[gmx-users] Optimum slice size (-sl)

2016-02-13 Thread Ashutosh Akshay Shah 
Hello GROMACS users,

What is the optimum slice size when trying to capture as much variation as
possible?

Consider a box with an electrolyte having anions and cations distributed in
it.


*Would be accurate to specify a slice size smaller than the diameter of the
ions while calculating the charge variation across the box?*
Thanks!

Ashutosh Shah
Joint School of Nanoscience and Nanoengineering
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Re: [gmx-users] Installation problem

2016-02-13 Thread Prof. Eddie 
Hi,
The system has a gpu (gtx 590) with cuda libraries installed (I've run namd
on the system). It also has mpi:
mpic++   mpiCCmpiCC.openmpimpicxx   mpiexec
 mpif77   mpif90   mpirun
mpiccmpicc.openmpimpic++.openmpi   mpicxx.openmpi
mpiexec.openmpi  mpif77.openmpi   mpif90.openmpi   mpirun.openmpi

CPU
Architecture:  x86_64
CPU op-mode(s):32-bit, 64-bit
Byte Order:Little Endian
CPU(s):8
On-line CPU(s) list:   0-7
Thread(s) per core:1
Core(s) per socket:8
Socket(s): 1
NUMA node(s):  2
Vendor ID: AuthenticAMD
CPU family:16
Model: 9
Stepping:  1
CPU MHz:   800.000
BogoMIPS:  4000.02
Virtualization:AMD-V
L1d cache: 64K
L1i cache: 64K
L2 cache:  512K
L3 cache:  5118K
NUMA node0 CPU(s): 0-3
NUMA node1 CPU(s): 4-7

gcc
gcc version 4.8.4 (Ubuntu 4.8.4-2ubuntu1~14.04.1)

The error was about ../../lib/libgromacs.so.1.2.0: undefined reference to
`clEnqueueMarkerWithWaitList'

Any idea what that belongs to? Any other details let me know.
Let me know
Thanks,
Eddie

On Fri, Feb 12, 2016 at 11:26 PM, Nikhil Maroli  wrote:

> Hi,
> What is your system details?Do you have GPU ,if yes CUDA library is
> installed?
> if not please install CUDA library and MPI packages too!
> hope it will fix
>
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Computational Nanophotonics
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[gmx-users] pulling simulation

2016-02-13 Thread Mehrnoosh Hazrati 
Dear all,

I'm trying to do umbrella sampling. But after running "perl distances.pl",
I get a "summary_distances.dat file which has NO distances! Before, I get
an error "pull reference distance for group 1 is negative" while I run
grompp and then mdrun for pulling simulation.

Below is my pull_md.mdp file.

Thank you for any help and suggestion.

Regards
Mehrnoosh

P.S.
I'm using gromacs v4.5.7


pull_md.mdp file:

title   = Umbrella pulling simulation
; Run parameters
integrator  = md
dt  = 0.001
tinit   = 0
nsteps  = 500; 5 ns
nstcomm = 10
; Output parameters
nstxout = 1000  ; every 10 ps
nstvout = 1000
nstfout = 500
nstxtcout   = 500   ; every 1 ps
nstenergy   = 500
; Bond parameters
constraint_algorithm= lincs
constraints = all-bonds
continuation= yes   ; continuing from NPT
; Single-range cutoff scheme
nstlist = 10
ns_type = grid
rlist   = 1
rcoulomb= 1
rvdw= 1
; PME electrostatics parameters
coulombtype = PME
fourierspacing  = 0.12
fourier_nx  = 0
fourier_ny  = 0
fourier_nz  = 0
pme_order   = 4
ewald_rtol  = 1e-5
optimize_fft= yes
; Berendsen temperature coupling is on in two groups
Tcoupl  = V-rescale
tc_grps = DPPC  DRG  SOL
tau_t   = 0.5   0.5  0.5
ref_t   = 310   310  310
; Pressure coupling is on
Pcoupl  = Parrinello-Rahman
pcoupltype  = semiisotropic
tau_p   = 2.0   2
compressibility = 4.5e-5  4.5e-5
ref_p   = 1.0 1.0
refcoord_scaling = com
; Generate velocities is off
gen_vel = no
; Periodic boundary conditions are on in all directions
pbc = xyz
; Long-range dispersion correction
DispCorr= EnerPres
; Pull code
pull= umbrella
pull_geometry   = distance
pull_dim= N N Y
pull_start  = yes
pull_ngroups= 1
pull_group0 = LIPID
pull_group1 = DRUG
pull_init1  =  0
pull_rate1  = -0.01
pull_k1 = 500 ; kJ mol^-1 nm^-2
pull_nstxout= 1000  ; every 2 ps
pull_nstfout= 1000  ; every 2 ps
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Re: [gmx-users] Optimum slice size (-sl)

