1
epsilon_r= 1
epsilon_rf = 50
vdwtype  = cut-off
rvdw = 1
fourierspacing = 0.12
pme-order = 4
ewald-rtol = 1e-5
couple-intramol = no

tcoupl   = v-rescale
tc-grps  = MMatoms QMatoms
tau_t= 0.1 0  ; uncoupled QM atoms
ref_t= 300 300
pcoupl   = Berendsen
pcoupltype   = isotropic
tau_p= 1.0
compressibility  = 4.5e-5
ref_p= 1.0

QMMM = yes
QMMM-grps= QMatoms
QMmethod = RHF
QMbasis  = STO-3G
QMMMscheme   = normal
QMcharge = 1
QMmult = 1

gen_vel  = no
gen_temp = 300
gen_seed = 173529

constraints  = all-bonds
constraint_algorithm = LINCS
continuation = no
shake_sor = no
shake_tol= 0.0005
lincs_order  = 4
lincs_iter = 1
lincs_warnangle  = 30
morse= no
*

***
here is my topol.top

; alkohol_GMX.top created by acpype (Rev: 403) on Wed Apr 20 20:48:03 2016

[ defaults ]
; nbfunccomb-rule   gen-pairs   fudgeLJ fudgeQQ
1   2   yes 0.5 0.8333

; Include alkohol_GMX.itp topology
#include "alkohol.acpype/alkohol_GMX.itp"

; Include Position restraint file
#ifdef POSRES_ALKOHOL
#include "posre_alkohol.itp"
#endif

#include 

Re: [gmx-users] mdrun -rerun does not reproduce itself

[Christopher Neale]

Dear Mark:

Thank you very much for the detailed reply. Everything that you say makes 
sense. My motivation to investigate this is to predict hamiltonian replica 
exchange acceptance probabilities in order to develop a good schedule for 
hamiltonian changes. The energy difference within a given CPU architecture is 
quite small so even though noise in energy computation will technically 
invalidate the ensemble I don't expect it to have any real effect except 
possibly near absolute zero ;) The 0.125 kJ/mol variability that one can get on 
GPUs might start to have an effect in realistic systems if one is doing 
something like Hamiltonian exchange for a small alchemical change where the 
absolute energy differences are quite a bit smaller (with intra-ensemble energy 
distributions that are quite a bit narrower) than what one would get with 
temperature REMD. I don't even know if it would be an issue in that case, but 
it seems at least possible.

Thanks again, I really appreciate it.
Chris.


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

Sent: 26 April 2016 16:48:18
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] mdrun -rerun does not reproduce itself

Hi,

Thanks (yet again) for your vigilance!

On Tue, Apr 26, 2016 at 7:44 PM Christopher Neale <
chris.ne...@alum.utoronto.ca> wrote:

> Dear Users:
>
> I find that running gromacs 5.1.2 mdrun -rerun many times gives different
> energies for some components.


Indeed. This is the intended behaviour.

Running floating-point code on different hardware is essentially guaranteed
to be non-reproducible, because the order of operations will be different.
In particular, accumulating hundreds of force components happens in a
different order, and that can cause different round-off effects. You can
certainly rotate your box 90 degrees and get a different energy. You can
minimize the size of the effect by running in double precision (which rules
out GPUs and gives up about half the speed on CPUs). We could re-write the
code to accumulate in fixed precision (as AMBER now does), which would give
reproducibility, subject to whatever rounding happens in practice (but this
is useless except for verification, or permitting certain kinds of
optimizations). Or you can run with mdrun -reprod, which is intended to
eliminate all the differences that are possible. (IIRC, that is not
implemented on GPUs, either.) All these implementations compute different
approximations to the same numerical result. The open question is what
quality of approximation is acceptable in practice. Merely implementing
reproducibility doesn't address the question at all. The answer is unclear
- one is typically anyway accepting error in
* whatever choice for the order of force and energy floating-point
reductions the code uses in practice
* how likely it is that particle pairs not in the short-range list might
drift inside the short-range interaction buffer (but this can't happen in
reruns)
* how faithfully PME models the full periodic electrostatics (ewald_rtol,
FFT grid size, and spline interpolation order matter here),
* the approximate enforcement of holonomic bond constraints (typical both
for SHAKE and LINCS), and
* using a model physics with static point partial charges (etc.)
so the answer has to be empirical - at what point do you start seeing
relevant differences in observables, and how much additional computer time
(= reduced sampling) are you prepared to pay to correct that? It does at
first seem reasonable to require that total energy (or the appropriate
conserved quantity for the integrator) is in fact conserved over the course
of the integration, but one still has to decide what tolerance is
acceptable, and I'm aware of no study that makes a defensible conclusion...

On GPUs I find that its the SR interactions (both LJ and q) that are
> inconsistent.


I believe that's because the scheduling of short-ranged kernels (and thus
the order of the accumulation) is up to the CUDA runtime (but maybe Szilard
will correct me).

On CPU only, I find that its the Coul. recip. that is inconsistent.


That is likely caused by FFTW's auto-tuning deciding on a different codelet
because whatever machine activity happens alongside mdrun was higher or
lower each run. This is suppressed by mdrun -reprod.


> On CPU only with NPME=1 I find consistency but I am surprised still by how
> much the coulombic SR depends on the approach (see differences in average
> value between the 3 approaches). Note that the issue here is not that the
> rerun energies differ from the runtime energies, but that mdrun rerun is
> not entirely reproducible compared to itself.


It's expected, normal, and intended. If there's a problem someone can show,
then we can discuss it. :-)

Also note that differences in the Coul. SR but not the LJ SR  changes are
> reflected in the last 

Re: [gmx-users] mdp options to generate xtc file but not trr file

[Justin Lemkul]

On 4/26/16 5:11 PM, Metallo Devasto wrote:

How can i set mdp option to have a simulation that generate only the xtc
file but without the trr file? ( i don't need trr and it has 2 times the
size of the xtc file)

my mdp option now are

nstxout = 1000
nstvout = 1000


Set the above two options to zero.


nstfout = 0
nstlog = 100
nstenergy = 100
nstxtcout = 100


This gets you an .xtc (in versions < 5.0, after that it's nstxout-compressed).


nstcalcenergy = -1
xtcprecision = 10


I would say it is unwise to reduce the .xtc precision by 100x.

-Justin


xtc-grps = system
energygrps = Protein Membrane Solvent


i cant figure out how to do it, pls help :(



--
==

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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* Please search the archive at 
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mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] DSSP with custom residues

[Justin Lemkul]

On 4/26/16 1:10 PM, leila salimi wrote:

Thanks very much.

I have one problem, I am trying to use xpm2ps to plot the secondary
structure!
I used the m2p file from this link:

http://ringo.ams.sunysb.edu/index.php/MD_Simulation:_Protein_in_Water_(Pt._2)

My problem is that the plot is not correct. I tried different xbox and ybox
but it is not working and I got confused!

I have 10 residues and 400 ns time simulations ( 80001 frames).
For this file how can I  fix the xbox and ybox parameters?



Well, your x-axis will be 800x longer than your y-axis by default, so do the 
math (simple proportions!) to generate a suitably sized rectangular plot.


-Justin



Thanks in advance,

On Tue, Apr 26, 2016 at 3:12 PM, Justin Lemkul  wrote:




On 4/26/16 9:10 AM, leila salimi wrote:


Hi Justin,

I am also busy by DSSP analysis. I am interested to know what the
difference between do_dssp and dssp is?



dssp is a binary that actually carries out the DSSP analysis; it is not a
GROMACS program but is downloaded from an external source.  do_dssp is a
GROMACS module that is just a wrapper - it runs through a trajectory, pulls
out the coordinates to a temporary file (those dd files that show up),
passes those coordinates to dssp, and records the output.  GROMACS doesn't
do secondary structure calculations natively, instead relying on dssp.

-Justin


Regards,

Leila

On Tue, Apr 26, 2016 at 3:00 PM, Justin Lemkul  wrote:




On 4/26/16 8:57 AM, Stephanie Jephthah wrote:

Hi!


I'm simulating a protein conjugate and thus uses custom residues. Is
there
any way to make the dssp program aware of the custom residues (and does
it
make sense to do so)? I'm using gromacs 4.6.7 and the "new" dssp. I'm
assuming that the problem is not with do_dssp but with dssp, but please
correct me if I'm wrong.


If you've got custom residues as integral parts of the protein, they

need
to be defined as such in residuetypes.dat, or otherwise defined in a
suitable custom index group.  Presumably you have to have done one or the
other before running the simulation.  If the custom residues have normal
amino acid backbone features, doing DSSP analysis makes sense.  If
something is failing, run dssp directly, not via do_dssp, to determine if
the failure is within dssp or do_dssp.

-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

==
--
Gromacs Users mailing list

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

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

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



--
==

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

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

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

==
--
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[gmx-users] mdp options to generate xtc file but not trr file

[Metallo Devasto]

How can i set mdp option to have a simulation that generate only the xtc
file but without the trr file? ( i don't need trr and it has 2 times the
size of the xtc file)

my mdp option now are

nstxout = 1000
nstvout = 1000
nstfout = 0
nstlog = 100
nstenergy = 100
nstxtcout = 100
nstcalcenergy = -1
xtcprecision = 10
xtc-grps = system
energygrps = Protein Membrane Solvent


i cant figure out how to do it, pls help :(
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Re: [gmx-users] mdrun -rerun does not reproduce itself

[Mark Abraham]

Hi,

Thanks (yet again) for your vigilance!

On Tue, Apr 26, 2016 at 7:44 PM Christopher Neale <
chris.ne...@alum.utoronto.ca> wrote:

> Dear Users:
>
> I find that running gromacs 5.1.2 mdrun -rerun many times gives different
> energies for some components.


Indeed. This is the intended behaviour.

Running floating-point code on different hardware is essentially guaranteed
to be non-reproducible, because the order of operations will be different.
In particular, accumulating hundreds of force components happens in a
different order, and that can cause different round-off effects. You can
certainly rotate your box 90 degrees and get a different energy. You can
minimize the size of the effect by running in double precision (which rules
out GPUs and gives up about half the speed on CPUs). We could re-write the
code to accumulate in fixed precision (as AMBER now does), which would give
reproducibility, subject to whatever rounding happens in practice (but this
is useless except for verification, or permitting certain kinds of
optimizations). Or you can run with mdrun -reprod, which is intended to
eliminate all the differences that are possible. (IIRC, that is not
implemented on GPUs, either.) All these implementations compute different
approximations to the same numerical result. The open question is what
quality of approximation is acceptable in practice. Merely implementing
reproducibility doesn't address the question at all. The answer is unclear
- one is typically anyway accepting error in
* whatever choice for the order of force and energy floating-point
reductions the code uses in practice
* how likely it is that particle pairs not in the short-range list might
drift inside the short-range interaction buffer (but this can't happen in
reruns)
* how faithfully PME models the full periodic electrostatics (ewald_rtol,
FFT grid size, and spline interpolation order matter here),
* the approximate enforcement of holonomic bond constraints (typical both
for SHAKE and LINCS), and
* using a model physics with static point partial charges (etc.)
so the answer has to be empirical - at what point do you start seeing
relevant differences in observables, and how much additional computer time
(= reduced sampling) are you prepared to pay to correct that? It does at
first seem reasonable to require that total energy (or the appropriate
conserved quantity for the integrator) is in fact conserved over the course
of the integration, but one still has to decide what tolerance is
acceptable, and I'm aware of no study that makes a defensible conclusion...

On GPUs I find that its the SR interactions (both LJ and q) that are
> inconsistent.


