date:20121217




On 12/16/12 11:55 PM, Shine A wrote:

Sir,

  I studying the dynamics of membrane proteins.First I did a 20 ns
simulation using GROMOS96 53a6.This force field cause some problems in the
helical part of the protein.Now I am trying to do the same simulation with
opls-aa force field.Is the changes I should have to do in ffnonbonded.itp
and ffbonded,itp is same as in the justin manual?



The concept is the same, but the actual information will be very different.  As 
I recall, there are OPLS-AA lipid parameters somewhere out there, but I've never 
used them personally.  One can also implement a hybrid approach wherein the 
Berger lipids can be made compatible with OPLS-AA.  There's a link to that 
method in my tutorial and it has been discussed on the mailing list at length.


For what it's worth, the helical instability is almost certainly due to the use 
of 53A6, which is known to over-stabilize extended configurations and 
under-stabilize helices.


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] error while running mdrun




On 12/17/12 5:57 AM, ananyachatterjee wrote:


Dear all,

While running mdrun using following mdpparameters:

title= Model MD
; Run parameters
integrator= md
nsteps= 500
dt= 0.002
; Output control
nstxout= 500
nstvout= 500
nstxtcout= 500
nstenergy= 500
nstlog= 500
nstcomm = 100
; Bond parameters
continuation= yes
constraint_algorithm = lincs
constraints= none
lincs_iter= 1
lincs_order= 4
ns_type= grid
nstlist= 5
rlist= 0.9
rcoulomb= 0.9
rvdw= 1.4
; Electrostatics
coulombtype= PME
pme_order= 4
fourierspacing= 0.15
optimize_fft= yes
; Temperature coupling is on
tcoupl= V-rescale
tc-grps= Protein Non-Protein
tau_t= 0.50.5
ref_t= 300 300
; Pressure coupling is on
pcoupl= Parrinello-Rahman
pcoupltype= isotropic
tau_p= 2.0
ref_p= 1.0
compressibility = 4.5e-5
; Periodic boundary conditions
pbc= xyz; 3-D PBC
; Dispersion correction
DispCorr= EnerPres
; Velocity generation
gen_vel= yes


Using multiple processor and I got this following error,

t = 239.934 ps: Water molecule starting at atom 75561 can not be settled.
Check for bad contacts and/or reduce the timestep.
Wrote pdb files with previous and current coordinates
[ganga:04205] *** Process received signal ***
[ganga:04205] Signal: Segmentation fault (11)
[ganga:04205] Signal code: Address not mapped (1)
[ganga:04205] Failing at address: 0x201a01c20
[ganga:04204] *** Process received signal ***
[ganga:04205] [ 0] /lib/libpthread.so.0(+0xfb40) [0x7fa773ac5b40]
[ganga:04205] [ 1] /usr/lib/libmd_mpi_openmpi.so.5(+0x73064) [0x7fa774749064]
[ganga:04205] [ 2] /usr/lib/libmd_mpi_openmpi.so.5(gmx_pme_do+0x323)
[0x7fa77474f420]
[ganga:04205] [ 3] /usr/lib/libmd_mpi_openmpi.so.5(gmx_pmeonly+0x1be)
[0x7fa77474f095]
[ganga:04205] [ 4] mdrun_mpi(mdrunner+0x13df) [0x416f1d]
[ganga:04205] [ 5] mdrun_mpi(main+0x797) [0x41c862]
[ganga:04205] [ 6] /lib/libc.so.6(__libc_start_main+0xfe) [0x7fa773750d8e]
[ganga:04205] [ 7] mdrun_mpi() [0x4056d9]
[ganga:04205] *** End of error message ***
[ganga:04204] Signal: Segmentation fault (11)
[ganga:04204] Signal code: Address not mapped (1)
[ganga:04204] Failing at address: 0x7518df0
--
mpirun noticed that process rank 10 with PID 4205 on node ganga exited on signal
11 (Segmentation fault).
--
[ganga:04204] [ 0] /lib/libpthread.so.0(+0xfb40) [0x7f488c4e3b40]
[ganga:04204] [ 1] /usr/lib/libgmx_mpi_openmpi.so.5(+0x10db29) [0x7f488cd2fb29]
[ganga:04204] *** End of error message ***
mani@ganga:~/project/gromacs/MUT$


Can any one help me where I am getting wrong.


Probably insufficient energy minimization.

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

-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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[gmx-users] mdp file warnings

2012-12-17 Thread Eduardo Oliveira

Hi,

I'm setting my system but when I run grompp I get a warning and the program 
terminates.  It says the following: 

You are using  pressure coupling with absolute position restraints, this will 
give artifacts. Use refcoord_scaling option.


I want to try it but i don't know where to change this term in the mdp file. 
Any help?

title                    = 500ps_pr_fixo
cpp                      = /lib/cpp
define                   = -DPOSRES
integrator               = md
tinit                    = 0
dt                       = 0.002
nsteps                   = 25 ; total 500 ps
comm-mode                = Linear
nstcomm                  = 1
nstxout                  = 500
nstvout                  = 2
nstfout                  = 2
nstlog                   = 1000
nstenergy                = 100
nstxtcout                = 500
xtc-precision            = 1000
energygrps               = Protein SOL NA 
nstlist                  = 5
ns_type                  = grid
pbc                      = xyz
rlist                    = 1.0
domain-decomposition     = no
coulombtype              = PME
rcoulomb                 = 1.0
epsilon-r                = 1
vdw-type                 = Cut-off
rvdw                     = 1.4
DispCorr                 = EnerPres
optimize_fft             = yes
Tcoupl                   = V-rescale ;berendsen
tc-grps                  = Protein Non-protein   
tau-t                    = .1 .1 
ref-t                    = 310 310
gen_vel                  = yes
gen_temp                 = 310
gen_seed                 = 173529
Pcoupl                   = berendsen
Pcoupltype               = Isotropic
tau-p                    = 1
compressibility          = 4.5e-5
ref-p                    = 1
constraints              = all-bonds
constraint-algorithm     = Lincs
unconstrained-start      = no
Shake-SOR                = no
shake-tol                = 1e-04
lincs-order              = 4
lincs-warnangle          = 30
morse                    = no
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Re: [gmx-users] error when running NVT equilibrium

On 12/17/12 8:53 AM, Kieu Thu Nguyen wrote:

Dear All,

I'm practising the tutorial 2a (protein in water) in the MARTINI tutorial.
After doing step 6 (Do a short energy minimization and position restrained
simulation),i carry out running NVT equilibrium. But it appears the error
in the terminal :

Fatal error:
There is no domain decomposition for 2 nodes that is compatible with the
given box and a minimum cell size of 5.2375 nm
Change the number of nodes or mdrun option -rcon or -dds or your LINCS
settings
Look in the log file for details on the domain decomposition

What can i do to fix this error ?

http://www.gromacs.org/Documentation/Errors#There_is_no_domain_decomposition_for_n_nodes_that_is_compatible_with_the_given_box_and_a_minimum_cell_size_of_x_nm

The fact that the minimum size is over 5 nm is very odd. Are there very
long-range bonded interactions of some sort? Normally the minimum box size is
very close to the value of the longest cutoff unless something abnormal is present.

-Justin

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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Re: [gmx-users] mdp file warnings




On 12/17/12 8:55 AM, Eduardo Oliveira wrote:

Hi,

I'm setting my system but when I run grompp I get a warning and the program 
terminates.  It says the following:

You are using  pressure coupling with absolute position restraints, this will 
give artifacts. Use refcoord_scaling option.