2016-02-13 Thread André Farias de Moura 
the ions may have a radius, but they are distributed continuously along the
system, so you may use slice thicknesses smaller than the ionic radius
you're interested in.

if the simulation was made on some sort of lattice system (which was very
common back in the 1990's), then the shortest, physically meaningful slice
thickness would be the lattice width. For simulations with freely-moving
species, you should only mind about precision: if thickness is too small,
density profiles may become too noisy, if it is too large you have loose
details of the density profile (maxima, minima, etc), so it's a matter or
trial and error to find out what slice thickness suites you better.

I hope it helps

Andre


On Sat, Feb 13, 2016 at 11:57 AM, Ashutosh Akshay Shah <
as...@aggies.ncat.edu> wrote:

> Hello GROMACS users,
>
> What is the optimum slice size when trying to capture as much variation as
> possible?
>
> Consider a box with an electrolyte having anions and cations distributed in
> it.
>
>
> *Would be accurate to specify a slice size smaller than the diameter of the
> ions while calculating the charge variation across the box?*
> Thanks!
>
> Ashutosh Shah
> Joint School of Nanoscience and Nanoengineering
> --
> 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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>



-- 
_

Prof. Dr. André Farias de Moura
Department of Chemistry
Federal University of São Carlos
São Carlos - Brazil
phone: +55-16-3351-8090
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Re: [gmx-users] Installation problem

2016-02-13 Thread Nikhil Maroli 
cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON



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Re: [gmx-users] DSSP secondary structure

2016-02-13 Thread Justin Lemkul 



On 2/13/16 1:33 AM, mohammad r wrote:

Hi,
I used the "gmx do_dssp" command to get the secondary structure of the protein 
during the simulation but the resolution of the resulted .xpm file is very low. how can I 
increase its resolution?


You can adjust the matrix proportions with an .m2p file passed to xpm2ps -di. 
These are almost always necessary as there are many more frames than residues in 
the protein, usually an order of magnitude or more.


-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] pulling simulation

2016-02-13 Thread Justin Lemkul 



On 2/13/16 10:24 AM, Mehrnoosh Hazrati wrote:

Dear all,

I'm trying to do umbrella sampling. But after running "perl distances.pl",
I get a "summary_distances.dat file which has NO distances! Before, I get
an error "pull reference distance for group 1 is negative" while I run
grompp and then mdrun for pulling simulation.


If grompp is warning you about problems or inconsistencies, don't just plow 
ahead.  It's trying to tell you that you're doing something either physically or 
algorithmically nonsensical.




Below is my pull_md.mdp file.

Thank you for any help and suggestion.

Regards
Mehrnoosh

P.S.
I'm using gromacs v4.5.7


Then my Perl script is useless to you; it's for version 5.1, which has a totally 
different syntax (gmx distance -select... rather than g_dist).  So naturally it 
returns nothing, because the commands it's calling don't exist.


-Justin




pull_md.mdp file:

title   = Umbrella pulling simulation
; Run parameters
integrator  = md
dt  = 0.001
tinit   = 0
nsteps  = 500; 5 ns
nstcomm = 10
; Output parameters
nstxout = 1000  ; every 10 ps
nstvout = 1000
nstfout = 500
nstxtcout   = 500   ; every 1 ps
nstenergy   = 500
; Bond parameters
constraint_algorithm= lincs
constraints = all-bonds
continuation= yes   ; continuing from NPT
; Single-range cutoff scheme
nstlist = 10
ns_type = grid
rlist   = 1
rcoulomb= 1
rvdw= 1
; PME electrostatics parameters
coulombtype = PME
fourierspacing  = 0.12
fourier_nx  = 0
fourier_ny  = 0
fourier_nz  = 0
pme_order   = 4
ewald_rtol  = 1e-5
optimize_fft= yes
; Berendsen temperature coupling is on in two groups
Tcoupl  = V-rescale
tc_grps = DPPC  DRG  SOL
tau_t   = 0.5   0.5  0.5
ref_t   = 310   310  310
; Pressure coupling is on
Pcoupl  = Parrinello-Rahman
pcoupltype  = semiisotropic
tau_p   = 2.0   2
compressibility = 4.5e-5  4.5e-5
ref_p   = 1.0 1.0
refcoord_scaling = com
; Generate velocities is off
gen_vel = no
; Periodic boundary conditions are on in all directions
pbc = xyz
; Long-range dispersion correction
DispCorr= EnerPres
; Pull code
pull= umbrella
pull_geometry   = distance
pull_dim= N N Y
pull_start  = yes
pull_ngroups= 1
pull_group0 = LIPID
pull_group1 = DRUG
pull_init1  =  0
pull_rate1  = -0.01
pull_k1 = 500 ; kJ mol^-1 nm^-2
pull_nstxout= 1000  ; every 2 ps
pull_nstfout= 1000  ; every 2 ps



--
==

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] Optimum slice size (-sl)

2016-02-13 Thread Warren Gallin 
If you are using a slice and PME, then wouldn’t the slice have to be thick 
enough to avoid any ion interacting with its own image in adjacent slices?

It seems to me that thickness would have to be greater than the ionic radius at 
the very least.

Warren Gallin

> On Feb 13, 2016, at 8:39 AM, André Farias de Moura  wrote:
> 
> the ions may have a radius, but they are distributed continuously along the
> system, so you may use slice thicknesses smaller than the ionic radius
> you're interested in.
> 
> if the simulation was made on some sort of lattice system (which was very
> common back in the 1990's), then the shortest, physically meaningful slice
> thickness would be the lattice width. For simulations with freely-moving
> species, you should only mind about precision: if thickness is too small,
> density profiles may become too noisy, if it is too large you have loose
> details of the density profile (maxima, minima, etc), so it's a matter or
> trial and error to find out what slice thickness suites you better.
> 
> I hope it helps
> 
> Andre
> 
> 
> On Sat, Feb 13, 2016 at 11:57 AM, Ashutosh Akshay Shah <
> as...@aggies.ncat.edu> wrote:
> 
>> Hello GROMACS users,
>> 
>> What is the optimum slice size when trying to capture as much variation as
>> possible?
>> 
>> Consider a box with an electrolyte having anions and cations distributed in
>> it.
>> 
>> 
>> *Would be accurate to specify a slice size smaller than the diameter of the
>> ions while calculating the charge variation across the box?*
>> Thanks!
>> 
>> Ashutosh Shah
>> Joint School of Nanoscience and Nanoengineering
>> --
>> 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.
>> 
> 
> 
> 
> -- 
> _
> 
> Prof. Dr. André Farias de Moura
> Department of Chemistry
> Federal University of São Carlos
> São Carlos - Brazil
> phone: +55-16-3351-8090
> -- 
> Gromacs Users mailing list
> 
> * Please search the archive at 
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Re: [gmx-users] Prodrg disturbed hybridization state of doubly bonded nitrogen

2016-02-13 Thread David van der Spoel 

On 13/02/16 08:11, Saman Yousuf ali wrote:

Dear all,I am a beginner here. I have prepared my ligand topology file using 
prodrg, it gave me the following error,
PRODRG> Starting up PRODRG version AA100323.0717PRODRG> Parameter set 'pd/gromos96' (fftype=2).PRODRG> PDB mode detected.PRODRG> 
WARNING: deleted hydrogen(s) from your input.PRODRG> Molecule complexity index: 2.11.PRODRG> WARNING: applied 1 unusual hybridisation 
fixup(s).PRODRG> 13 hydrogen(s) added.PRODRG> Using charge groups.PRODRG> Net charge on molecule: 0.000PRODRG> 19 partial charges 1 
ambiguousPRODRG> 33 bonds 10 ambiguousPRODRG> 55 bond angles 34 ambiguousPRODRG> 17 improper dihedrals 2 ambiguousPRODRG> 11 dihedrals 5 
ambiguousPRODRG> Writing GROMACS topology.PRODRG> GROMACS topology quality on 0-10 scale: 5.8PRODRG> Keeping old coordinates.PRODRG> 
RMSD from GROMOS bond ideality (Angstrom) : 0.060PRODRG> RMSD from GROMOS angle ideality (degrees) : 5.631PRODRG> RMSD from GROMOS plane 
ideality (degrees) : 2.317PRODRG> Number of improper improper dihedrals : 0PRODRG> Writing: SCRTHOWMMPGPRODRG> Normal program end.
Prodrg disturbed hybridization state of doubly bonded nitrogen atom and it 
remove double bond and attach hydrogen on this atom. Kindly suggest me how can 
I fix this problem.
Thank you.


Your mail is unreadable and you do not mention the name of the molecule.
Unless there is a very strong reason to use the gromos force field you 
probably want to consider using Amber tools with the acpype tool to make 
a gromacs compatible topology, or Charmm with the CGENff tool.




  Best Regards, Saman Yousuf AliJunior Research Fellow,
| Lab No. P-133, Computational Chemistry Laboratory
Dr. Panjwani Center for Molecular Medicine & Drug Research,
International Center for Chemical & Biological Sciences,
University of Karachi – 75270.Karachi-Pakistan.

Contact No:
Office (92-21) 11192 (Ext 309)
Email ID: saman.yousufal...@yahoo.com
  saman@iccs.edu

|




--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
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Re: [gmx-users] Optimum slice size (-sl)

2016-02-13 Thread Ashutosh Akshay Shah 
50 slices corresponds to a slice size slightly smaller than the smallest
ions' diameter.

On Sat, Feb 13, 2016 at 4:40 PM, Ashutosh Akshay Shah  wrote:

> Thank you Andre and Warren!
>
> A note about PME-
> The basic principle is that a system of particles is converted into a grid
> (or "mesh") of density values. The potential is then solved for this
> density grid, and forces are applied to each particle based on what cell it
> is in, and where in the cell it lies. - from wikipedia
>
> This is a graph of potential across a box that I am simulating, using
> different number of slices. I have used the PME method in all cases. The
> minimum ion diameter is 0.25 nm. Note that my box is 12 nm in z-direction,
> but only the 3 to 9 nm portion is of significance (rest is vacuum).
>
> http://s21.postimg.org/s75ck7tdj/potentialslicescomparison.png
>
> The graph shows that more the slice size, better the resolution, even for
> PME. (no visible noise at higher slice numbers)
>
> What should I conclude out of this? Higher the number of slices, better?
> Even using PME?
>
> Ashutosh Shah
> Joint School of Nanoscience and Nanoengineering
>
>
>
>
> On Sat, Feb 13, 2016 at 1:56 PM, Warren Gallin 
> wrote:
>
>> If you are using a slice and PME, then wouldn’t the slice have to be
>> thick enough to avoid any ion interacting with its own image in adjacent
>> slices?
>>
>> It seems to me that thickness would have to be greater than the ionic
>> radius at the very least.
>>
>> Warren Gallin
>>
>> > On Feb 13, 2016, at 8:39 AM, André Farias de Moura 
>> wrote:
>> >
>> > the ions may have a radius, but they are distributed continuously along
>> the
>> > system, so you may use slice thicknesses smaller than the ionic radius
>> > you're interested in.
>> >
>> > if the simulation was made on some sort of lattice system (which was
>> very
>> > common back in the 1990's), then the shortest, physically meaningful
>> slice
>> > thickness would be the lattice width. For simulations with freely-moving
>> > species, you should only mind about precision: if thickness is too
>> small,
>> > density profiles may become too noisy, if it is too large you have loose
>> > details of the density profile (maxima, minima, etc), so it's a matter
>> or
>> > trial and error to find out what slice thickness suites you better.
>> >
>> > I hope it helps
>> >
>> > Andre
>> >
>> >
>> > On Sat, Feb 13, 2016 at 11:57 AM, Ashutosh Akshay Shah <
>> > as...@aggies.ncat.edu> wrote:
>> >
>> >> Hello GROMACS users,
>> >>
>> >> What is the optimum slice size when trying to capture as much
>> variation as
>> >> possible?
>> >>
>> >> Consider a box with an electrolyte having anions and cations
>> distributed in
>> >> it.
>> >>
>> >>
>> >> *Would be accurate to specify a slice size smaller than the diameter
>> of the
>> >> ions while calculating the charge variation across the box?*
>> >> Thanks!
>> >>
>> >> Ashutosh Shah
>> >> Joint School of Nanoscience and Nanoengineering
>> >> --
>> >> 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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>> >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> >> send a mail to gmx-users-requ...@gromacs.org.
>> >>
>> >
>> >
>> >
>> > --
>> > _
>> >
>> > Prof. Dr. André Farias de Moura
>> > Department of Chemistry
>> > Federal University of São Carlos
>> > São Carlos - Brazil
>> > phone: +55-16-3351-8090
>> > --
>> > 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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>
>
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[gmx-users] energygrps