I believe that's because the scheduling of short-ranged kernels (and thus
the order of the accumulation) is up to the CUDA runtime (but maybe Szilard
will correct me).

On CPU only, I find that its the Coul. recip. that is inconsistent.


That is likely caused by FFTW's auto-tuning deciding on a different codelet
because whatever machine activity happens alongside mdrun was higher or
lower each run. This is suppressed by mdrun -reprod.


> On CPU only with NPME=1 I find consistency but I am surprised still by how
> much the coulombic SR depends on the approach (see differences in average
> value between the 3 approaches). Note that the issue here is not that the
> rerun energies differ from the runtime energies, but that mdrun rerun is
> not entirely reproducible compared to itself.


It's expected, normal, and intended. If there's a problem someone can show,
then we can discuss it. :-)

Also note that differences in the Coul. SR but not the LJ SR  changes are
> reflected in the last column, which is the total potential energy...
> strange, and possibly off-topic to this post, but I note it in case some of
> these differences might just be output related.


Single-precision floating-point arithmetic is only accurate to about one
part in 10^-7, so the round-off accumulated in the component (Coul. SR) of
largest magnitude tends to dominate the round-off in the total.


> There's also the difference between rows 5 and 6, where none of the
> potential energy components changes, but the total does ch
>  ange.
>

I can't think of a reason for that one.


>
> ### [GPU TEST] Note the differences down column 8 (LJ SR) and column 9 (q
> SR)
>
> $ for((i=1;i<=10;i++)); do
> ~/exec/GROMACS/exec/gromacs-5.1.2/gpu_serial/bin/gmx mdrun -notunepme -dlb
> yes -npme 0 -cpt 60 -gpu_id 0123 -ntmpi 4 -ntomp 6 -rerun TEMP.xtc -s
> MD2.tpr -deffnm SAME >/dev/null 2>&1; echo "1 2 3 4 5 6 7 8 9 10" | gmx
> energy -f SAME.edr -o epot_SAME.xvg -xvg none >/dev/null 2>&1; tail -n 1
> epot_SAME.xvg; done
>
>  2000.00  22256.701172  121366.734375  69411.359375  813.758789
> 12650.896484  -141897.171875  23329.945312  -932386.625000  4761.907227
> -819692.50
>  2000.00  22256.701172  121366.734375  69411.359375  813.758789
> 12650.896484  -141897.171875  23329.947266  -932386.75  4761.907227
> 

[gmx-users] mdrun -rerun does not reproduce itself

[Christopher Neale]

Dear Users:

I find that running gromacs 5.1.2 mdrun -rerun many times gives different 
energies for some components. On GPUs I find that its the SR interactions (both 
LJ and q) that are inconsistent. On CPU only, I find that its the Coul. recip. 
that is inconsistent. On CPU only with NPME=1 I find consistency but I am 
surprised still by how much the coulombic SR depends on the approach (see 
differences in average value between the 3 approaches). Note that the issue 
here is not that the rerun energies differ from the runtime energies, but that 
mdrun rerun is not entirely reproducible compared to itself. Also note that 
differences in the Coul. SR but not the LJ SR  changes are reflected in the 
last column, which is the total potential energy... strange, and possibly 
off-topic to this post, but I note it in case some of these differences might 
just be output related. There's also the difference between rows 5 and 6, where 
none of the potential energy components changes, but the total does ch
 ange.

### [GPU TEST] Note the differences down column 8 (LJ SR) and column 9 (q SR)

$ for((i=1;i<=10;i++)); do ~/exec/GROMACS/exec/gromacs-5.1.2/gpu_serial/bin/gmx 
mdrun -notunepme -dlb yes -npme 0 -cpt 60 -gpu_id 0123 -ntmpi 4 -ntomp 6 -rerun 
TEMP.xtc -s MD2.tpr -deffnm SAME >/dev/null 2>&1; echo "1 2 3 4 5 6 7 8 9 10" | 
gmx energy -f SAME.edr -o epot_SAME.xvg -xvg none >/dev/null 2>&1; tail -n 1 
epot_SAME.xvg; done

 2000.00  22256.701172  121366.734375  69411.359375  813.758789  
12650.896484  -141897.171875  23329.945312  -932386.625000  4761.907227  
-819692.50
 2000.00  22256.701172  121366.734375  69411.359375  813.758789  
12650.896484  -141897.171875  23329.947266  -932386.75  4761.907227  
-819692.625000
 2000.00  22256.701172  121366.734375  69411.359375  813.758789  
12650.896484  -141897.171875  23329.945312  -932386.75  4761.907227  
-819692.625000
 2000.00  22256.701172  121366.734375  69411.359375  813.758789  
12650.896484  -141897.171875  23329.943359  -932386.75  4761.907227  
-819692.625000
 2000.00  22256.701172  121366.734375  69411.359375  813.758789  
12650.896484  -141897.171875  23329.945312  -932386.75  4761.907227  
-819692.625000
 2000.00  22256.701172  121366.734375  69411.359375  813.758789  
12650.896484  -141897.171875  23329.945312  -932386.75  4761.907227  
-819692.687500
 2000.00  22256.701172  121366.734375  69411.359375  813.758789  
12650.896484  -141897.171875  23329.945312  -932386.75  4761.907227  
-819692.625000
 2000.00  22256.701172  121366.734375  69411.359375  813.758789  
12650.896484  -141897.171875  23329.945312  -932386.687500  4761.907227  
-819692.562500
 2000.00  22256.701172  121366.734375  69411.359375  813.758789  
12650.896484  -141897.171875  23329.945312  -932386.75  4761.907227  
-819692.625000
 2000.00  22256.701172  121366.734375  69411.359375  813.758789  
12650.896484  -141897.171875  23329.943359  -932386.625000  4761.907227  
-819692.50


### [CPU TEST] Note the differences down column 9 (Coul. recip.). However, note 
that Coul. recip. changes are again not reflected in the last column, which is 
the total potential energy.

$ for((i=1;i<=10;i++)); do ~/exec/GROMACS/exec/gromacs-5.1.2/serial/bin/gmx 
mdrun -notunepme -dlb yes -npme 0 -cpt 60 -ntmpi 4 -ntomp 6 -rerun TEMP.xtc -s 
MD2.tpr -deffnm SAME >/dev/null 2>&1; echo "1 2 3 4 5 6 7 8 9 10" | gmx energy 
-f SAME.edr -o epot_SAME.xvg -xvg none >/dev/null 2>&1; tail -n 1 
epot_SAME.xvg; done

 2000.00  22256.705078  121366.718750  69411.343750  813.758789  
12650.895508  -141897.234375  23329.876953  -932379.437500  4761.906738  
-819685.437500
 2000.00  22256.705078  121366.718750  69411.343750  813.758789  
12650.895508  -141897.234375  23329.876953  -932379.437500  4761.907227  
-819685.437500
 2000.00  22256.705078  121366.718750  69411.343750  813.758789  
12650.895508  -141897.234375  23329.876953  -932379.437500  4761.907227  
-819685.437500
 2000.00  22256.705078  121366.718750  69411.343750  813.758789  
12650.895508  -141897.234375  23329.876953  -932379.437500  4761.907227  
-819685.437500
 2000.00  22256.705078  121366.718750  69411.343750  813.758789  
12650.895508  -141897.234375  23329.876953  -932379.437500  4761.906738  
-819685.437500
 2000.00  22256.705078  121366.718750  69411.343750  813.758789  
12650.895508  -141897.234375  23329.876953  -932379.437500  4761.907227  
-819685.437500
 2000.00  22256.705078  121366.718750  69411.343750  813.758789  
12650.895508  -141897.234375  23329.876953  -932379.437500  4761.907227  
-819685.437500
 2000.00  22256.705078  121366.718750  69411.343750  813.758789  
12650.895508  -141897.234375  23329.876953  -932379.437500  4761.907227  
-819685.437500
 2000.00  22256.705078  121366.718750  69411.343750  813.758789  
12650.895508  -141897.234375  23329.876953  -932379.437500  4761.907227  
-819685.437500
 2000.00  

Re: [gmx-users] DSSP with custom residues

[leila salimi]

Thanks very much.

I have one problem, I am trying to use xpm2ps to plot the secondary
structure!
I used the m2p file from this link:

http://ringo.ams.sunysb.edu/index.php/MD_Simulation:_Protein_in_Water_(Pt._2)

My problem is that the plot is not correct. I tried different xbox and ybox
but it is not working and I got confused!

I have 10 residues and 400 ns time simulations ( 80001 frames).
For this file how can I  fix the xbox and ybox parameters?


Thanks in advance,

On Tue, Apr 26, 2016 at 3:12 PM, Justin Lemkul  wrote:

>
>
> On 4/26/16 9:10 AM, leila salimi wrote:
>
>> Hi Justin,
>>
>> I am also busy by DSSP analysis. I am interested to know what the
>> difference between do_dssp and dssp is?
>>
>>
> dssp is a binary that actually carries out the DSSP analysis; it is not a
> GROMACS program but is downloaded from an external source.  do_dssp is a
> GROMACS module that is just a wrapper - it runs through a trajectory, pulls
> out the coordinates to a temporary file (those dd files that show up),
> passes those coordinates to dssp, and records the output.  GROMACS doesn't
> do secondary structure calculations natively, instead relying on dssp.
>
> -Justin
>
>
> Regards,
>> Leila
>>
>> On Tue, Apr 26, 2016 at 3:00 PM, Justin Lemkul  wrote:
>>
>>
>>>
>>> On 4/26/16 8:57 AM, Stephanie Jephthah wrote:
>>>
>>> Hi!

 I'm simulating a protein conjugate and thus uses custom residues. Is
 there
 any way to make the dssp program aware of the custom residues (and does
 it
 make sense to do so)? I'm using gromacs 4.6.7 and the "new" dssp. I'm
 assuming that the problem is not with do_dssp but with dssp, but please
 correct me if I'm wrong.


 If you've got custom residues as integral parts of the protein, they
>>> need
>>> to be defined as such in residuetypes.dat, or otherwise defined in a
>>> suitable custom index group.  Presumably you have to have done one or the
>>> other before running the simulation.  If the custom residues have normal
>>> amino acid backbone features, doing DSSP analysis makes sense.  If
>>> something is failing, run dssp directly, not via do_dssp, to determine if
>>> the failure is within dssp or do_dssp.
>>>
>>> -Justin
>>>
>>> --
>>> ==
>>>
>>> Justin A. Lemkul, Ph.D.
>>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>>
>>> Department of Pharmaceutical Sciences
>>> School of Pharmacy
>>> Health Sciences Facility II, Room 629
>>> University of Maryland, Baltimore
>>> 20 Penn St.
>>> Baltimore, MD 21201
>>>
>>> jalem...@outerbanks.umaryland.edu | (410) 706-7441
>>> http://mackerell.umaryland.edu/~jalemkul
>>>
>>> ==
>>>
>>> --
>>> Gromacs Users mailing list
>>>
>>> * Please search the archive at
>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>>> posting!
>>>
>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>
>>> * For (un)subscribe requests visit
>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>>> send a mail to gmx-users-requ...@gromacs.org.
>>>
>>>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
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>
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Re: [gmx-users] Constant Density

[Smith, Micholas D.]

Hi Anthony,

One possible way I can think of to get the water to redistribute is to perform 
some temperature annealing of just the solvent, i.e. raise the temperature 
every so many steps to a max ~500K then quickly quench (lower the temperature) 
the solvent back to the physiological regime. Repeat this a few cycles to make 
sure you've redistributed the water as you expect. Just make sure to hold the 
protein fixed with restraints. After it has done a few cycles (maybe 5 or so), 
try running with NVT at the proper temperature for both protein+solvent 
(typical NVT simulation). You should note that the water will not remain 
"uniformly" distributed; though, as it will tend toward its equilibrium values 
so your system should be considered non-equilibrium MD (thought the extent of 
how long it takes to relax to the standard state, may allow you to approximate 
it as quasi-equilibrium)

There may be other ways to do this as well.