I want to try it but i don't know where to change this term in the mdp file. 
Any help?



Location within the file is irrelevant.  For most cases, you want 
refcoord_scaling = com.  See the numerous discussions on this topic in the 
list archive.


-Justin


title= 500ps_pr_fixo
cpp  = /lib/cpp
define   = -DPOSRES
integrator   = md
tinit= 0
dt   = 0.002
nsteps   = 25 ; total 500 ps
comm-mode= Linear
nstcomm  = 1
nstxout  = 500
nstvout  = 2
nstfout  = 2
nstlog   = 1000
nstenergy= 100
nstxtcout= 500
xtc-precision= 1000
energygrps   = Protein SOL NA
nstlist  = 5
ns_type  = grid
pbc  = xyz
rlist= 1.0
domain-decomposition = no
coulombtype  = PME
rcoulomb = 1.0
epsilon-r= 1
vdw-type = Cut-off
rvdw = 1.4
DispCorr = EnerPres
optimize_fft = yes
Tcoupl   = V-rescale ;berendsen
tc-grps  = Protein Non-protein
tau-t= .1 .1
ref-t= 310 310
gen_vel  = yes
gen_temp = 310
gen_seed = 173529
Pcoupl   = berendsen
Pcoupltype   = Isotropic
tau-p= 1
compressibility  = 4.5e-5
ref-p= 1
constraints  = all-bonds
constraint-algorithm = Lincs
unconstrained-start  = no
Shake-SOR= no
shake-tol= 1e-04
lincs-order  = 4
lincs-warnangle  = 30
morse= no



--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] mdp file warnings

2012-12-17 Thread Eduardo Oliveira

OK, so if i got this right all I have to do is add another line in the mdp file 
with refcoord_scaling = com?  I thought that i had to make a substitution in 
one of the existing terms.

Thanks.



 De: Justin Lemkul jalem...@vt.edu
Para: Eduardo Oliveira eduardo...@yahoo.com.br; Discussion list for GROMACS 
users gmx-users@gromacs.org 
Enviadas: Segunda-feira, 17 de Dezembro de 2012 11:57
Assunto: Re: [gmx-users] mdp file warnings
 


On 12/17/12 8:55 AM, Eduardo Oliveira wrote:
 Hi,

 I'm setting my system but when I run grompp I get a warning and the program 
 terminates.  It says the following:

 You are using  pressure coupling with absolute position restraints, this will 
 give artifacts. Use refcoord_scaling option.


 I want to try it but i don't know where to change this term in the mdp file. 
 Any help?


Location within the file is irrelevant.  For most cases, you want 
refcoord_scaling = com.  See the numerous discussions on this topic in the 
list archive.

-Justin

 title                    = 500ps_pr_fixo
 cpp                      = /lib/cpp
 define                   = -DPOSRES
 integrator               = md
 tinit                    = 0
 dt                       = 0.002
 nsteps                   = 25 ; total 500 ps
 comm-mode                = Linear
 nstcomm                  = 1
 nstxout                  = 500
 nstvout                  = 2
 nstfout                  = 2
 nstlog                   = 1000
 nstenergy                = 100
 nstxtcout                = 500
 xtc-precision            = 1000
 energygrps               = Protein SOL NA
 nstlist                  = 5
 ns_type                  = grid
 pbc                      = xyz
 rlist                    = 1.0
 domain-decomposition     = no
 coulombtype              = PME
 rcoulomb                 = 1.0
 epsilon-r                = 1
 vdw-type                 = Cut-off
 rvdw                     = 1.4
 DispCorr                 = EnerPres
 optimize_fft             = yes
 Tcoupl                   = V-rescale ;berendsen
 tc-grps                  = Protein Non-protein
 tau-t                    = .1 .1
 ref-t                    = 310 310
 gen_vel                  = yes
 gen_temp                 = 310
 gen_seed                 = 173529
 Pcoupl                   = berendsen
 Pcoupltype               = Isotropic
 tau-p                    = 1
 compressibility          = 4.5e-5
 ref-p                    = 1
 constraints              = all-bonds
 constraint-algorithm     = Lincs
 unconstrained-start      = no
 Shake-SOR                = no
 shake-tol                = 1e-04
 lincs-order              = 4
 lincs-warnangle          = 30
 morse                    = no


-- 


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] mdp file warnings




On 12/17/12 9:06 AM, Eduardo Oliveira wrote:

OK, so if i got this right all I have to do is add another line in the mdp file
with refcoord_scaling = com?  I thought that i had to make a substitution in one
of the existing terms.



Right, it's a new term entirely (see the manual).  All keywords have a default 
setting that is accepted if not explicitly given in the .mdp file.  For 
refcoord_scaling, the default is no, which will trigger the warning you got 
when used with position restraints.


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] error when running NVT equilibrium

Dear Justin,

The nvt.mdp file is:

define= -DPOSRES; position restrain the protein
; Run parameters
integrator= md; leap-frog integrator
nsteps= 5; 2 * 5 = 100 ps
dt= 0.002; 2 fs
; Output control
nstxout= 100; save coordinates every 0.2 ps
nstvout= 100; save velocities every 0.2 ps
nstenergy= 100; save energies every 0.2 ps
nstlog= 100; update log file every 0.2 ps
; Bond parameters
continuation= no; first dynamics run
constraint_algorithm = lincs; holonomic constraints
constraints= all-bonds; all bonds (even heavy atom-H bonds)
constrained
lincs_iter= 1; accuracy of LINCS
lincs_order= 4; also related to accuracy
; Neighborsearching
ns_type= grid; search neighboring grid cells
nstlist= 5; 10 fs
rlist= 1.2; short-range neighborlist cutoff (in nm)
rcoulomb= 1.2; short-range electrostatic cutoff (in nm)
rvdw= 1.2; short-range van der Waals cutoff (in nm)
; Electrostatics
coulombtype= PME; Particle Mesh Ewald for long-range
electrostatics
pme_order= 4; cubic interpolation
fourierspacing= 0.16; grid spacing for FFT
; Temperature coupling is on
tcoupl= V-rescale; modified Berendsen thermostat
tc-grps= Protein Non-Protein; two coupling groups - more
accurate
tau_t= 0.10.1; time constant, in ps
ref_t= 300 300; reference temperature, one for each group,
in K
; Pressure coupling is off
pcoupl= no ; no pressure coupling in NVT
; Periodic boundary conditions
pbc= xyz; 3-D PBC
; Dispersion correction
DispCorr= EnerPres; account for cut-off vdW scheme
; Velocity generation
gen_vel= yes; assign velocities from Maxwell distribution
gen_temp= 300; temperature for Maxwell distribution
gen_seed= -1; generate a random seed


Are there any something abnormal ?


On Mon, Dec 17, 2012 at 8:56 PM, Justin Lemkul jalem...@vt.edu wrote:



 On 12/17/12 8:53 AM, Kieu Thu Nguyen wrote:

 Dear All,

 I'm practising the tutorial 2a (protein in water) in the MARTINI tutorial.
 After doing step 6 (Do a short energy minimization and position restrained
 simulation),i carry out running NVT equilibrium. But it appears the error
 in the terminal :

 Fatal error:
 There is no domain decomposition for 2 nodes that is compatible with the
 given box and a minimum cell size of 5.2375 nm
 Change the number of nodes or mdrun option -rcon or -dds or your LINCS
 settings
 Look in the log file for details on the domain decomposition

 What can i do to fix this error ?


 http://www.gromacs.org/**Documentation/Errors#There_is_**
 no_domain_decomposition_for_n_**nodes_that_is_compatible_with_**
 the_given_box_and_a_minimum_**cell_size_of_x_nmhttp://www.gromacs.org/Documentation/Errors#There_is_no_domain_decomposition_for_n_nodes_that_is_compatible_with_the_given_box_and_a_minimum_cell_size_of_x_nm

 The fact that the minimum size is over 5 nm is very odd.  Are there very
 long-range bonded interactions of some sort?  Normally the minimum box size
 is very close to the value of the longest cutoff unless something abnormal
 is present.