2016-02-13 Thread Alexander Alexander 
Dear Gromacs user,

By using
"energygrps = A SOL"
We can have SR-NB potential energies between "SOL"-"A" in the energy file,
now suppose that there are three elements with different population in our
system like "A", "B" and "SOL", my question is that what should I
write as "energygrps"
if the SR-NB energies between "(AB)" and "SOL" are required to know? not
"A"-"SOL" interaction and "B"-"SOL" interaction separately.

Best regards,
Alex
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Re: [gmx-users] Optimum slice size (-sl)

2016-02-13 Thread Ashutosh Akshay Shah 
Thank you Andre and Warren!

A note about PME-
The basic principle is that a system of particles is converted into a grid
(or "mesh") of density values. The potential is then solved for this
density grid, and forces are applied to each particle based on what cell it
is in, and where in the cell it lies. - from wikipedia

This is a graph of potential across a box that I am simulating, using
different number of slices. I have used the PME method in all cases. The
minimum ion diameter is 0.25 nm. Note that my box is 12 nm in z-direction,
but only the 3 to 9 nm portion is of significance (rest is vacuum).

http://s21.postimg.org/s75ck7tdj/potentialslicescomparison.png

The graph shows that more the slice size, better the resolution, even for
PME. (no visible noise at higher slice numbers)

What should I conclude out of this? Higher the number of slices, better?
Even using PME?

Ashutosh Shah
Joint School of Nanoscience and Nanoengineering




On Sat, Feb 13, 2016 at 1:56 PM, Warren Gallin  wrote:

> If you are using a slice and PME, then wouldn’t the slice have to be thick
> enough to avoid any ion interacting with its own image in adjacent slices?
>
> It seems to me that thickness would have to be greater than the ionic
> radius at the very least.
>
> Warren Gallin
>
> > On Feb 13, 2016, at 8:39 AM, André Farias de Moura 
> wrote:
> >
> > the ions may have a radius, but they are distributed continuously along
> the
> > system, so you may use slice thicknesses smaller than the ionic radius
> > you're interested in.
> >
> > if the simulation was made on some sort of lattice system (which was very
> > common back in the 1990's), then the shortest, physically meaningful
> slice
> > thickness would be the lattice width. For simulations with freely-moving
> > species, you should only mind about precision: if thickness is too small,
> > density profiles may become too noisy, if it is too large you have loose
> > details of the density profile (maxima, minima, etc), so it's a matter or
> > trial and error to find out what slice thickness suites you better.
> >
> > I hope it helps
> >
> > Andre
> >
> >
> > On Sat, Feb 13, 2016 at 11:57 AM, Ashutosh Akshay Shah <
> > as...@aggies.ncat.edu> wrote:
> >
> >> Hello GROMACS users,
> >>
> >> What is the optimum slice size when trying to capture as much variation
> as
> >> possible?
> >>
> >> Consider a box with an electrolyte having anions and cations
> distributed in
> >> it.
> >>
> >>
> >> *Would be accurate to specify a slice size smaller than the diameter of
> the
> >> ions while calculating the charge variation across the box?*
> >> Thanks!
> >>
> >> Ashutosh Shah
> >> Joint School of Nanoscience and Nanoengineering
> >> --
> >> Gromacs Users mailing list
> >>
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> >> 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.
> >>
> >
> >
> >
> > --
> > _
> >
> > Prof. Dr. André Farias de Moura
> > Department of Chemistry
> > Federal University of São Carlos
> > São Carlos - Brazil
> > phone: +55-16-3351-8090
> > --
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Re: [gmx-users] energygrps