-Micholas


From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on behalf of Nash, Anthony 

Sent: Tuesday, April 26, 2016 9:29 AM
To: gmx-us...@gromacs.org
Subject: [gmx-users] Constant Density

Hi all,

At the risk of bending the rules of thermodynamics, I¹m wondering whether
Gromacs can maintain density of a water box (0.750 g/L density of water in
a collagen fibril environment) whilst applying an NPT ensemble?

gmx_d solvate, fills up to 2/3 of my truncated oct cell, with my protein
at the centre. An NVT simulation does not redistribute the water. To do
this I need to perform an NPT run, but even so this rapidly shrinks the
box.

I have considering looking up the necessary pressure value for this
density, however I¹m a bit uncertain whether this maintains any
physiological realism for the protein itself.

I¹ve tried googling with little success.

Any thoughts are appreciated.
Thanks
Anthony

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Re: [gmx-users] Bash scripting and Gromacs

[Mark Abraham]

Or since you have a highly predictable sequence of integers, use a loop
over them! Bash built in printf can also be useful here. Stackoverflow.com
is a good friend for recipes.

Mark

On Tue, 26 Apr 2016 17:52 Fabricio Cannini  wrote:

> On 26-04-2016 10:33, James Starlight wrote:
> > No, in my case it recognize ? like a ?
> >
> > in script I have
> >
> > for sim in ${HOME}/${tit}* ; do
> >   if [[ -d $sim ]]; then
> >simulation=$(basename "$sim")
> >cd ${sim}
> >rm dd_dump_err*.pdb
> >trjconv -s md_${tit}?.tpr -f md_${tit}?.trr -o
> > ${HOME}/output/${simulation}.xtc -n -pbc mol -ur compact -fit trans  <
> > ${HOME}/enter.txt
> >
> > and gromacs sent
> >
> >trjconv -s md_resp_complex?.tpr -f md_resp_complex?.trr -o
> >
> /nfs_homes/clouddyn/MD_bench/Resp_cyt_cluster/output/resp_complex_conf7.xtc
> > -n -pbc mol -ur compact -fit trans
> >
> >
> > Is it possible specify more flexible e.g 1 of any character or 2 of
> > any characters within the file name etc like REGEX syntax
> >
> > Thanks!
>
> Brace expansion can be useful in such cases too:
> http://www.thegeekstuff.com/2010/06/bash-shell-brace-expansion/
>
> --
> 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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>
> * 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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Re: [gmx-users] Bash scripting and Gromacs

[Fabricio Cannini]

On 26-04-2016 10:33, James Starlight wrote:

No, in my case it recognize ? like a ?

in script I have

for sim in ${HOME}/${tit}* ; do
  if [[ -d $sim ]]; then
   simulation=$(basename "$sim")
   cd ${sim}
   rm dd_dump_err*.pdb
   trjconv -s md_${tit}?.tpr -f md_${tit}?.trr -o
${HOME}/output/${simulation}.xtc -n -pbc mol -ur compact -fit trans  <
${HOME}/enter.txt

and gromacs sent

   trjconv -s md_resp_complex?.tpr -f md_resp_complex?.trr -o
/nfs_homes/clouddyn/MD_bench/Resp_cyt_cluster/output/resp_complex_conf7.xtc
-n -pbc mol -ur compact -fit trans


Is it possible specify more flexible e.g 1 of any character or 2 of
any characters within the file name etc like REGEX syntax

Thanks!


Brace expansion can be useful in such cases too:
http://www.thegeekstuff.com/2010/06/bash-shell-brace-expansion/

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Re: [gmx-users] DSSP with custom residues

[Stephanie Jephthah]

Ok. Thank you very much!

//Stephanie
Den 26 apr 2016 15:00 skrev "Justin Lemkul" :

>
>
> On 4/26/16 8:57 AM, Stephanie Jephthah wrote:
>
>> Hi!
>>
>> I'm simulating a protein conjugate and thus uses custom residues. Is there
>> any way to make the dssp program aware of the custom residues (and does it
>> make sense to do so)? I'm using gromacs 4.6.7 and the "new" dssp. I'm
>> assuming that the problem is not with do_dssp but with dssp, but please
>> correct me if I'm wrong.
>>
>>
> If you've got custom residues as integral parts of the protein, they need
> to be defined as such in residuetypes.dat, or otherwise defined in a
> suitable custom index group.  Presumably you have to have done one or the
> other before running the simulation.  If the custom residues have normal
> amino acid backbone features, doing DSSP analysis makes sense.  If
> something is failing, run dssp directly, not via do_dssp, to determine if
> the failure is within dssp or do_dssp.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==
> --
> Gromacs Users mailing list
>
> * Please search the archive at
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> posting!
>
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[gmx-users] LINCS warning of QMMM simulation

[andrian]

Dear gromacs users

i was trying to simulate simple QMMM of 2-chlorobutanol versus 
protonated water... my simulation was going well until LINCS warning 
appeared.


"Step 34, time 0.017 (ps)  LINCS WARNING relative constraint deviation 
after LINCS: rms 0.19, max 0.231421 (between atoms 2 and 6) bonds 
that rotated more than 30 degrees"


i dont know whats the problem with the system or mdp setting...

any kind of help is really appreciated... thank you

cheers

*
here is my mdp file
title= my_mdp_file
cpp  = /lib/cpp
include  =
define   =

integrator   = md
tinit= 0
dt   = 0.0005
nsteps   = 1000 ; 2ps
nstcomm  = 10
comm_grps= system

nstxout  = 10
nstvout  = 10
nstfout  = 10
nstlog   = 10
nstenergy= 10
nstcalcenergy = 10
nstxtcout= 10
xtc_grps = system
energygrps   = QMatoms MMatoms

nstlist  = 10
ns_type  = grid
pbc  = xyz
rlist= 1

coulombtype  = Reaction-Field
rcoulomb = 1
epsilon_r= 1
epsilon_rf = 50
vdwtype  = cut-off
rvdw = 1
fourierspacing = 0.12
pme-order = 4
ewald-rtol = 1e-5
couple-intramol = no

tcoupl   = v-rescale
tc-grps  = MMatoms QMatoms
tau_t= 0.1 0  ; uncoupled QM atoms
ref_t= 300 300
pcoupl   = Berendsen
pcoupltype   = isotropic
tau_p= 1.0
compressibility  = 4.5e-5
ref_p= 1.0

QMMM = yes
QMMM-grps= QMatoms
QMmethod = RHF
QMbasis  = STO-3G
QMMMscheme   = normal
QMcharge = 1
QMmult = 1

gen_vel  = no
gen_temp = 300
gen_seed = 173529

constraints  = all-bonds
constraint_algorithm = LINCS
continuation = no
shake_sor = no
shake_tol= 0.0005
lincs_order  = 4
lincs_iter = 1
lincs_warnangle  = 30
morse= no
*

***
here is my topol.top

; alkohol_GMX.top created by acpype (Rev: 403) on Wed Apr 20 20:48:03 2016

[ defaults ]
; nbfunccomb-rule   gen-pairs   fudgeLJ fudgeQQ
1   2   yes 0.5 0.8333

; Include alkohol_GMX.itp topology
#include "alkohol.acpype/alkohol_GMX.itp"

; Include Position restraint file
#ifdef POSRES_ALKOHOL
#include "posre_alkohol.itp"
#endif

#include "waterH.acpype/waterH_GMX.itp"

; Include Position restraint file
#ifdef POSRES_WATER
#include "posre_water.itp"
#endif

[ system ]
 alkohol

[ molecules ]
; Compoundnmols
alkohol   1
waterH  1


*
here is my alkohol itp file

; alkohol_GMX.itp created by acpype (Rev: 403) on Wed Apr 20 20:48:03 2016

[ atomtypes ]
;name   bond_type at.nummass charge   ptype   sigma 
epsilon   Amb
 c3   c3  60.0  0.0   A 3.39967e-01 4.57730e-01 
; 1.91  0.1094
 h1   h1  10.0  0.0   A 2.47135e-01 6.56888e-02 
; 1.39  0.0157
 oh   oh  80.0  0.0   A 3.06647e-01 8.80314e-01 
; 1.72  0.2104
 cl   cl 170.0  0.0   A 3.47094e-01 1.10876e+00 
; 1.95  0.2650
 hc   hc  10.0  0.0   A 2.64953e-01 6.56888e-02 
; 1.49  0.0157
 ho   ho  10.0  0.0   A 0.0e+00 0.0e+00 
; 0.00  0.

 LA  LA  10.0  0.0   A 0.00+00 0.0e+00

[ moleculetype ]
;namenrexcl
 alkohol  3

[ atoms ]
;   nr  type  resi  res  atom  cgnr charge  mass   ; qtot   
bond_type

 1   c3 1   UNL C1 0.122400 12.01000 ; qtot 0.122
 2   c3 1   UNLC12 0.015700 12.01000 ; qtot 0.138
 3   h1 1   UNL H3 0.058200  1.00800 ; qtot 0.196
 4   oh 1   UNL O4-0.593801 16.0 ; qtot -0.398
 5   h1 1   UNLH15 0.058200  1.00800 ; qtot -0.339
 6   c3 1   UNLC26-0.083400 12.01000 ; qtot -0.423
 7   h1 1   UNLH27 0.086700  1.00800 ; qtot -0.336
 8   cl 1   UNLCL8-0.208400 35.45000 ; qtot -0.544
 9   c3 1   UNLC39-0.097100 12.01000 ; qtot -0.642
10   hc 1   UNLH3   10 0.053700  1.00800 ; qtot -0.588
11   hc 

Re: [gmx-users] Higher Density than Expected

[Tsjerk Wassenaar]

Hey :)

Salt water has a higher density than pure water anyway.