 -Justin

 --
 ==**==

 Justin A. Lemkul, Ph.D.
 Research Scientist
 Department of Biochemistry
 Virginia Tech
 Blacksburg, VA
 jalemkul[at]vt.edu | (540) 231-9080
 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

 ==**==
 --
 gmx-users mailing listgmx-users@gromacs.org
 http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users
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 Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore
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Re: [gmx-users] error when running NVT equilibrium




On 12/17/12 9:14 AM, Kieu Thu Nguyen wrote:

Dear Justin,

The nvt.mdp file is:

define= -DPOSRES; position restrain the protein
; Run parameters
integrator= md; leap-frog integrator
nsteps= 5; 2 * 5 = 100 ps
dt= 0.002; 2 fs
; Output control
nstxout= 100; save coordinates every 0.2 ps
nstvout= 100; save velocities every 0.2 ps
nstenergy= 100; save energies every 0.2 ps
nstlog= 100; update log file every 0.2 ps
; Bond parameters
continuation= no; first dynamics run
constraint_algorithm = lincs; holonomic constraints
constraints= all-bonds; all bonds (even heavy atom-H bonds)
constrained
lincs_iter= 1; accuracy of LINCS
lincs_order= 4; also related to accuracy
; Neighborsearching
ns_type= grid; search neighboring grid cells
nstlist= 5; 10 fs
rlist= 1.2; short-range neighborlist cutoff (in nm)
rcoulomb= 1.2; short-range electrostatic cutoff (in nm)
rvdw= 1.2; short-range van der Waals cutoff (in nm)
; Electrostatics
coulombtype= PME; Particle Mesh Ewald for long-range
electrostatics
pme_order= 4; cubic interpolation
fourierspacing= 0.16; grid spacing for FFT
; Temperature coupling is on
tcoupl= V-rescale; modified Berendsen thermostat
tc-grps= Protein Non-Protein; two coupling groups - more
accurate
tau_t= 0.10.1; time constant, in ps
ref_t= 300 300; reference temperature, one for each group,
in K
; Pressure coupling is off
pcoupl= no ; no pressure coupling in NVT
; Periodic boundary conditions
pbc= xyz; 3-D PBC
; Dispersion correction
DispCorr= EnerPres; account for cut-off vdW scheme
; Velocity generation
gen_vel= yes; assign velocities from Maxwell distribution
gen_temp= 300; temperature for Maxwell distribution
gen_seed= -1; generate a random seed


Are there any something abnormal ?



Not here.  The log file should have a breakdown of the interaction ranges, which 
it establishes right before the fatal error.  That would be much more 
informative.  It could be any number of things - pair interaction, restraint in 
the topology, broken starting structure, etc.


-Justin



On Mon, Dec 17, 2012 at 8:56 PM, Justin Lemkul jalem...@vt.edu wrote:




On 12/17/12 8:53 AM, Kieu Thu Nguyen wrote:


Dear All,

I'm practising the tutorial 2a (protein in water) in the MARTINI tutorial.
After doing step 6 (Do a short energy minimization and position restrained
simulation),i carry out running NVT equilibrium. But it appears the error
in the terminal :

Fatal error:
There is no domain decomposition for 2 nodes that is compatible with the
given box and a minimum cell size of 5.2375 nm
Change the number of nodes or mdrun option -rcon or -dds or your LINCS
settings
Look in the log file for details on the domain decomposition

What can i do to fix this error ?



http://www.gromacs.org/**Documentation/Errors#There_is_**
no_domain_decomposition_for_n_**nodes_that_is_compatible_with_**
the_given_box_and_a_minimum_**cell_size_of_x_nmhttp://www.gromacs.org/Documentation/Errors#There_is_no_domain_decomposition_for_n_nodes_that_is_compatible_with_the_given_box_and_a_minimum_cell_size_of_x_nm

The fact that the minimum size is over 5 nm is very odd.  Are there very
long-range bonded interactions of some sort?  Normally the minimum box size
is very close to the value of the longest cutoff unless something abnormal
is present.

-Justin

--
==**==

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] mdp file warnings

2012-12-17 Thread Eduardo Oliveira

Ok,

Thanks a lot!



 De: Justin Lemkul jalem...@vt.edu
Para: Discussion list for GROMACS users gmx-users@gromacs.org 
Enviadas: Segunda-feira, 17 de Dezembro de 2012 12:08
Assunto: Re: [gmx-users] mdp file warnings
 


On 12/17/12 9:06 AM, Eduardo Oliveira wrote:
 OK, so if i got this right all I have to do is add another line in the mdp 
 file
 with refcoord_scaling = com?  I thought that i had to make a substitution in 
 one
 of the existing terms.
 

Right, it's a new term entirely (see the manual).  All keywords have a default 
setting that is accepted if not explicitly given in the .mdp file.  For 
refcoord_scaling, the default is no, which will trigger the warning you got 
when used with position restraints.

-Justin

-- 

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] error No such moleculetype W




On 12/17/12 9:24 AM, Kieu Thu Nguyen wrote:

Dear All,

When i do the Step Four: Adding Ionsin the tutorial KALP-15 in DPPC, it
appears the error:

Fatal error:
No such moleculetype W

I checked .top file and included.itp files, they have definded water
molecule type name is W.

What happens ?



There's got to be something wrong with what's #included or how it's named.  The 
error is pretty straightforward.


Also note that you are not, in fact, doing the tutorial - you are following its 
suggested method with some different system.  I cannot guarantee that the 
tutorial is suited for whatever you're trying to do.  The workflow might be 
similar, but other aspects (practical considerations, .mdp files, etc) may be 
different.


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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[gmx-users] extract dihedrals from ALAD.pdb

2012-12-17 Thread Antonia Mey

Hi,
I am trying to simulate alanine dipeptide with the CHARMM27 force field
I have downloaded the ALAD file provided here:

http://www.charmm-gui.org/?doc=archivelib=csml

And the run pdb2gmx, solvation, minimization and nvt equilibration
Everything worked fine, but when I want to use g_rama to extract the dihedral 
angle pairs, none are found.
how and where do I need to add the information manually so that the dihedral 
phi and psi pair around 5 7 9 15 and 7 9 15 17 is found?

Adding the following line to the topology file did not solve the problem:
[ dihedrals]

  5  7 9 15 1
  7  9 1517 1

Any help would be greatly appreciated!

Best,
AntoniaThis message and any attachment are intended solely for the addressee 
and may contain confidential information. If you have received this message in 
error, please send it back to me, and immediately delete it.   Please do not 
use, copy or disclose the information contained in this message or in any 
attachment.  Any views or opinions expressed by the author of this email do not 
necessarily reflect the views of the University of Nottingham.

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[gmx-users] virtual site generation for backbone hydrogen

2012-12-17 Thread Jochen Hub


Hi all,

I try to generate a topology using pdb2gmx of a protein that contains a 
non-native amino acid, that is lysine with some more atoms, which is 
treated a one amino acid RETK.