2016-02-13 Thread Justin Lemkul 



On 2/13/16 5:43 PM, Alexander Alexander wrote:

Dear Gromacs user,

By using
"energygrps = A SOL"
We can have SR-NB potential energies between "SOL"-"A" in the energy file,
now suppose that there are three elements with different population in our
system like "A", "B" and "SOL", my question is that what should I
write as "energygrps"
if the SR-NB energies between "(AB)" and "SOL" are required to know? not
"A"-"SOL" interaction and "B"-"SOL" interaction separately.



Then you need an index group that defines AB and energygrps = AB SOL.

-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] Simulation Terminated on Clusters Due to "cannot rename checkpoint file"

2016-02-13 Thread Ray Chao 
D​ear gmx users,

Just a little revision for my last question.

I am running my cases on the cluster. The simulation was always terminated
after running for a while. The error was always "
*cannot rename checkpoint file: maybe you are out of disk space*". However,
I have 1TB of disk
allocation, which is enough,  and the disk is in good condition. Besides, I
created the .top .gro .mdp files on my own workstation and also changed the
permission from "read-only" to "read and write".  The gromacs version is
5.0.2 or 5.1.2 on the clusters.

Is there any specific requirement about running gromacs on clusters? Your
response is very much appreciated.​

You all have a good Valentine's day.
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Re: [gmx-users] DSSP secondary structure

2016-02-13 Thread mohammad r 
Thank you Justin,
I used xpm2ps command with below m2p file but the resolution was not changed. 
I've attached the xpm file, even the legend can't be seen.is there anyway to 
get the result file in pdf format?
m2p file (I found it in the gromacs website):
black = no ; Obsoletetitlefont = Times‐Roman ; A PostScript 
Fonttitlefontsize = 20 ; Font size (pt)legend = yes ; Show the legendlegendfont 
= Times‐Roman ; A PostScript Fontlegendlabel = ; Used when there is none in the 
.xpmlegend2label = ; Used when merging two xpm'slegendfontsize = 14 ; Font size 
(pt)xbox = 2.0 ; x‐size of a matrix elementybox = 2.0 ; y‐size of a matrix 
elementmatrixspacing = 20.0 ; Space between 2 matricesxoffset = 0.0 ; Between 
matrix and bounding boxyoffset = 0.0 ; Between matrix and bounding boxx‐major = 
20 ; Major ticks on x axis every .. framesx‐minor = 5 ; Id. Minor 
ticksx‐firstmajor = 0 ; First frame for major tickx‐majorat0 = no ; Major tick 
at first framex‐majorticklen = 8.0 ; x‐majorticklengthx‐minorticklen = 4.0 ; 
x‐minorticklengthx‐label = ; Used when there is none in the .xpmx‐fontsize = 16 
; Font size (pt)x‐font = Times‐Roman ; A PostScript Fontx‐tickfontsize = 10 ; 
Font size (pt)x‐tickfont = Helvetica ; A PostScript Fonty‐major = 20y‐minor = 
5y‐firstmajor = 0y‐majorat0 = noy‐majorticklen = 8.0y‐minorticklen = 4.0y‐label 
=y‐fontsize = 16y‐font = Times‐Romany‐tickfontsize = 10y‐tickfont = Helvetica
 

On Saturday, February 13, 2016 9:44 PM, Justin Lemkul  
wrote:
 

 

On 2/13/16 1:33 AM, mohammad r wrote:
> Hi,
> I used the "gmx do_dssp" command to get the secondary structure of the 
> protein during the simulation but the resolution of the resulted .xpm file is 
> very low. how can I increase its resolution?

You can adjust the matrix proportions with an .m2p file passed to xpm2ps -di. 
These are almost always necessary as there are many more frames than residues 
in 
the protein, usually an order of magnitude or more.

-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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