Cheers,

Tsjerk
On Apr 26, 2016 5:19 PM, "Christopher Schlicksup" 
wrote:

> Thanks Justin. I was expecting closer to 1000kg/m^3. My reading about the
> tip3p water model found approximately this value at 300K, and it is also
> the approximate experimental value. So I guess my question was whether
> 1025kg/m^3 was off enough to be a concern.
>
> I think you answered the question: that the system is too inhomogeneous to
> pay that close attention to the absolute density value. Thanks again.
>
>
>
> > Date: Mon, 25 Apr 2016 17:13:01 -0400
> > From: Justin Lemkul 
> > To: gmx-us...@gromacs.org
> > Subject: Re: [gmx-users] Higher Density than Expected
> > Message-ID: <571e885d.2030...@vt.edu>
> > Content-Type: text/plain; charset=windows-1252; format=flowed
> >
> >
> >
> > On 4/25/16 5:09 PM, Christopher Schlicksup wrote:
> > > Hi, I am fairly new to simulation, and would like some input about
> > whether
> > > I have set up Gromacs correcly. I am using version 5.0.4 with the
> > > CHARMM36-Jun2015 force field and the TIP3P water model. I am
> simulating a
> > > 35kDa protein in a dodecahedron box (-d 1.6) with 150mM NaCl plus
> > > neutralizing ions.
> > >
> > > I do a 200ps NVT equilibration followed by a 500ps NPT equilibration
> > > followed by 230ps of production run where the protein is unrestrained.
> My
> > > observations so far are that the density is higher than I would expect
> > from
> > > reading literature. I would appreciate any insight into whether I have
> a
> > > problem, or if my density and pressure values look acceptable. Thanks
> in
> > > advance
> > >
> >
> > What value do you expect from the literature?  The density of such an
> > inhomogeneous system is rather useless.  Everything looks fine to me.
> >
> > -Justin
> >
> > > Here are my results from gmx energy:
> > >
> > > *Energy minimization*
> > >
> > > Energy  Average   Err.Est.   RMSD  Tot-Drift
> > >
> >
> ---
> > > Potential-1.93229e+06  2900077735.5-189748
> > > (kJ/mol)
> > >
> > >
> > > *NVT Equilibration 200ps*
> > >
> > > Energy  Average   Err.Est.   RMSD  Tot-Drift
> > >
> >
> ---
> > > Temperature   299.9  0.0992.59846   0.560458
> (K)
> > >
> > >
> > > *NPT Equilibration 500ps*
> > >
> > > Energy  Average   Err.Est.   RMSD  Tot-Drift
> > >
> >
> ---
> > > Pressure1.528921.781.007911.2974
> > (bar)
> > > Density 1024.74  0.0571.70907 -0.0499058
> > > (kg/m^3)
> > > Volume  1168.76  0.0651.96293  0.0505822
> > (nm^3)
> > >
> > >
> > > *Production Run 230ps*
> > >
> > > Energy  Average   Err.Est.   RMSD  Tot-Drift
> > >
> >
> ---
> > > Pressure   0.450022   0.6575.3012   0.157248
> > (bar)
> > > Density  1025.4  0.0481.39937  -0.209504
> > > (kg/m^3)
> > > Volume  1168.01  0.0551.59374   0.238338
> > (nm^3)
> > >
> >
> > --
> > ==
> >
> > Justin A. Lemkul, Ph.D.
> > Ruth L. Kirschstein NRSA Postdoctoral Fellow
> >
> > Department of Pharmaceutical Sciences
> > School of Pharmacy
> > Health Sciences Facility II, Room 629
> > University of Maryland, Baltimore
> > 20 Penn St.
> > Baltimore, MD 21201
> >
> > jalem...@outerbanks.umaryland.edu | (410) 706-7441
> > http://mackerell.umaryland.edu/~jalemkul
> >
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
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Re: [gmx-users] Higher Density than Expected

[Christopher Schlicksup]

Thanks Justin. I was expecting closer to 1000kg/m^3. My reading about the
tip3p water model found approximately this value at 300K, and it is also
the approximate experimental value. So I guess my question was whether
1025kg/m^3 was off enough to be a concern.

I think you answered the question: that the system is too inhomogeneous to
pay that close attention to the absolute density value. Thanks again.



> Date: Mon, 25 Apr 2016 17:13:01 -0400
> From: Justin Lemkul 
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] Higher Density than Expected
> Message-ID: <571e885d.2030...@vt.edu>
> Content-Type: text/plain; charset=windows-1252; format=flowed
>
>
>
> On 4/25/16 5:09 PM, Christopher Schlicksup wrote:
> > Hi, I am fairly new to simulation, and would like some input about
> whether
> > I have set up Gromacs correcly. I am using version 5.0.4 with the
> > CHARMM36-Jun2015 force field and the TIP3P water model. I am simulating a
> > 35kDa protein in a dodecahedron box (-d 1.6) with 150mM NaCl plus
> > neutralizing ions.
> >
> > I do a 200ps NVT equilibration followed by a 500ps NPT equilibration
> > followed by 230ps of production run where the protein is unrestrained. My
> > observations so far are that the density is higher than I would expect
> from
> > reading literature. I would appreciate any insight into whether I have a
> > problem, or if my density and pressure values look acceptable. Thanks in
> > advance
> >
>
> What value do you expect from the literature?  The density of such an
> inhomogeneous system is rather useless.  Everything looks fine to me.
>
> -Justin
>
> > Here are my results from gmx energy:
> >
> > *Energy minimization*
> >
> > Energy  Average   Err.Est.   RMSD  Tot-Drift
> >
> ---
> > Potential-1.93229e+06  2900077735.5-189748
> > (kJ/mol)
> >
> >
> > *NVT Equilibration 200ps*
> >
> > Energy  Average   Err.Est.   RMSD  Tot-Drift
> >
> ---
> > Temperature   299.9  0.0992.59846   0.560458  (K)
> >
> >
> > *NPT Equilibration 500ps*
> >
> > Energy  Average   Err.Est.   RMSD  Tot-Drift
> >
> ---
> > Pressure1.528921.781.007911.2974
> (bar)
> > Density 1024.74  0.0571.70907 -0.0499058
> > (kg/m^3)
> > Volume  1168.76  0.0651.96293  0.0505822
> (nm^3)
> >
> >
> > *Production Run 230ps*
> >
> > Energy  Average   Err.Est.   RMSD  Tot-Drift
> >
> ---
> > Pressure   0.450022   0.6575.3012   0.157248
> (bar)
> > Density  1025.4  0.0481.39937  -0.209504
> > (kg/m^3)
> > Volume  1168.01  0.0551.59374   0.238338
> (nm^3)
> >
>
> --
> ==
>
> 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] Bash scripting and Gromacs

[Kutzner, Carsten]

> On 26 Apr 2016, at 15:33, James Starlight  wrote:
> 
> No, in my case it recognize ? like a ?
> 
> in script I have
> 
> for sim in ${HOME}/${tit}* ; do
> if [[ -d $sim ]]; then
>  simulation=$(basename "$sim")
>  cd ${sim}
>  rm dd_dump_err*.pdb
>  trjconv -s md_${tit}?.tpr -f md_${tit}?.trr -o
> ${HOME}/output/${simulation}.xtc -n -pbc mol -ur compact -fit trans  <
> ${HOME}/enter.txt
> 
> and gromacs sent
> 
>  trjconv -s md_resp_complex?.tpr -f md_resp_complex?.trr -o
> /nfs_homes/clouddyn/MD_bench/Resp_cyt_cluster/output/resp_complex_conf7.xtc
> -n -pbc mol -ur compact -fit trans
> 
> 
> Is it possible specify more flexible e.g 1 of any character or 2 of
> any characters within the file name etc like REGEX syntax
http://www.tldp.org/LDP/Bash-Beginners-Guide/html/sect_04_01.html

Good luck :)

Carsten


> 
> Thanks!
> 
> J.
> 
> 2016-04-26 12:45 GMT+02:00 Kutzner, Carsten :
>> 
>>> On 26 Apr 2016, at 11:22, James Starlight  wrote:
>>> 
>>> Exactly the problem was there!
>>> 
>>> BTW how to define selection more carefully (avoiding using *) tpr and
>>> trr to be sure that always only 1 file is selected assuming that all
>>> relevant trajectories and topologies are differs only on the digit e.g
>>> 
>>> resp_complex_conf7/md_resp_complex_conf7.tpr
>>> resp_complex_conf7/md_resp_complex_conf6.tpr
>>> ..
>>> resp_complex_conf7/md_resp_complex_conf1.tpr
>> For a single-character wildcard you can use a '?',
>> e.g.
>> 
>>> resp_complex_conf7/md_resp_complex_conf?.tpr
>> 
>> 
>> Carsten
>> 
>> 
>>> 
>>> the same for trr
>>> 
>>> J.
>>> 
>>> 2016-04-26 11:11 GMT+02:00 Kutzner, Carsten :
 
> On 26 Apr 2016, at 11:00, James Starlight  wrote:
> 
> Hello,
> 
> I faced with the folliwing problem:
> 
> I try to make small script which will loop several folders
> corresponded to the invididual simulations and procecc each trajectory
> searching them by the keyword
> trr_file="md_resp_complex_conf"
> 
> 
> #!/bin/bash
> 
> HOME="/nfs_homes/clouddyn/MD_bench/Resp_cyt_cluster"
> trr_file="md_resp_complex_conf"
> tit="resp_complex"
> 
> rm -r ${HOME}/output
> mkdir ${HOME}/output
> source /prog/gm502/bin/GMXRC
> 
> for sim in ${HOME}/${tit}* ; do
> if [[ -d $sim ]]; then
> simulation=$(basename "$sim")
> pushd ${sim}
> rm dd_dump_err*.pdb
> trjconv -s ${HOME}/ref.gro -f ${trr_file}*.trr -o
 if there are several files that match your ${trr_file}* pattern, then
 bash will give you all of those. Try leaving away the *
 or delete the other .trr files in that dir to make get only
 one file there.
 
 Carsten
 
> ${HOME}/output/${simulation}.xtc -n
> popd
> fi
> done
> 
> 
> 
> finally I ontained
> 
> trjconv -s /nfs_homes/clouddyn/MD_bench/Resp_cyt_cluster/ref.gro -f
> md_resp_complex_conf7_go.trr md_resp_complex_conf7.trr -o
> /nfs_homes/clouddyn/MD_bench/Resp_cyt_cluster/output/resp_complex_conf7.xtc
> -n -pbc nojump -ur compact -fit trans
> 
> 
> here you see that the problem that the trajectory is repeated twisely
> after -f which is the source of the error:
> 
> -f md_resp_complex_conf7_go.trr md_resp_complex_conf7.trr
> 
> Why this issue occures? As you see in my scriopt I defined all proprly
> 
> trjconv -s ${HOME}/ref.gro -f ${trr_file}*.trr -o
> ${HOME}/output/${simulation}.xtc -n
> 
> 
> Thanks!
> 
> J,
> --
> 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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> 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 
>> 

[gmx-users] Constant Density

[Nash, Anthony]

Hi all,

At the risk of bending the rules of thermodynamics, I¹m wondering whether
Gromacs can maintain density of a water box (0.750 g/L density of water in
a collagen fibril environment) whilst applying an NPT ensemble?

gmx_d solvate, fills up to 2/3 of my truncated oct cell, with my protein
at the centre. An NVT simulation does not redistribute the water. To do
this I need to perform an NPT run, but even so this rapidly shrinks the
box. 

I have considering looking up the necessary pressure value for this
density, however I¹m a bit uncertain whether this maintains any
physiological realism for the protein itself.

I¹ve tried googling with little success.

Any thoughts are appreciated.
Thanks
Anthony 

-- 
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Re: [gmx-users] Bash scripting and Gromacs

[James Starlight]

No, in my case it recognize ? like a ?

in script I have

for sim in ${HOME}/${tit}* ; do
 if [[ -d $sim ]]; then
  simulation=$(basename "$sim")
  cd ${sim}
  rm dd_dump_err*.pdb
  trjconv -s md_${tit}?.tpr -f md_${tit}?.trr -o
${HOME}/output/${simulation}.xtc -n -pbc mol -ur compact -fit trans  <
${HOME}/enter.txt

and gromacs sent

  trjconv -s md_resp_complex?.tpr -f md_resp_complex?.trr -o
/nfs_homes/clouddyn/MD_bench/Resp_cyt_cluster/output/resp_complex_conf7.xtc
-n -pbc mol -ur compact -fit trans


Is it possible specify more flexible e.g 1 of any character or 2 of
any characters within the file name etc like REGEX syntax

Thanks!

J.