Without vsites, everything works fine. With pdb2gmx -vsite hydrogen, a 
constraint is generated between the backbone CA and H (that gives an 
error later grompp since the constraint type CT-H is not defined).


[ atoms ]
...
  3603  H216   RETK  H   3241 0.2747  1.008
  3604 CT216   RETK CA   3242  -0.24 13.018
[ constraints ]
 3603  3604 2

If the non-native aa is replaced by a LYS, pdb2gmx generates instead:

[ virtual_sites3 ]
 3603  3602  3600  3604 2

I now wonder how to tell pdb2gmx that RETK should be treated as any 
other amino acid, that is that the backbone-H should be turned into a 
virtual_site3.


I have already added RETK into residuetypes.dat, and there are entries 
in the rtp and hdb.


Many thanks in advance for any help,
Jochen



--
---
Dr. Jochen Hub
Computational Molecular Biophysics Group
Institute for Microbiology and Genetics
Georg-August-University of Göttingen
Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany.
Phone: +49-551-39-14189
http://cmb.bio.uni-goettingen.de/
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[gmx-users] GPU running problem with GMX-4.6 beta2


hello:

 I am running GMX-4.6 beta2 GPU work in a 24 CPU core workstation with 
two GTX590, it stacked there without any output i.e the .xtc file size 
is always 0 after hours of running. Here is the md.log file I found:



Using CUDA 8x8x8 non-bonded kernels

Potential shift: LJ r^-12: 0.112 r^-6 0.335, Ewald 1.000e-05
Initialized non-bonded Ewald correction tables, spacing: 7.82e-04 size: 1536

Removing pbc first time
Pinning to Hyper-Threading cores with 12 physical cores in a compute node
There are 1 flexible constraints

WARNING: step size for flexible constraining = 0
 All flexible constraints will be rigid.
 Will try to keep all flexible constraints at their original 
length,

 but the lengths may exhibit some drift.

Initializing Parallel LINear Constraint Solver
Linking all bonded interactions to atoms
There are 161872 inter charge-group exclusions,
will use an extra communication step for exclusion forces for PME

The initial number of communication pulses is: X 1
The initial domain decomposition cell size is: X 1.83 nm

The maximum allowed distance for charge groups involved in interactions is:
 non-bonded interactions   1.200 nm
(the following are initial values, they could change due to box deformation)
two-body bonded interactions  (-rdd)   1.200 nm
  multi-body bonded interactions  (-rdd)   1.200 nm
  atoms separated by up to 5 constraints  (-rcon)  1.826 nm

When dynamic load balancing gets turned on, these settings will change to:
The maximum number of communication pulses is: X 1
The minimum size for domain decomposition cells is 1.200 nm
The requested allowed shrink of DD cells (option -dds) is: 0.80
The allowed shrink of domain decomposition cells is: X 0.66
The maximum allowed distance for charge groups involved in interactions is:
 non-bonded interactions   1.200 nm
two-body bonded interactions  (-rdd)   1.200 nm
  multi-body bonded interactions  (-rdd)   1.200 nm
  atoms separated by up to 5 constraints  (-rcon)  1.200 nm

Making 1D domain decomposition grid 4 x 1 x 1, home cell index 0 0 0

Center of mass motion removal mode is Linear
We have the following groups for center of mass motion removal:
  0:  Protein_LIG_POPC
  1:  Water_and_ions

 PLEASE READ AND CITE THE FOLLOWING REFERENCE 
G. Bussi, D. Donadio and M. Parrinello
Canonical sampling through velocity rescaling
J. Chem. Phys. 126 (2007) pp. 014101
  --- Thank You ---  



THX
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Re: [gmx-users] error No such moleculetype W

Thank Justin ! I found my mistake. But when i type the next command line

 genion -s ions.tpr -o system_solv_ions.gro -p topol.top -pname NA -nname
CL -nn 4

and choose group 0 (system), the error is

Fatal error:
No line with moleculetype 'System' found the [ molecules ] section of file
'topol.top'

the section [molecules] in my tolpol.top file is

[ molecules ]
; Compound#mols
Protein1
DPPC126
SOL  15628

Should i add System into topol.top file ?

Regards
KT


On Mon, Dec 17, 2012 at 9:31 PM, Justin Lemkul jalem...@vt.edu wrote:



 On 12/17/12 9:24 AM, Kieu Thu Nguyen wrote:

 Dear All,

 When i do the Step Four: Adding Ionsin the tutorial KALP-15 in DPPC,
 it
 appears the error:

 Fatal error:
 No such moleculetype W

 I checked .top file and included.itp files, they have definded water
 molecule type name is W.

 What happens ?


 There's got to be something wrong with what's #included or how it's named.
  The error is pretty straightforward.

 Also note that you are not, in fact, doing the tutorial - you are
 following its suggested method with some different system.  I cannot
 guarantee that the tutorial is suited for whatever you're trying to do.
  The workflow might be similar, but other aspects (practical
 considerations, .mdp files, etc) may be different.

 -Justin

 --
 ==**==

 Justin A. Lemkul, Ph.D.
 Research Scientist
 Department of Biochemistry
 Virginia Tech
 Blacksburg, VA
 jalemkul[at]vt.edu | (540) 231-9080
 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

 ==**==
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Re: [gmx-users] GPU running problem with GMX-4.6 beta2

Hi,

That unfortunately tell exactly about the reason why mdrun is stuck. Can
you reproduce the issue on another machines or with different launch
configurations? At which step does it get stuck (-stepout 1 can help)?

Please try the following:
- try running on a single GPU;
- try running on CPUs only (-nb cpu and to match closer the GPU setup with
-ntomp 12);
- try running in GPU emulation mode with the GMX_EMULATE_GPU=1 env. var
set (and to match closer the GPU setup with -ntomp 12)
- provide a backtrace (using gdb).

Cheers,

--
Szilárd



On Mon, Dec 17, 2012 at 5:37 PM, Albert mailmd2...@gmail.com wrote:

 hello:

  I am running GMX-4.6 beta2 GPU work in a 24 CPU core workstation with two
 GTX590, it stacked there without any output i.e the .xtc file size is
 always 0 after hours of running. Here is the md.log file I found:


 Using CUDA 8x8x8 non-bonded kernels

 Potential shift: LJ r^-12: 0.112 r^-6 0.335, Ewald 1.000e-05
 Initialized non-bonded Ewald correction tables, spacing: 7.82e-04 size:
 1536

 Removing pbc first time
 Pinning to Hyper-Threading cores with 12 physical cores in a compute node
 There are 1 flexible constraints

 WARNING: step size for flexible constraining = 0
  All flexible constraints will be rigid.
  Will try to keep all flexible constraints at their original
 length,
  but the lengths may exhibit some drift.