2016-04-26 12:45 GMT+02:00 Kutzner, Carsten :
>
>> On 26 Apr 2016, at 11:22, James Starlight  wrote:
>>
>> Exactly the problem was there!
>>
>> BTW how to define selection more carefully (avoiding using *) tpr and
>> trr to be sure that always only 1 file is selected assuming that all
>> relevant trajectories and topologies are differs only on the digit e.g
>>
>> resp_complex_conf7/md_resp_complex_conf7.tpr
>> resp_complex_conf7/md_resp_complex_conf6.tpr
>> ..
>> resp_complex_conf7/md_resp_complex_conf1.tpr
> For a single-character wildcard you can use a '?',
> e.g.
>
>> resp_complex_conf7/md_resp_complex_conf?.tpr
>
>
> Carsten
>
>
>>
>> the same for trr
>>
>> J.
>>
>> 2016-04-26 11:11 GMT+02:00 Kutzner, Carsten :
>>>
 On 26 Apr 2016, at 11:00, James Starlight  wrote:

 Hello,

 I faced with the folliwing problem:

 I try to make small script which will loop several folders
 corresponded to the invididual simulations and procecc each trajectory
 searching them by the keyword
 trr_file="md_resp_complex_conf"


 #!/bin/bash

 HOME="/nfs_homes/clouddyn/MD_bench/Resp_cyt_cluster"
 trr_file="md_resp_complex_conf"
 tit="resp_complex"

 rm -r ${HOME}/output
 mkdir ${HOME}/output
 source /prog/gm502/bin/GMXRC

 for sim in ${HOME}/${tit}* ; do
 if [[ -d $sim ]]; then
 simulation=$(basename "$sim")
 pushd ${sim}
 rm dd_dump_err*.pdb
 trjconv -s ${HOME}/ref.gro -f ${trr_file}*.trr -o
>>> if there are several files that match your ${trr_file}* pattern, then
>>> bash will give you all of those. Try leaving away the *
>>> or delete the other .trr files in that dir to make get only
>>> one file there.
>>>
>>> Carsten
>>>
 ${HOME}/output/${simulation}.xtc -n
 popd
 fi
 done



 finally I ontained

 trjconv -s /nfs_homes/clouddyn/MD_bench/Resp_cyt_cluster/ref.gro -f
 md_resp_complex_conf7_go.trr md_resp_complex_conf7.trr -o
 /nfs_homes/clouddyn/MD_bench/Resp_cyt_cluster/output/resp_complex_conf7.xtc
 -n -pbc nojump -ur compact -fit trans


 here you see that the problem that the trajectory is repeated twisely
 after -f which is the source of the error:

 -f md_resp_complex_conf7_go.trr md_resp_complex_conf7.trr

 Why this issue occures? As you see in my scriopt I defined all proprly

 trjconv -s ${HOME}/ref.gro -f ${trr_file}*.trr -o
 ${HOME}/output/${simulation}.xtc -n


 Thanks!

 J,
 --
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Re: [gmx-users] DSSP with custom residues

[Justin Lemkul]

On 4/26/16 9:10 AM, leila salimi wrote:

Hi Justin,

I am also busy by DSSP analysis. I am interested to know what the
difference between do_dssp and dssp is?



dssp is a binary that actually carries out the DSSP analysis; it is not a 
GROMACS program but is downloaded from an external source.  do_dssp is a GROMACS 
module that is just a wrapper - it runs through a trajectory, pulls out the 
coordinates to a temporary file (those dd files that show up), passes those 
coordinates to dssp, and records the output.  GROMACS doesn't do secondary 
structure calculations natively, instead relying on dssp.


-Justin


Regards,
Leila

On Tue, Apr 26, 2016 at 3:00 PM, Justin Lemkul  wrote:




On 4/26/16 8:57 AM, Stephanie Jephthah wrote:


Hi!

I'm simulating a protein conjugate and thus uses custom residues. Is there
any way to make the dssp program aware of the custom residues (and does it
make sense to do so)? I'm using gromacs 4.6.7 and the "new" dssp. I'm
assuming that the problem is not with do_dssp but with dssp, but please
correct me if I'm wrong.



If you've got custom residues as integral parts of the protein, they need
to be defined as such in residuetypes.dat, or otherwise defined in a
suitable custom index group.  Presumably you have to have done one or the
other before running the simulation.  If the custom residues have normal
amino acid backbone features, doing DSSP analysis makes sense.  If
something is failing, run dssp directly, not via do_dssp, to determine if
the failure is within dssp or do_dssp.

-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] DSSP with custom residues

[leila salimi]

Hi Justin,

I am also busy by DSSP analysis. I am interested to know what the
difference between do_dssp and dssp is?

Regards,
Leila

On Tue, Apr 26, 2016 at 3:00 PM, Justin Lemkul  wrote:

>
>
> On 4/26/16 8:57 AM, Stephanie Jephthah wrote:
>
>> Hi!
>>
>> I'm simulating a protein conjugate and thus uses custom residues. Is there
>> any way to make the dssp program aware of the custom residues (and does it
>> make sense to do so)? I'm using gromacs 4.6.7 and the "new" dssp. I'm
>> assuming that the problem is not with do_dssp but with dssp, but please
>> correct me if I'm wrong.
>>
>>
> If you've got custom residues as integral parts of the protein, they need
> to be defined as such in residuetypes.dat, or otherwise defined in a
> suitable custom index group.  Presumably you have to have done one or the
> other before running the simulation.  If the custom residues have normal
> amino acid backbone features, doing DSSP analysis makes sense.  If
> something is failing, run dssp directly, not via do_dssp, to determine if
> the failure is within dssp or do_dssp.
>
> -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] DSSP with custom residues

[Justin Lemkul]

On 4/26/16 8:57 AM, Stephanie Jephthah wrote:

Hi!

I'm simulating a protein conjugate and thus uses custom residues. Is there
any way to make the dssp program aware of the custom residues (and does it
make sense to do so)? I'm using gromacs 4.6.7 and the "new" dssp. I'm
assuming that the problem is not with do_dssp but with dssp, but please
correct me if I'm wrong.



If you've got custom residues as integral parts of the protein, they need to be 
defined as such in residuetypes.dat, or otherwise defined in a suitable custom 
index group.  Presumably you have to have done one or the other before running 
the simulation.  If the custom residues have normal amino acid backbone 
features, doing DSSP analysis makes sense.  If something is failing, run dssp 
directly, not via do_dssp, to determine if the failure is within dssp or do_dssp.


-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] DSSP with custom residues

[Stephanie Jephthah]

Hi!

I'm simulating a protein conjugate and thus uses custom residues. Is there
any way to make the dssp program aware of the custom residues (and does it
make sense to do so)? I'm using gromacs 4.6.7 and the "new" dssp. I'm
assuming that the problem is not with do_dssp but with dssp, but please
correct me if I'm wrong.

Kind regards,
Stephanie Jephthah
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Re: [gmx-users] Topology include file " " not found

[Mark Abraham]

Yeah, don't use wysiwyg word processors for editing plain text files (else
you will get such smartness tripping you up). Use an editor aimed at them.

Mark

On Tue, 26 Apr 2016 13:59 gozde ergin  wrote:

> Ok I found the error. I put “cis-pinonic.itp” instead of
> ”cis-pinonic.itp”. The problem is quote.
>
> On 26 Apr 2016, at 13:35, gozde ergin  wrote:
> >
> > I checked it and there is no #include statement in cis-pinonic.itp file.
> >> On 26 Apr 2016, at 13:24, Justin Lemkul  wrote:
> >>
> >>
> >>
> >> On 4/26/16 5:57 AM, gozde ergin wrote:
> >>> Dear all,
> >>>
> >>> I am trying to simulate organic system.
> >>> Here is my tool.top file, and cis-pionic,its is in the same folder
> with the tool.top.
> >>>
> >>> ;
> >>> ; Topology from .mol2 file
> >>> ; topolbuild
> >>> ;
> >>> ; The force field files to be included
> >>> #include "charmm27.ff/forcefield.itp"
> >>>
> >>> ; Include chain topologies
> >>> #include “cis-pinonic.itp"
> >>>
> >>> ; Include water topology
> >>> #include "charmm27.ff/tip3p.itp"
> >>>
> >>> #ifdef POSRES_WATER
> >>> ; Position restraint for each water oxygen
> >>> [ position_restraints ]
> >>> ;  i funct   fcxfcyfcz
> >>>   11   1000   1000   1000
> >>> #endif
> >>>
> >>> ; Include topology for ions
> >>> #include "charmm27.ff/ions.itp"
> >>>
> >>> [ system ]
> >>> ; title from mol2 input
> >>> LIG
> >>>
> >>> [ molecules ]
> >>> ; molecule namenr.
> >>> cis-pinonic   64
> >>>
> >>>
> >>> When I try to minimize the system this is the error that I’m getting,
> >>>
> >>> grompp -f minim.mdp  -c lig.gro -p topol.top -o em.tpr
> >>>
> >>> Fatal error:
> >>> Topology include file "   " not found
> >>> For more information and tips for troubleshooting, please check the
> GROMACS
> >>> website at http://www.gromacs.org/Documentation/Errors
> >>>
> >>> What is that mean?
> >>> I thought maybe there is an invisible line so I did also dos2unix
> however the error is still there.
> >>>
> >>
> >> Are there any #include statements within your .itp files (e.g.
> cis-pinonic.itp) that might be triggering this?
> >>
> >> -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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Re: [gmx-users] REMD--how to determine the temperature distribution

[YanhuaOuyang]

When I choose NVT, it appear like this: "ERROR: Can not do constant volume 
yet!”, do you have other ways to determine the temperature except the two 
websites?
> 在 2016年4月26日，下午8:16，Mark Abraham  写道：
> 
> No, just choose NVT.
> 
> Mark
> 
> On Tue, 26 Apr 2016 13:42 YanhuaOuyang <15901283...@163.com> wrote:
> 
>> Thank you so much, but the latter one is only suitable for REMD in NPT
>> ensemble.
>>> 在 2016年4月26日，上午1:20，Christopher Neale  写道：
>>> 
>>> There are many published approaches. Here is the one that I use:
>> http://origami.phys.rpi.edu/racc/rate_of_acceptance.php
>>> Another example is here: http://folding.bmc.uu.se/remd/
>>> 
>>> 
>>> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <
>> gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of
>> YanhuaOuyang <15901283...@163.com>
>>> Sent: 25 April 2016 10:36
>>> To: gmx-us...@gromacs.org
>>> Subject: [gmx-users] REMD--how to determine the temperature distribution
>>> 
>>> Dear all,
>>>   I am going to run a REMD of a protein(explicit solvent) in NVT
>> ensemble with gromacs, but I have trouble in determining a optimum
>> temperature  distribution.Can anybody know the ways to determine the
>> temperature?
>>> --
>>> 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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>> send a mail to gmx-users-requ...@gromacs.org.
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>> send a mail to gmx-users-requ...@gromacs.org.
>> 
>> 
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Re: [gmx-users] REMD--how to determine the temperature distribution

[Mark Abraham]

No, just choose NVT.

Mark

On Tue, 26 Apr 2016 13:42 YanhuaOuyang <15901283...@163.com> wrote:

> Thank you so much, but the latter one is only suitable for REMD in NPT
> ensemble.
> > 在 2016年4月26日，上午1:20，Christopher Neale  写道：
> >
> > There are many published approaches. Here is the one that I use:
> http://origami.phys.rpi.edu/racc/rate_of_acceptance.php
> > Another example is here: http://folding.bmc.uu.se/remd/
> >
> > 
> > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <
> gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of
> YanhuaOuyang <15901283...@163.com>
> > Sent: 25 April 2016 10:36
> > To: gmx-us...@gromacs.org
> > Subject: [gmx-users] REMD--how to determine the temperature distribution
> >
> > Dear all,
> >I am going to run a REMD of a protein(explicit solvent) in NVT
> ensemble with gromacs, but I have trouble in determining a optimum
> temperature  distribution.Can anybody know the ways to determine the
> temperature?
> > --
> > 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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Re: [gmx-users] g_hbond: range checking error

[Erik Marklund]

Hi,

Strange. Do you get the same error with 5.1.2? If so, can you please file a 
redmine issue (http://redmine.gromacs.org/) and upload the input files that 
generate this error? Assign the issue to me.

Kind regards
Erik Marklund

On 26 Apr 2016, at 12:01, Shubhangi Gupta 
> wrote:

Hi all,


I want to calculate the number of hydrogen bonds between protein
and solvent. I am using g_hbond (gromacs 5.0.2) with the two groups -
protein and SOL. When i run the command, I get a *Range Checking error*

*Variable gx has value -3. It should have been within [0 ..19]*

However when i do the same and choose the two groups as protein and
protein, the command goes through.

Any help is greatly appreciated.

Thanks


Regards,
Shubhangi Gupta
PhD Research Scholar (YUS lab)
Dept of Chemistry
Indian Institute of Technology Bombay
Powai, Mumbai-400076.


e-mail ID: ignahbuhs.gup...@gmail.com
  144033...@iitb.ac.in
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Re: [gmx-users] Topology include file " " not found

[gozde ergin]

Ok I found the error. I put “cis-pinonic.itp” instead of ”cis-pinonic.itp”. The 
problem is quote.

On 26 Apr 2016, at 13:35, gozde ergin  wrote:
> 
> I checked it and there is no #include statement in cis-pinonic.itp file.
>> On 26 Apr 2016, at 13:24, Justin Lemkul  wrote:
>> 
>> 
>> 
>> On 4/26/16 5:57 AM, gozde ergin wrote:
>>> Dear all,
>>> 
>>> I am trying to simulate organic system.
>>> Here is my tool.top file, and cis-pionic,its is in the same folder with the 
>>> tool.top.
>>> 
>>> ;
>>> ; Topology from .mol2 file
>>> ; topolbuild
>>> ;
>>> ; The force field files to be included
>>> #include "charmm27.ff/forcefield.itp"
>>> 
>>> ; Include chain topologies
>>> #include “cis-pinonic.itp"
>>> 
>>> ; Include water topology
>>> #include "charmm27.ff/tip3p.itp"
>>> 
>>> #ifdef POSRES_WATER
>>> ; Position restraint for each water oxygen
>>> [ position_restraints ]
>>> ;  i funct   fcxfcyfcz
>>>   11   1000   1000   1000
>>> #endif
>>> 
>>> ; Include topology for ions
>>> #include "charmm27.ff/ions.itp"
>>> 
>>> [ system ]
>>> ; title from mol2 input
>>> LIG
>>> 
>>> [ molecules ]
>>> ; molecule namenr.
>>> cis-pinonic   64
>>> 
>>> 
>>> When I try to minimize the system this is the error that I’m getting,
>>> 
>>> grompp -f minim.mdp  -c lig.gro -p topol.top -o em.tpr
>>> 
>>> Fatal error:
>>> Topology include file "   " not found
>>> For more information and tips for troubleshooting, please check the GROMACS
>>> website at http://www.gromacs.org/Documentation/Errors
>>> 
>>> What is that mean?
>>> I thought maybe there is an invisible line so I did also dos2unix however 
>>> the error is still there.
>>> 
>> 
>> Are there any #include statements within your .itp files (e.g. 
>> cis-pinonic.itp) that might be triggering this?
>> 
>> -Justin
>> 
>> -- 
>> ==
>> 
>> Justin A. Lemkul, Ph.D.
>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>> 
>> Department of Pharmaceutical Sciences
>> School of Pharmacy
>> Health Sciences Facility II, Room 629
>> University of Maryland, Baltimore
>> 20 Penn St.
>> Baltimore, MD 21201
>> 
>> jalem...@outerbanks.umaryland.edu | (410) 706-7441
>> http://mackerell.umaryland.edu/~jalemkul
>> 
>> ==
>> -- 
>> Gromacs Users mailing list
>> 
>> * Please search the archive at 
>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
>> 
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>> mail to gmx-users-requ...@gromacs.org.
> 

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Re: [gmx-users] Free energy including change in temperature

[Justin Lemkul]

On 4/26/16 7:48 AM, Andreas Mecklenfeld wrote:

Dear Gromacs users,

I would like to try a free energy calculation including a change in temperature
using the temperature-lambdas-vector. It says in the online manual that each
entry has to be between 0 and 1. How can I define the corresponding temperatures
(something like couple-lambda0 / couple-lambda1)?



http://manual.gromacs.org/documentation/5.1.2/user-guide/mdp-options.html#expanded-ensemble-calculations

-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] Free energy including change in temperature

[Andreas Mecklenfeld]

Dear Gromacs users,

I would like to try a free energy calculation including a change in 
temperature using the temperature-lambdas-vector. It says in the online 
manual that each entry has to be between 0 and 1. How can I define the 
corresponding temperatures (something like couple-lambda0 / 
couple-lambda1)?


Thanks & regards,
Andreas


--
M. Sc. Andreas Mecklenfeld
Stipendiat

Technische Universität Braunschweig
Institut für Thermodynamik
Hans-Sommer-Straße 5
38106 Braunschweig
Deutschland / Germany

Tel: +49 (0)531 391-2634
Fax: +49 (0)531 391-7814

http://www.ift-bs.de

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Re: [gmx-users] REMD--how to determine the temperature distribution

[YanhuaOuyang]

Thank you so much, but the latter one is only suitable for REMD in NPT ensemble.
> 在 2016年4月26日，上午1:20，Christopher Neale  写道：
> 
> There are many published approaches. Here is the one that I use: 
> http://origami.phys.rpi.edu/racc/rate_of_acceptance.php
> Another example is here: http://folding.bmc.uu.se/remd/
> 
> 
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
>  on behalf of YanhuaOuyang 
> <15901283...@163.com>
> Sent: 25 April 2016 10:36
> To: gmx-us...@gromacs.org
> Subject: [gmx-users] REMD--how to determine the temperature distribution
> 
> Dear all,
>I am going to run a REMD of a protein(explicit solvent) in NVT 
> ensemble with gromacs, but I have trouble in determining a optimum 
> temperature  distribution.Can anybody know the ways to determine the 
> temperature?
> --
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Re: [gmx-users] Topology include file " " not found

[gozde ergin]

I checked it and there is no #include statement in cis-pinonic.itp file.
>  On 26 Apr 2016, at 13:24, Justin Lemkul  wrote:
> 
> 
> 
> On 4/26/16 5:57 AM, gozde ergin wrote:
>> Dear all,
>> 
>> I am trying to simulate organic system.
>> Here is my tool.top file, and cis-pionic,its is in the same folder with the 
>> tool.top.
>> 
>> ;
>> ; Topology from .mol2 file
>> ; topolbuild
>> ;
>> ; The force field files to be included
>> #include "charmm27.ff/forcefield.itp"
>> 
>> ; Include chain topologies
>> #include “cis-pinonic.itp"
>> 
>> ; Include water topology
>> #include "charmm27.ff/tip3p.itp"
>> 
>> #ifdef POSRES_WATER
>> ; Position restraint for each water oxygen
>> [ position_restraints ]
>> ;  i funct   fcxfcyfcz
>>11   1000   1000   1000
>> #endif
>> 
>> ; Include topology for ions
>> #include "charmm27.ff/ions.itp"
>> 
>>  [ system ]
>> ; title from mol2 input
>> LIG
>> 
>>  [ molecules ]
>> ; molecule namenr.
>>  cis-pinonic   64
>> 
>> 
>> When I try to minimize the system this is the error that I’m getting,
>> 
>> grompp -f minim.mdp  -c lig.gro -p topol.top -o em.tpr
>> 
>> Fatal error:
>> Topology include file "   " not found
>> For more information and tips for troubleshooting, please check the GROMACS
>> website at http://www.gromacs.org/Documentation/Errors
>> 
>> What is that mean?
>> I thought maybe there is an invisible line so I did also dos2unix however 
>> the error is still there.
>> 
> 
> Are there any #include statements within your .itp files (e.g. 
> cis-pinonic.itp) that might be triggering this?
> 
> -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] Topology include file " " not found

[Justin Lemkul]

On 4/26/16 5:57 AM, gozde ergin wrote:

Dear all,

I am trying to simulate organic system.
Here is my tool.top file, and cis-pionic,its is in the same folder with the 
tool.top.

;
; Topology from .mol2 file
; topolbuild
;
; The force field files to be included
#include "charmm27.ff/forcefield.itp"

; Include chain topologies
#include “cis-pinonic.itp"

; Include water topology
#include "charmm27.ff/tip3p.itp"

#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
;  i funct   fcxfcyfcz
11   1000   1000   1000
#endif

; Include topology for ions
#include "charmm27.ff/ions.itp"

  [ system ]
; title from mol2 input
LIG

  [ molecules ]
; molecule namenr.
  cis-pinonic   64


When I try to minimize the system this is the error that I’m getting,

grompp -f minim.mdp  -c lig.gro -p topol.top -o em.tpr

Fatal error:
Topology include file "   " not found
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors

What is that mean?
I thought maybe there is an invisible line so I did also dos2unix however the 
error is still there.



Are there any #include statements within your .itp files (e.g. cis-pinonic.itp) 
that might be triggering this?


-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] g_hbond: range checking error

[Shubhangi Gupta]

Hi all,


 I want to calculate the number of hydrogen bonds between protein
and solvent. I am using g_hbond (gromacs 5.0.2) with the two groups -
protein and SOL. When i run the command, I get a *Range Checking error*

*Variable gx has value -3. It should have been within [0 ..19]*

However when i do the same and choose the two groups as protein and
protein, the command goes through.

Any help is greatly appreciated.

Thanks


Regards,
Shubhangi Gupta
PhD Research Scholar (YUS lab)
Dept of Chemistry
Indian Institute of Technology Bombay
Powai, Mumbai-400076.


e-mail ID: ignahbuhs.gup...@gmail.com
   144033...@iitb.ac.in
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Re: [gmx-users] Bash scripting and Gromacs

[Kutzner, Carsten]

> On 26 Apr 2016, at 11:22, James Starlight  wrote:
> 
> Exactly the problem was there!
> 
> BTW how to define selection more carefully (avoiding using *) tpr and
> trr to be sure that always only 1 file is selected assuming that all
> relevant trajectories and topologies are differs only on the digit e.g
> 
> resp_complex_conf7/md_resp_complex_conf7.tpr
> resp_complex_conf7/md_resp_complex_conf6.tpr
> ..
> resp_complex_conf7/md_resp_complex_conf1.tpr
For a single-character wildcard you can use a '?',
e.g.