 Initializing Parallel LINear Constraint Solver
 Linking all bonded interactions to atoms
 There are 161872 inter charge-group exclusions,
 will use an extra communication step for exclusion forces for PME

 The initial number of communication pulses is: X 1
 The initial domain decomposition cell size is: X 1.83 nm

 The maximum allowed distance for charge groups involved in interactions is:
  non-bonded interactions   1.200 nm
 (the following are initial values, they could change due to box
 deformation)
 two-body bonded interactions  (-rdd)   1.200 nm
   multi-body bonded interactions  (-rdd)   1.200 nm
   atoms separated by up to 5 constraints  (-rcon)  1.826 nm

 When dynamic load balancing gets turned on, these settings will change to:
 The maximum number of communication pulses is: X 1
 The minimum size for domain decomposition cells is 1.200 nm
 The requested allowed shrink of DD cells (option -dds) is: 0.80
 The allowed shrink of domain decomposition cells is: X 0.66
 The maximum allowed distance for charge groups involved in interactions is:
  non-bonded interactions   1.200 nm
 two-body bonded interactions  (-rdd)   1.200 nm
   multi-body bonded interactions  (-rdd)   1.200 nm
   atoms separated by up to 5 constraints  (-rcon)  1.200 nm

 Making 1D domain decomposition grid 4 x 1 x 1, home cell index 0 0 0

 Center of mass motion removal mode is Linear
 We have the following groups for center of mass motion removal:
   0:  Protein_LIG_POPC
   1:  Water_and_ions

  PLEASE READ AND CITE THE FOLLOWING REFERENCE 
 G. Bussi, D. Donadio and M. Parrinello
 Canonical sampling through velocity rescaling
 J. Chem. Phys. 126 (2007) pp. 014101
   --- Thank You ---  



 THX
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Re: [gmx-users] error No such moleculetype W

I have just found the right group is 15 (SOL) :-)

Thanks so much and sorry about my stupid question !


On Mon, Dec 17, 2012 at 11:40 PM, Justin Lemkul jalem...@vt.edu wrote:



 On 12/17/12 11:38 AM, Kieu Thu Nguyen wrote:

 Thank Justin ! I found my mistake. But when i type the next command line

   genion -s ions.tpr -o system_solv_ions.gro -p topol.top -pname NA -nname
 CL -nn 4

 and choose group 0 (system), the error is

 Fatal error:
 No line with moleculetype 'System' found the [ molecules ] section of file
 'topol.top'

 the section [molecules] in my tolpol.top file is

 [ molecules ]
 ; Compound#mols
 Protein1
 DPPC126
 SOL  15628

 Should i add System into topol.top file ?


 Absolutely not.  Read what genion does - it replaces solvent molecules
 with ions.  If you choose System (which you can't, because that's a group,
 not a [moleculetype]) you'll start haphazardly replacing random molecules
 with ions. Definitely not what you want.


 -Justin

 --
 ==**==

 Justin A. Lemkul, Ph.D.
 Research Scientist
 Department of Biochemistry
 Virginia Tech
 Blacksburg, VA
 jalemkul[at]vt.edu | (540) 231-9080
 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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Re: [gmx-users] GPU running problem with GMX-4.6 beta2


hello:

 I reduced the GPU to two, and it said:

Back Off! I just backed up nvt.log to ./#nvt.log.1#
Reading file nvt.tpr, VERSION 4.6-dev-20121004-5d6c49d (single precision)

NOTE: GPU(s) found, but the current simulation can not use GPUs
  To use a GPU, set the mdp option: cutoff-scheme = Verlet
  (for quick performance testing you can use the -testverlet option)

Using 2 MPI processes

4 GPUs detected on host CUDANodeA:
  #0: NVIDIA GeForce GTX 590, compute cap.: 2.0, ECC:  no, stat: compatible
  #1: NVIDIA GeForce GTX 590, compute cap.: 2.0, ECC:  no, stat: compatible
  #2: NVIDIA GeForce GTX 590, compute cap.: 2.0, ECC:  no, stat: compatible
  #3: NVIDIA GeForce GTX 590, compute cap.: 2.0, ECC:  no, stat: compatible

Making 1D domain decomposition 2 x 1 x 1

* WARNING * WARNING * WARNING * WARNING * WARNING * WARNING *
We have just committed the new CPU detection code in this branch,
and will commit new SSE/AVX kernels in a few days. However, this
means that currently only the NxN kernels are accelerated!
In the mean time, you might want to avoid production runs in 4.6.


when I run it with single GPU, it produced lots of pdb file with prefix 
step, and then it crashed with messages:


Wrote pdb files with previous and current coordinates
Warning: 1-4 interaction between 4674 and 4706 at distance 434.986 which 
is larger than the 1-4 table size 2.200 nm

These are ignored for the rest of the simulation
This usually means your system is exploding,
if not, you should increase table-extension in your mdp file
or with user tables increase the table size
[CUDANodeA:20659] *** Process received signal ***
[CUDANodeA:20659] Signal: Segmentation fault (11)
[CUDANodeA:20659] Signal code: Address not mapped (1)
[CUDANodeA:20659] Failing at address: 0xc7aa00dc
[CUDANodeA:20659] [ 0] /lib64/libpthread.so.0(+0xf2d0) [0x2ab25c76d2d0]
[CUDANodeA:20659] [ 1] /opt/gromacs-4.6/lib/libmd_mpi.so.6(+0x11020f) 
[0x2ab259e0720f]
[CUDANodeA:20659] [ 2] /opt/gromacs-4.6/lib/libmd_mpi.so.6(+0x111c94) 
[0x2ab259e08c94]
[CUDANodeA:20659] [ 3] 
/opt/gromacs-4.6/lib/libmd_mpi.so.6(gmx_pme_do+0x1d2e) [0x2ab259e0cbae]
[CUDANodeA:20659] [ 4] 
/opt/gromacs-4.6/lib/libmd_mpi.so.6(do_force_lowlevel+0x1eef) 
[0x2ab259ddd62f]
[CUDANodeA:20659] [ 5] 
/opt/gromacs-4.6/lib/libmd_mpi.so.6(do_force_cutsGROUP+0x1495) 
[0x2ab259e72a45]

[CUDANodeA:20659] [ 6] mdrun_mpi(do_md+0x8133) [0x4334c3]
[CUDANodeA:20659] [ 7] mdrun_mpi(mdrunner+0x19e9) [0x411639]
[CUDANodeA:20659] [ 8] mdrun_mpi(main+0x17db) [0x4373db]
[CUDANodeA:20659] [ 9] /lib64/libc.so.6(__libc_start_main+0xfd) 
[0x2ab25c999bfd]

[CUDANodeA:20659] [10] mdrun_mpi() [0x407f09]
[CUDANodeA:20659] *** End of error message ***

[1]Segmentation faultmdrun_mpi -v -s nvt.tpr -c nvt.gro 
-g nvt.log -x nvt.xtc




here is the .mdp file I used:

title   = NVT equilibration for OR-POPC system
define  = -DPOSRES -DPOSRES_LIG ; Protein is position restrained 
(uses the posres.itp file information)

; Parameters describing the details of the NVT simulation protocol
integrator  = md; Algorithm (md = molecular dynamics 
[leap-frog integrator]; md-vv = md using velocity verlet; sd = 
stochastic dynamics)

dt  = 0.002 ; Time-step (ps)
nsteps  = 25; Number of steps to run (0.002 * 25 
= 500 ps)


; Parameters controlling output writing
nstxout = 0 ; Write coordinates to output .trr file 
every 2 ps
nstvout = 0 ; Write velocities to output .trr file 
every 2 ps

nstfout = 0

nstxtcout   = 1000
nstenergy   = 1000  ; Write energies to output .edr file 
every 2 ps

nstlog  = 1000  ; Write output to .log file every 2 ps

; Parameters describing neighbors searching and details about 
interaction calculations

ns_type = grid  ; Neighbor list search method (simple, grid)
nstlist = 50; Neighbor list update frequency (after 
every given number of steps)

rlist   = 1.2   ; Neighbor list search cut-off distance (nm)
rlistlong   = 1.4
rcoulomb= 1.2   ; Short-range Coulombic interactions 
cut-off distance (nm)
rvdw= 1.2   ; Short-range van der Waals cutoff 
distance (nm)
pbc = xyz   ; Direction in which to use Perodic 
Boundary Conditions (xyz, xy, no)

cutoff-scheme   =Verlet  ; GPU running

; Parameters for treating bonded interactions
continuation= no; Whether a fresh start or a 
continuation from a previous run (yes/no)

constraint_algorithm = LINCS; Constraint algorithm (LINCS / SHAKE)
constraints = all-bonds ; Which bonds/angles to constrain 
(all-bonds / hbonds / none / all-angles / h-angles)
lincs_iter  = 1 ; Number of iterations to correct for 
rotational lengthening in LINCS (related to accuracy)
lincs_order = 4 ; Highest order in the expansion of the 
constraint

Re: [gmx-users] GPU running problem with GMX-4.6 beta2

Hi,

How about GPU emulation or CPU-only runs? Also, please try setting the
number of therads to 1 (-ntomp 1).