> resp_complex_conf7/md_resp_complex_conf?.tpr


Carsten


> 
> the same for trr
> 
> J.
> 
> 2016-04-26 11:11 GMT+02:00 Kutzner, Carsten :
>> 
>>> On 26 Apr 2016, at 11:00, James Starlight  wrote:
>>> 
>>> Hello,
>>> 
>>> I faced with the folliwing problem:
>>> 
>>> I try to make small script which will loop several folders
>>> corresponded to the invididual simulations and procecc each trajectory
>>> searching them by the keyword
>>> trr_file="md_resp_complex_conf"
>>> 
>>> 
>>> #!/bin/bash
>>> 
>>> HOME="/nfs_homes/clouddyn/MD_bench/Resp_cyt_cluster"
>>> trr_file="md_resp_complex_conf"
>>> tit="resp_complex"
>>> 
>>> rm -r ${HOME}/output
>>> mkdir ${HOME}/output
>>> source /prog/gm502/bin/GMXRC
>>> 
>>> for sim in ${HOME}/${tit}* ; do
>>> if [[ -d $sim ]]; then
>>> simulation=$(basename "$sim")
>>> pushd ${sim}
>>> rm dd_dump_err*.pdb
>>> trjconv -s ${HOME}/ref.gro -f ${trr_file}*.trr -o
>> if there are several files that match your ${trr_file}* pattern, then
>> bash will give you all of those. Try leaving away the *
>> or delete the other .trr files in that dir to make get only
>> one file there.
>> 
>> Carsten
>> 
>>> ${HOME}/output/${simulation}.xtc -n
>>> popd
>>> fi
>>> done
>>> 
>>> 
>>> 
>>> finally I ontained
>>> 
>>> trjconv -s /nfs_homes/clouddyn/MD_bench/Resp_cyt_cluster/ref.gro -f
>>> md_resp_complex_conf7_go.trr md_resp_complex_conf7.trr -o
>>> /nfs_homes/clouddyn/MD_bench/Resp_cyt_cluster/output/resp_complex_conf7.xtc
>>> -n -pbc nojump -ur compact -fit trans
>>> 
>>> 
>>> here you see that the problem that the trajectory is repeated twisely
>>> after -f which is the source of the error:
>>> 
>>> -f md_resp_complex_conf7_go.trr md_resp_complex_conf7.trr
>>> 
>>> Why this issue occures? As you see in my scriopt I defined all proprly
>>> 
>>> trjconv -s ${HOME}/ref.gro -f ${trr_file}*.trr -o
>>> ${HOME}/output/${simulation}.xtc -n
>>> 
>>> 
>>> Thanks!
>>> 
>>> J,
>>> --
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>>> 
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>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
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>>> a mail to gmx-users-requ...@gromacs.org.
>> 
>> --
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[gmx-users] Topology include file " " not found

[gozde ergin]

Dear all,

I am trying to simulate organic system.
Here is my tool.top file, and cis-pionic,its is in the same folder with the 
tool.top.

;
; Topology from .mol2 file
; topolbuild
;
; The force field files to be included
#include "charmm27.ff/forcefield.itp"

; Include chain topologies
#include “cis-pinonic.itp"   

; Include water topology
#include "charmm27.ff/tip3p.itp"

#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
;  i funct   fcxfcyfcz
   11   1000   1000   1000
#endif

; Include topology for ions
#include "charmm27.ff/ions.itp"

 [ system ]
; title from mol2 input
LIG

 [ molecules ]
; molecule namenr.
 cis-pinonic   64


When I try to minimize the system this is the error that I’m getting,

grompp -f minim.mdp  -c lig.gro -p topol.top -o em.tpr

Fatal error:
Topology include file "   " not found
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors

What is that mean? 
I thought maybe there is an invisible line so I did also dos2unix however the 
error is still there.
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Re: [gmx-users] Adding Residue in .rtp file.

[Justin Lemkul]

On 4/26/16 2:57 AM, Md. Imrul Reza Shishir wrote:

Dear All
​I have a ​structure file(pdb) cellulose fibril with unknown residue and
atom type. I want to add this residue in the .rtp file and .hdb file. As i
am new in gromacs. Is there any tutorial how i parameterize the structure
file with force field. Is there any tutorial or guideline how to add
residue in gromacs in details.



http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field
http://www.gromacs.org/Documentation/How-tos/Polymers

As far as the parametrization itself, that's not a GROMACS-specific issue (or 
any software for that matter).  You'll have to refer to the primary literature 
for your chosen force field for the actual mechanics of what you need to do.


-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] Bash scripting and Gromacs

[James Starlight]

Exactly the problem was there!

BTW how to define selection more carefully (avoiding using *) tpr and
trr to be sure that always only 1 file is selected assuming that all
relevant trajectories and topologies are differs only on the digit e.g

resp_complex_conf7/md_resp_complex_conf7.tpr
 resp_complex_conf7/md_resp_complex_conf6.tpr
..
resp_complex_conf7/md_resp_complex_conf1.tpr

the same for trr

J.

2016-04-26 11:11 GMT+02:00 Kutzner, Carsten :
>
>> On 26 Apr 2016, at 11:00, James Starlight  wrote:
>>
>> Hello,
>>
>> I faced with the folliwing problem:
>>
>> I try to make small script which will loop several folders
>> corresponded to the invididual simulations and procecc each trajectory
>> searching them by the keyword
>> trr_file="md_resp_complex_conf"
>>
>>
>> #!/bin/bash
>>
>> HOME="/nfs_homes/clouddyn/MD_bench/Resp_cyt_cluster"
>> trr_file="md_resp_complex_conf"
>> tit="resp_complex"
>>
>> rm -r ${HOME}/output
>> mkdir ${HOME}/output
>> source /prog/gm502/bin/GMXRC
>>
>> for sim in ${HOME}/${tit}* ; do
>> if [[ -d $sim ]]; then
>>  simulation=$(basename "$sim")
>>  pushd ${sim}
>>  rm dd_dump_err*.pdb
>>  trjconv -s ${HOME}/ref.gro -f ${trr_file}*.trr -o
> if there are several files that match your ${trr_file}* pattern, then
> bash will give you all of those. Try leaving away the *
> or delete the other .trr files in that dir to make get only
> one file there.
>
> Carsten
>
>> ${HOME}/output/${simulation}.xtc -n
>>  popd
>> fi
>> done
>>
>>
>>
>> finally I ontained
>>
>>  trjconv -s /nfs_homes/clouddyn/MD_bench/Resp_cyt_cluster/ref.gro -f
>> md_resp_complex_conf7_go.trr md_resp_complex_conf7.trr -o
>> /nfs_homes/clouddyn/MD_bench/Resp_cyt_cluster/output/resp_complex_conf7.xtc
>> -n -pbc nojump -ur compact -fit trans
>>
>>
>> here you see that the problem that the trajectory is repeated twisely
>> after -f which is the source of the error:
>>
>> -f md_resp_complex_conf7_go.trr md_resp_complex_conf7.trr
>>
>> Why this issue occures? As you see in my scriopt I defined all proprly
>>
>>  trjconv -s ${HOME}/ref.gro -f ${trr_file}*.trr -o
>> ${HOME}/output/${simulation}.xtc -n
>>
>>
>> Thanks!
>>
>> J,
>> --
>> 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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>> mail to gmx-users-requ...@gromacs.org.
>
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Re: [gmx-users] Bash scripting and Gromacs

[Kutzner, Carsten]

> On 26 Apr 2016, at 11:00, James Starlight  wrote:
> 
> Hello,
> 
> I faced with the folliwing problem:
> 
> I try to make small script which will loop several folders
> corresponded to the invididual simulations and procecc each trajectory
> searching them by the keyword
> trr_file="md_resp_complex_conf"
> 
> 
> #!/bin/bash
> 
> HOME="/nfs_homes/clouddyn/MD_bench/Resp_cyt_cluster"
> trr_file="md_resp_complex_conf"
> tit="resp_complex"
> 
> rm -r ${HOME}/output
> mkdir ${HOME}/output
> source /prog/gm502/bin/GMXRC
> 
> for sim in ${HOME}/${tit}* ; do
> if [[ -d $sim ]]; then
>  simulation=$(basename "$sim")
>  pushd ${sim}
>  rm dd_dump_err*.pdb
>  trjconv -s ${HOME}/ref.gro -f ${trr_file}*.trr -o
if there are several files that match your ${trr_file}* pattern, then
bash will give you all of those. Try leaving away the * 
or delete the other .trr files in that dir to make get only
one file there.

Carsten

> ${HOME}/output/${simulation}.xtc -n
>  popd
> fi
> done
> 
> 
> 
> finally I ontained
> 
>  trjconv -s /nfs_homes/clouddyn/MD_bench/Resp_cyt_cluster/ref.gro -f
> md_resp_complex_conf7_go.trr md_resp_complex_conf7.trr -o
> /nfs_homes/clouddyn/MD_bench/Resp_cyt_cluster/output/resp_complex_conf7.xtc
> -n -pbc nojump -ur compact -fit trans
> 
> 
> here you see that the problem that the trajectory is repeated twisely
> after -f which is the source of the error:
> 
> -f md_resp_complex_conf7_go.trr md_resp_complex_conf7.trr
> 
> Why this issue occures? As you see in my scriopt I defined all proprly
> 
>  trjconv -s ${HOME}/ref.gro -f ${trr_file}*.trr -o
> ${HOME}/output/${simulation}.xtc -n
> 
> 
> Thanks!
> 
> J,
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[gmx-users] Bash scripting and Gromacs

[James Starlight]

Hello,

I faced with the folliwing problem:

I try to make small script which will loop several folders
corresponded to the invididual simulations and procecc each trajectory
searching them by the keyword
trr_file="md_resp_complex_conf"


#!/bin/bash

HOME="/nfs_homes/clouddyn/MD_bench/Resp_cyt_cluster"
trr_file="md_resp_complex_conf"
tit="resp_complex"

rm -r ${HOME}/output
mkdir ${HOME}/output
source /prog/gm502/bin/GMXRC

for sim in ${HOME}/${tit}* ; do
 if [[ -d $sim ]]; then
  simulation=$(basename "$sim")
  pushd ${sim}
  rm dd_dump_err*.pdb
  trjconv -s ${HOME}/ref.gro -f ${trr_file}*.trr -o
${HOME}/output/${simulation}.xtc -n
  popd
 fi
done



finally I ontained

  trjconv -s /nfs_homes/clouddyn/MD_bench/Resp_cyt_cluster/ref.gro -f
md_resp_complex_conf7_go.trr md_resp_complex_conf7.trr -o
/nfs_homes/clouddyn/MD_bench/Resp_cyt_cluster/output/resp_complex_conf7.xtc
-n -pbc nojump -ur compact -fit trans


here you see that the problem that the trajectory is repeated twisely
after -f which is the source of the error:

-f md_resp_complex_conf7_go.trr md_resp_complex_conf7.trr

Why this issue occures? As you see in my scriopt I defined all proprly

  trjconv -s ${HOME}/ref.gro -f ${trr_file}*.trr -o
${HOME}/output/${simulation}.xtc -n


Thanks!

J,
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Re: [gmx-users] Syntax error

[Roshan Shrestha]

Sorry, I found my mistake. Should have read the instructions properly. My bad 

On 4/26/16, Roshan Shrestha  wrote:
> I am currently working on KALP-15 tutorial. After I typed-
>
> gmx editconf -f protein.gro -o protein_newbox.gro -box (membrane box
> vectors) -center x y z
> I got bash: syntax error near unexpected token `('
> What is the remedy to this problem ?
>


-- 
*Roshan Shrestha*
Graduate Student
Central Department of Physics,Tribhuvan University
Kathmandu,Nepal
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Re: [gmx-users] Standard volume of the simulation box

[Tsjerk Wassenaar]

Hi Sana,

There's no such thing as a standard volume. The key decision you have to
take is what distance there should be between periodic images, for which
the consensus view is that you need at least 2.0 nm. I typically use 2.25,
corresponding roughly to 9 layers of water, so the protein can stretch
without significant risk of direct interactions. That means setting up the
unit cell with a distance to the wall of 1.125 nm.

Hope it helps,

Tsjerk

On Mon, Apr 25, 2016 at 5:27 AM, Sana Saeed 
wrote:

> hi
> how can i find the standard volume of the simulation box, that includes
> ligand, protein and water.
>
>  Sana Saeed Khan,
> Research Assistant
> Chemoinformatics Lab
> Graduate Student, MS bioinfo
> Department of Bioinformatics
> Soongsil University, Seoul, South Korea.
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>



-- 
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Re: [gmx-users] Syntax error

[Sarath Chandra]

You have to provide the actual box vectors value in numbers

eg: -box 9 5 6

regards,

Sarath

-- 
Sarath Chandra Dantu, PhD, ELS
Room No. 606, New BSBE Building
Department of Biosciences and Bioengineering
Indian Institute of Technology Bombay
Powai Mumbai, 400-076, India


On 26 April 2016 at 13:06, Roshan Shrestha  wrote:

> I am currently working on KALP-15 tutorial. After I typed-
>
> gmx editconf -f protein.gro -o protein_newbox.gro -box (membrane box
> vectors) -center x y z
> I got bash: syntax error near unexpected token `('
> What is the remedy to this problem ?
> --
> 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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[gmx-users] Syntax error

[Roshan Shrestha]

I am currently working on KALP-15 tutorial. After I typed-

gmx editconf -f protein.gro -o protein_newbox.gro -box (membrane box
vectors) -center x y z
I got bash: syntax error near unexpected token `('
What is the remedy to this problem ?
-- 
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[gmx-users] Adding Residue in .rtp file.

[Md. Imrul Reza Shishir]

Dear All
​I have a ​structure file(pdb) cellulose fibril with unknown residue and
atom type. I want to add this residue in the .rtp file and .hdb file. As i
am new in gromacs. Is there any tutorial how i parameterize the structure
file with force field. Is there any tutorial or guideline how to add
residue in gromacs in details.

-- 
*Md Imrul Reza Shishir*
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Re: [gmx-users] Gromacs-5.1.2 Checkpoint/restart example

[Mark Abraham]

Yes

On Tue, 26 Apr 2016 08:12 Husen R  wrote:

> Hi,
>
>
> Thanks for your reply.
>
> There is no state.cpt or state_prev.cpt file.
>
> In equilibration part 1 the resulting checkpoint files : nvt.cpt and
> nvt_prev.cpt
> In equilibration part 2 the resulting checkpoint files : npt.cpt and
> npt_prev.cpt
> In Production MD the resulting checkpoint files  : md_0_1.cpt and
> md_0_1_prev.cpt
>
> is this because of -deffnm option ?
> I just want to make sure.
>
> Regards,
>
>
> Husen
>
>
> On Tue, Apr 26, 2016 at 11:45 AM, Mark Abraham 
> wrote:
>
> > Hi,
> >
> > On Tue, 26 Apr 2016 06:19 Husen R  wrote:
> >
> > > Hi all,
> > >
> > > I tried to run this gromacs tutorial (
> > >
> > >
> >
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/01_pdb2gmx.html
> > > )
> > > in order to understand how checkpoint/restart works in Gromacs-5.1.2.
> > >
> > > Based on running that tutorial I found that mdrun automatically
> > checkpoint
> > > even though I didn't specify -cpt option (based on mdrun manual page,
> by
> > > default checkpoint every 15 minutes)
> > >
> >
> > Yes, as that webpage suggests.
> >
> > 1. What if I specify -cpt option with a value longer than or smaller than
> > > 15 minutes ? does -cpt value will automatically override the default ?
> > >
> >
> > Yes, the default is used when you don't supply a value. But usually you
> > don't need to think about this.
> >
> > 2. I run the following command to restart production MD step (using
> SLURM)
> > > from checkpoint file. md_0_1_prev.cpt is .cpt file resulting from
> > previous
> > > mdrun execution. is my command right ? I just want to make sure.
> > >
> >
> > Not quite. From that webpage: "Note that mdrun will write state.cpt and
> > state_prev.cpt files. As you can see from their time stamps, one was
> > written approximately at the checkpoint interval before the other (15
> mins
> > by default). Or you can use gmxcheck to see what is in them." You want to
> > follow the examples there and do your restart from the most recent file,
> > which is state.cpt. The older file is just kept for safety. Your command
> > will lead to wasting 15 minutes of simulation.
> >
> > Mark
> >
> > #!/bin/bash
> > > #SBATCH -J Lysozyme
> > > #SBATCH -o md-%j.out
> > > #SBATCH -A necis
> > > #SBATCH -N 3
> > > #SBATCH -n 24
> > > #SBATCH --time=144:00:00
> > > #SBATCH --mail-user=hus...@gmail.com
> > > #SBATCH --mail-type=begin
> > > #SBATCH --mail-type=end
> > >
> > > mpirun gmx_mpi mdrun -cpi md_0_1_prev.cpt -deffnm md_0_1
> > >
> > >
> > > Thank you in advance
> > >
> > > Regards,
> > >
> > >
> > > Husen
> > >
> > >
> > > On Sun, Apr 24, 2016 at 7:57 PM, Husen R  wrote:
> > >
> > > > Hi,
> > > >
> > > > Thanks a lot !
> > > > I'll try it,..
> > > >
> > > > Regards,
> > > >
> > > >
> > > > Husen
> > > >
> > > > On Sun, Apr 24, 2016 at 6:54 PM, Justin Lemkul 
> > wrote:
> > > >
> > > >>
> > > >>
> > > >> On 4/24/16 12:04 AM, Husen R wrote:
> > > >>
> > > >>> Dear all,
> > > >>>
> > > >>> is there any complete documentation discussing checkpoint/restart
> in
> > > >>> Gromacs-5.1.2 ?
> > > >>> I found this link that discuss checkpoint (
> > > >>> http://www.gromacs.org/Documentation/How-tos/Extending_Simulations
> )
> > > and
> > > >>> this link that discuss restart (
> > > >>> http://www.gromacs.org/Documentation/How-tos/Doing_Restarts) but
> > these
> > > >>> are
> > > >>> not specifically for gromacs 5.1.2.
> > > >>>
> > > >>>
> > > >> There are no differences for 5.1.2, so that information is all
> > relevant.
> > > >>
> > > >> -Justin
> > > >>
> > > >> --
> > > >> ==
> > > >>
> > > >> Justin A. Lemkul, Ph.D.
> > > >> Ruth L. Kirschstein NRSA Postdoctoral Fellow
> > > >>
> > > >> Department of Pharmaceutical Sciences
> > > >> School of Pharmacy
> > > >> Health Sciences Facility II, Room 629
> > > >> University of Maryland, Baltimore
> > > >> 20 Penn St.
> > > >> Baltimore, MD 21201
> > > >>
> > > >> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> > > >> http://mackerell.umaryland.edu/~jalemkul
> > > >>
> > > >> ==
> > > >> --
> > > >> Gromacs Users mailing list
> > > >>
> > > >> * Please search the archive at
> > > >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > > >> posting!
> > > >>
> > > >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > > >>
> > > >> * For (un)subscribe requests visit
> > > >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> or
> > > >> send a mail to gmx-users-requ...@gromacs.org.
> > > >>
> > > >
> > > >
> > > --
> > > Gromacs Users mailing list
> > >
> > > * Please search the archive at
> > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > > posting!
> > >
> > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > 

Re: [gmx-users] Gromacs-5.1.2 Checkpoint/restart example

[Husen R]

Hi,


Thanks for your reply.

There is no state.cpt or state_prev.cpt file.

In equilibration part 1 the resulting checkpoint files : nvt.cpt and
nvt_prev.cpt
In equilibration part 2 the resulting checkpoint files : npt.cpt and
npt_prev.cpt
In Production MD the resulting checkpoint files  : md_0_1.cpt and
md_0_1_prev.cpt

is this because of -deffnm option ?
I just want to make sure.

Regards,


Husen


On Tue, Apr 26, 2016 at 11:45 AM, Mark Abraham 
wrote:

> Hi,
>
> On Tue, 26 Apr 2016 06:19 Husen R  wrote:
>
> > Hi all,
> >
> > I tried to run this gromacs tutorial (
> >
> >
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/01_pdb2gmx.html
> > )
> > in order to understand how checkpoint/restart works in Gromacs-5.1.2.
> >
> > Based on running that tutorial I found that mdrun automatically
> checkpoint
> > even though I didn't specify -cpt option (based on mdrun manual page, by
> > default checkpoint every 15 minutes)
> >
>
> Yes, as that webpage suggests.
>
> 1. What if I specify -cpt option with a value longer than or smaller than
> > 15 minutes ? does -cpt value will automatically override the default ?
> >
>
> Yes, the default is used when you don't supply a value. But usually you
> don't need to think about this.
>
> 2. I run the following command to restart production MD step (using SLURM)
> > from checkpoint file. md_0_1_prev.cpt is .cpt file resulting from
> previous
> > mdrun execution. is my command right ? I just want to make sure.
> >
>
> Not quite. From that webpage: "Note that mdrun will write state.cpt and
> state_prev.cpt files. As you can see from their time stamps, one was
> written approximately at the checkpoint interval before the other (15 mins
> by default). Or you can use gmxcheck to see what is in them." You want to
> follow the examples there and do your restart from the most recent file,
> which is state.cpt. The older file is just kept for safety. Your command
> will lead to wasting 15 minutes of simulation.
>
> Mark
>
> #!/bin/bash
> > #SBATCH -J Lysozyme
> > #SBATCH -o md-%j.out
> > #SBATCH -A necis
> > #SBATCH -N 3
> > #SBATCH -n 24
> > #SBATCH --time=144:00:00
> > #SBATCH --mail-user=hus...@gmail.com
> > #SBATCH --mail-type=begin
> > #SBATCH --mail-type=end
> >
> > mpirun gmx_mpi mdrun -cpi md_0_1_prev.cpt -deffnm md_0_1
> >
> >
> > Thank you in advance
> >
> > Regards,
> >
> >
> > Husen
> >
> >
> > On Sun, Apr 24, 2016 at 7:57 PM, Husen R  wrote:
> >
> > > Hi,
> > >
> > > Thanks a lot !
> > > I'll try it,..
> > >
> > > Regards,
> > >
> > >
> > > Husen
> > >
> > > On Sun, Apr 24, 2016 at 6:54 PM, Justin Lemkul 
> wrote:
> > >
> > >>
> > >>
> > >> On 4/24/16 12:04 AM, Husen R wrote:
> > >>
> > >>> Dear all,
> > >>>
> > >>> is there any complete documentation discussing checkpoint/restart in
> > >>> Gromacs-5.1.2 ?
> > >>> I found this link that discuss checkpoint (
> > >>> http://www.gromacs.org/Documentation/How-tos/Extending_Simulations)
> > and
> > >>> this link that discuss restart (
> > >>> http://www.gromacs.org/Documentation/How-tos/Doing_Restarts) but
> these
> > >>> are
> > >>> not specifically for gromacs 5.1.2.
> > >>>
> > >>>
> > >> There are no differences for 5.1.2, so that information is all
> relevant.
> > >>
> > >> -Justin
> > >>
> > >> --
> > >> ==
> > >>
> > >> Justin A. Lemkul, Ph.D.
> > >> Ruth L. Kirschstein NRSA Postdoctoral Fellow
> > >>
> > >> Department of Pharmaceutical Sciences
> > >> School of Pharmacy
> > >> Health Sciences Facility II, Room 629
> > >> University of Maryland, Baltimore
> > >> 20 Penn St.
> > >> Baltimore, MD 21201
> > >>
> > >> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> > >> http://mackerell.umaryland.edu/~jalemkul
> > >>
> > >> ==
> > >> --
> > >> Gromacs Users mailing list
> > >>
> > >> * Please search the archive at
> > >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > >> posting!
> > >>
> > >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > >>
> > >> * For (un)subscribe requests visit
> > >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > >> send a mail to gmx-users-requ...@gromacs.org.
> > >>
> > >
> > >
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
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> >
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> > 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
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