--
Szilárd



On Mon, Dec 17, 2012 at 6:01 PM, Albert mailmd2...@gmail.com wrote:

 hello:

  I reduced the GPU to two, and it said:

 Back Off! I just backed up nvt.log to ./#nvt.log.1#
 Reading file nvt.tpr, VERSION 4.6-dev-20121004-5d6c49d (single precision)

 NOTE: GPU(s) found, but the current simulation can not use GPUs
   To use a GPU, set the mdp option: cutoff-scheme = Verlet
   (for quick performance testing you can use the -testverlet option)

 Using 2 MPI processes

 4 GPUs detected on host CUDANodeA:
   #0: NVIDIA GeForce GTX 590, compute cap.: 2.0, ECC:  no, stat: compatible
   #1: NVIDIA GeForce GTX 590, compute cap.: 2.0, ECC:  no, stat: compatible
   #2: NVIDIA GeForce GTX 590, compute cap.: 2.0, ECC:  no, stat: compatible
   #3: NVIDIA GeForce GTX 590, compute cap.: 2.0, ECC:  no, stat: compatible

 Making 1D domain decomposition 2 x 1 x 1

 * WARNING * WARNING * WARNING * WARNING * WARNING * WARNING *
 We have just committed the new CPU detection code in this branch,
 and will commit new SSE/AVX kernels in a few days. However, this
 means that currently only the NxN kernels are accelerated!
 In the mean time, you might want to avoid production runs in 4.6.


 when I run it with single GPU, it produced lots of pdb file with prefix
 step, and then it crashed with messages:

 Wrote pdb files with previous and current coordinates
 Warning: 1-4 interaction between 4674 and 4706 at distance 434.986 which
 is larger than the 1-4 table size 2.200 nm
 These are ignored for the rest of the simulation
 This usually means your system is exploding,
 if not, you should increase table-extension in your mdp file
 or with user tables increase the table size
 [CUDANodeA:20659] *** Process received signal ***
 [CUDANodeA:20659] Signal: Segmentation fault (11)
 [CUDANodeA:20659] Signal code: Address not mapped (1)
 [CUDANodeA:20659] Failing at address: 0xc7aa00dc
 [CUDANodeA:20659] [ 0] /lib64/libpthread.so.0(+**0xf2d0) [0x2ab25c76d2d0]
 [CUDANodeA:20659] [ 1] /opt/gromacs-4.6/lib/libmd_**mpi.so.6(+0x11020f)
 [0x2ab259e0720f]
 [CUDANodeA:20659] [ 2] /opt/gromacs-4.6/lib/libmd_**mpi.so.6(+0x111c94)
 [0x2ab259e08c94]
 [CUDANodeA:20659] [ 3] 
 /opt/gromacs-4.6/lib/libmd_**mpi.so.6(gmx_pme_do+0x1d2e)
 [0x2ab259e0cbae]
 [CUDANodeA:20659] [ 4] /opt/gromacs-4.6/lib/libmd_**
 mpi.so.6(do_force_lowlevel+**0x1eef) [0x2ab259ddd62f]
 [CUDANodeA:20659] [ 5] /opt/gromacs-4.6/lib/libmd_**
 mpi.so.6(do_force_cutsGROUP+**0x1495) [0x2ab259e72a45]
 [CUDANodeA:20659] [ 6] mdrun_mpi(do_md+0x8133) [0x4334c3]
 [CUDANodeA:20659] [ 7] mdrun_mpi(mdrunner+0x19e9) [0x411639]
 [CUDANodeA:20659] [ 8] mdrun_mpi(main+0x17db) [0x4373db]
 [CUDANodeA:20659] [ 9] /lib64/libc.so.6(__libc_start_**main+0xfd)
 [0x2ab25c999bfd]
 [CUDANodeA:20659] [10] mdrun_mpi() [0x407f09]
 [CUDANodeA:20659] *** End of error message ***

 [1]Segmentation faultmdrun_mpi -v -s nvt.tpr -c nvt.gro -g
 nvt.log -x nvt.xtc



 here is the .mdp file I used:

 title   = NVT equilibration for OR-POPC system
 define  = -DPOSRES -DPOSRES_LIG ; Protein is position restrained
 (uses the posres.itp file information)
 ; Parameters describing the details of the NVT simulation protocol
 integrator  = md; Algorithm (md = molecular dynamics
 [leap-frog integrator]; md-vv = md using velocity verlet; sd = stochastic
 dynamics)
 dt  = 0.002 ; Time-step (ps)
 nsteps  = 25; Number of steps to run (0.002 * 25 =
 500 ps)

 ; Parameters controlling output writing
 nstxout = 0 ; Write coordinates to output .trr file
 every 2 ps
 nstvout = 0 ; Write velocities to output .trr file
 every 2 ps
 nstfout = 0

 nstxtcout   = 1000
 nstenergy   = 1000  ; Write energies to output .edr file every
 2 ps
 nstlog  = 1000  ; Write output to .log file every 2 ps

 ; Parameters describing neighbors searching and details about interaction
 calculations
 ns_type = grid  ; Neighbor list search method (simple,
 grid)
 nstlist = 50; Neighbor list update frequency (after
 every given number of steps)
 rlist   = 1.2   ; Neighbor list search cut-off distance
 (nm)
 rlistlong   = 1.4
 rcoulomb= 1.2   ; Short-range Coulombic interactions
 cut-off distance (nm)
 rvdw= 1.2   ; Short-range van der Waals cutoff
 distance (nm)
 pbc = xyz   ; Direction in which to use Perodic
 Boundary Conditions (xyz, xy, no)
 cutoff-scheme   =Verlet  ; GPU running

 ; Parameters for treating bonded interactions
 continuation= no; Whether a fresh start or a continuation
 from a previous run (yes/no)
 constraint_algorithm = LINCS; Constraint algorithm (LINCS / SHAKE)
 constraints = all-bonds ; Which bonds/angles

Re: [gmx-users] GPU running problem with GMX-4.6 beta2


On 12/17/2012 06:08 PM, Szilárd Páll wrote:

Hi,

How about GPU emulation or CPU-only runs? Also, please try setting the
number of therads to 1 (-ntomp 1).


--
Szilárd



hello:

I am running in GPU emulation mode with the GMX_EMULATE_GPU=1 env. var
set (and to match closer the GPU setup with -ntomp 12), it failed with log:

Back Off! I just backed up step33b.pdb to ./#step33b.pdb.2#

Back Off! I just backed up step33c.pdb to ./#step33c.pdb.2#
Wrote pdb files with previous and current coordinates
[CUDANodeA:20753] *** Process received signal ***
[CUDANodeA:20753] Signal: Segmentation fault (11)
[CUDANodeA:20753] Signal code: Address not mapped (1)
[CUDANodeA:20753] Failing at address: 0x106ae6a00

[1]Segmentation faultmdrun_mpi -v -s nvt.tpr -c nvt.gro -g 
nvt.log -x nvt.xtc -ntomp 12




I also tried , number of therads to 1 (-ntomp 1), it failed with following 
messages:


Back Off! I just backed up step33c.pdb to ./#step33c.pdb.1#
Wrote pdb files with previous and current coordinates
[CUDANodeA:20740] *** Process received signal ***
[CUDANodeA:20740] Signal: Segmentation fault (11)
[CUDANodeA:20740] Signal code: Address not mapped (1)
[CUDANodeA:20740] Failing at address: 0x1f74a96ec
[CUDANodeA:20740] [ 0] /lib64/libpthread.so.0(+0xf2d0) [0x2b351d3022d0]
[CUDANodeA:20740] [ 1] /opt/gromacs-4.6/lib/libmd_mpi.so.6(+0x11020f) 
[0x2b351a99c20f]
[CUDANodeA:20740] [ 2] /opt/gromacs-4.6/lib/libmd_mpi.so.6(+0x111c94) 
[0x2b351a99dc94]
[CUDANodeA:20740] [ 3] 
/opt/gromacs-4.6/lib/libmd_mpi.so.6(gmx_pme_do+0x1d2e) [0x2b351a9a1bae]
[CUDANodeA:20740] [ 4] 
/opt/gromacs-4.6/lib/libmd_mpi.so.6(do_force_lowlevel+0x1eef) 
[0x2b351a97262f]
[CUDANodeA:20740] [ 5] 
/opt/gromacs-4.6/lib/libmd_mpi.so.6(do_force_cutsVERLET+0x1756) 
[0x2b351aa04736]
[CUDANodeA:20740] [ 6] 
/opt/gromacs-4.6/lib/libmd_mpi.so.6(do_force+0x3bf) [0x2b351aa0a0df]

[CUDANodeA:20740] [ 7] mdrun_mpi(do_md+0x8133) [0x4334c3]
[CUDANodeA:20740] [ 8] mdrun_mpi(mdrunner+0x19e9) [0x411639]
[CUDANodeA:20740] [ 9] mdrun_mpi(main+0x17db) [0x4373db]
[CUDANodeA:20740] [10] /lib64/libc.so.6(__libc_start_main+0xfd) 
[0x2b351d52ebfd]

[CUDANodeA:20740] [11] mdrun_mpi() [0x407f09]
[CUDANodeA:20740] *** End of error message ***

[1]Segmentation faultmdrun_mpi -v -s nvt.tpr -c nvt.gro 
-g nvt.log -x nvt.xtc -ntomp 1




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[gmx-users] (no subject)

2012-12-17 Thread Shine A

sir,

I am studying dynamics of a membrane protein using oplsaa force field.
Energy minimization during nvt equilibration getting error like this.
  Fatal error:
1 particles communicated to PME node 1 are more than 2/3 times the cut-off
out of the domain decomposition cell of their charge group in dimension x.
This usually means that your system is not well equilibrated.
plz give me a way to solve this problem?
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Re: [gmx-users] (no subject)




On 12/17/12 12:53 PM, Shine A wrote:

sir,

 I am studying dynamics of a membrane protein using oplsaa force field.
Energy minimization during nvt equilibration getting error like this.
   Fatal error:
1 particles communicated to PME node 1 are more than 2/3 times the cut-off
out of the domain decomposition cell of their charge group in dimension x.
This usually means that your system is not well equilibrated.
plz give me a way to solve this problem?



http://www.gromacs.org/Documentation/Errors#X_particles_communicated_to_PME_node_Y_are_more_than_a_cell_length_out_of_the_domain_decomposition_cell_of_their_charge_group

-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] GPU running problem with GMX-4.6 beta2

Hi Albert,

Thanks for the testing.

Last questions.
- What version are you using? Is it beta2 release or latest git? if it's
the former, getting the latest git might help if...
-  (do) you happen to be using GMX_GPU_ACCELERATION=None (you shouldn't!)?
A bug triggered only with this setting has been fixed recently.

If the above doesn't help, please file a bug report and attach a tpr so we
can reproduce.

Cheers,

--
Szilárd



On Mon, Dec 17, 2012 at 6:21 PM, Albert mailmd2...@gmail.com wrote:

 On 12/17/2012 06:08 PM, Szilárd Páll wrote:

 Hi,

 How about GPU emulation or CPU-only runs? Also, please try setting the
 number of therads to 1 (-ntomp 1).


 --
 Szilárd


 hello:

 I am running in GPU emulation mode with the GMX_EMULATE_GPU=1 env. var
 set (and to match closer the GPU setup with -ntomp 12), it failed with log:

 Back Off! I just backed up step33b.pdb to ./#step33b.pdb.2#

 Back Off! I just backed up step33c.pdb to ./#step33c.pdb.2#

 Wrote pdb files with previous and current coordinates
 [CUDANodeA:20753] *** Process received signal ***
 [CUDANodeA:20753] Signal: Segmentation fault (11)
 [CUDANodeA:20753] Signal code: Address not mapped (1)
 [CUDANodeA:20753] Failing at address: 0x106ae6a00

 [1]Segmentation faultmdrun_mpi -v -s nvt.tpr -c nvt.gro -g
 nvt.log -x nvt.xtc -ntomp 12




 I also tried , number of therads to 1 (-ntomp 1), it failed with following
 messages:


 Back Off! I just backed up step33c.pdb to ./#step33c.pdb.1#

 Wrote pdb files with previous and current coordinates
 [CUDANodeA:20740] *** Process received signal ***
 [CUDANodeA:20740] Signal: Segmentation fault (11)
 [CUDANodeA:20740] Signal code: Address not mapped (1)
 [CUDANodeA:20740] Failing at address: 0x1f74a96ec
 [CUDANodeA:20740] [ 0] /lib64/libpthread.so.0(+**0xf2d0) [0x2b351d3022d0]
 [CUDANodeA:20740] [ 1] /opt/gromacs-4.6/lib/libmd_**mpi.so.6(+0x11020f)
 [0x2b351a99c20f]
 [CUDANodeA:20740] [ 2] /opt/gromacs-4.6/lib/libmd_**mpi.so.6(+0x111c94)
 [0x2b351a99dc94]
 [CUDANodeA:20740] [ 3] 
 /opt/gromacs-4.6/lib/libmd_**mpi.so.6(gmx_pme_do+0x1d2e)
 [0x2b351a9a1bae]
 [CUDANodeA:20740] [ 4] /opt/gromacs-4.6/lib/libmd_**
 mpi.so.6(do_force_lowlevel+**0x1eef) [0x2b351a97262f]
 [CUDANodeA:20740] [ 5] /opt/gromacs-4.6/lib/libmd_**
 mpi.so.6(do_force_cutsVERLET+**0x1756) [0x2b351aa04736]
 [CUDANodeA:20740] [ 6] /opt/gromacs-4.6/lib/libmd_**mpi.so.6(do_force+0x3bf)
 [0x2b351aa0a0df]
 [CUDANodeA:20740] [ 7] mdrun_mpi(do_md+0x8133) [0x4334c3]
 [CUDANodeA:20740] [ 8] mdrun_mpi(mdrunner+0x19e9) [0x411639]
 [CUDANodeA:20740] [ 9] mdrun_mpi(main+0x17db) [0x4373db]
 [CUDANodeA:20740] [10] /lib64/libc.so.6(__libc_start_**main+0xfd)
 [0x2b351d52ebfd]
 [CUDANodeA:20740] [11] mdrun_mpi() [0x407f09]
 [CUDANodeA:20740] *** End of error message ***

 [1]Segmentation faultmdrun_mpi -v -s nvt.tpr -c nvt.gro -g
 nvt.log -x nvt.xtc -ntomp 1




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[gmx-users] Actual box size

2012-12-17 Thread zugunder

Hi,

I want to simulate a water soluble protein of approx. 160aa size and its
shape from a .pdb looks a little elongated (if rotated around the longest
axis, it roughly occupies a cylinder with length to diameter ratio 1.8 -
1.9). Would it be considered globular enough to try dodecahedron box?

Out of curiosity, I compared the triclinic and dodecahedral boxes created
for my protein.

After I created a triclinic box with g_editconf, I got this:

Read 2406 atoms
Volume: 83.8247 nm^3, corresponds to roughly 37700 electrons
No velocities found
system size :  4.830  3.541  4.901 (nm)
center  : 19.439-14.327 13.948 (nm)
box vectors :  4.830  3.541  4.901 (nm)
box angles  :  90.00  90.00  90.00 (degrees)
box volume  :  83.82   (nm^3)
shift   :-16.024 17.097-10.498 (nm)
new center  :  3.415  2.771  3.451 (nm)
new box vectors :  6.830  5.541  6.901 (nm)
new box angles  :  90.00  90.00  90.00 (degrees)
new box volume  : 261.17   (nm^3)

Dodecahedron:

Volume: 83.8247 nm^3, corresponds to roughly 37700 electrons
No velocities found
system size :  4.830  3.541  4.901 (nm)
diameter:  5.907   (nm)
center  : 19.439-14.327 13.948 (nm)
box vectors :  4.830  3.541  4.901 (nm)
box angles  :  90.00  90.00  90.00 (degrees)
box volume  :  83.82   (nm^3)
shift   :-13.508 20.257-11.153 (nm)
new center  :  5.931  5.931  2.796 (nm)
new box vectors :  7.907  7.907  7.907 (nm)
new box angles  :  60.00  60.00  90.00 (degrees)
new box volume  : 349.61   (nm^3)

So from the box volumes I see that in this case a triclinic box is a
preferred choice. However, as I am aware that dodecahedral box
representation (as seen in VMD for example) is subject to periodicity
effects, I am not completely sure if exactly these box sizes will be used in
simulations. If not, how could I estimate the actual box volumes before I
start simulation (to maximize performance)?

And I have one more short question:
Is it possible somehow to visualize the actual dodecahedral box at this
stage (i.e. right after adding water, having no trajectory file yet)?

Thank you.



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Re: [gmx-users] Actual box size




On 12/17/12 1:48 PM, zugunder wrote:

Hi,

I want to simulate a water soluble protein of approx. 160aa size and its
shape from a .pdb looks a little elongated (if rotated around the longest
axis, it roughly occupies a cylinder with length to diameter ratio 1.8 -
1.9). Would it be considered globular enough to try dodecahedron box?



In almost all cases, a dodecahedral box is the optimal choice.  A cubic box with 
the same periodic distance for an elongated protein would be much larger.



Out of curiosity, I compared the triclinic and dodecahedral boxes created
for my protein.

After I created a triclinic box with g_editconf, I got this:

Read 2406 atoms
Volume: 83.8247 nm^3, corresponds to roughly 37700 electrons
No velocities found
 system size :  4.830  3.541  4.901 (nm)
 center  : 19.439-14.327 13.948 (nm)
 box vectors :  4.830  3.541  4.901 (nm)
 box angles  :  90.00  90.00  90.00 (degrees)
 box volume  :  83.82   (nm^3)
 shift   :-16.024 17.097-10.498 (nm)
new center  :  3.415  2.771  3.451 (nm)
new box vectors :  6.830  5.541  6.901 (nm)
new box angles  :  90.00  90.00  90.00 (degrees)
new box volume  : 261.17   (nm^3)

Dodecahedron:

Volume: 83.8247 nm^3, corresponds to roughly 37700 electrons
No velocities found
 system size :  4.830  3.541  4.901 (nm)
 diameter:  5.907   (nm)
 center  : 19.439-14.327 13.948 (nm)
 box vectors :  4.830  3.541  4.901 (nm)
 box angles  :  90.00  90.00  90.00 (degrees)
 box volume  :  83.82   (nm^3)
 shift   :-13.508 20.257-11.153 (nm)
new center  :  5.931  5.931  2.796 (nm)
new box vectors :  7.907  7.907  7.907 (nm)
new box angles  :  60.00  60.00  90.00 (degrees)
new box volume  : 349.61   (nm^3)



In the absence of the actual editconf commands, it's hard to judge the utility 
of each of these setups.



So from the box volumes I see that in this case a triclinic box is a
preferred choice. However, as I am aware that dodecahedral box
representation (as seen in VMD for example) is subject to periodicity
effects, I am not completely sure if exactly these box sizes will be used in
simulations. If not, how could I estimate the actual box volumes before I
start simulation (to maximize performance)?



The box vectors shown are the ones that will be used unless you manipulate them 
in some way.



And I have one more short question:
Is it possible somehow to visualize the actual dodecahedral box at this
stage (i.e. right after adding water, having no trajectory file yet)?



You need a .tpr file and can re-wrap the periodic image with trjconv -pbc mol 
-ur compact.


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] GPU running problem with GMX-4.6 beta2

2012-12-17 Thread Mark Abraham

On Mon, Dec 17, 2012 at 6:01 PM, Albert mailmd2...@gmail.com wrote:

 hello:

  I reduced the GPU to two, and it said:

 Back Off! I just backed up nvt.log to ./#nvt.log.1#
 Reading file nvt.tpr, VERSION 4.6-dev-20121004-5d6c49d (single precision)


This is a development version from October 1. Please use the mdrun version
you think you're using :-)

Mark
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Re: [gmx-users] GPU running problem with GMX-4.6 beta2

On Mon, Dec 17, 2012 at 7:56 PM, Mark Abraham mark.j.abra...@gmail.comwrote:

 On Mon, Dec 17, 2012 at 6:01 PM, Albert mailmd2...@gmail.com wrote:

  hello:
 
   I reduced the GPU to two, and it said:
 
  Back Off! I just backed up nvt.log to ./#nvt.log.1#
  Reading file nvt.tpr, VERSION 4.6-dev-20121004-5d6c49d (single precision)
 

 This is a development version from October 1. Please use the mdrun version
 you think you're using :-)


Thanks Mark, good catch!

--
Szilárd




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Re: [gmx-users] GPU running problem with GMX-4.6 beta2


well, that's one of the log files.
I've tried both

VERSION 4.6-dev-20121004-5d6c49d
VERSION 4.6-beta1
VERSION 4.6-beta2
and the latest 5.0 by git.

the problems are the same.:-(




On 12/17/2012 07:56 PM, Mark Abraham wrote:

On Mon, Dec 17, 2012 at 6:01 PM, Albertmailmd2...@gmail.com  wrote:


hello:

  I reduced the GPU to two, and it said:

Back Off! I just backed up nvt.log to ./#nvt.log.1#
Reading file nvt.tpr, VERSION 4.6-dev-20121004-5d6c49d (single precision)


This is a development version from October 1. Please use the mdrun version
you think you're using:-)

Mark
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Re: [gmx-users] GPU running problem with GMX-4.6 beta2




On 12/17/12 2:03 PM, Albert wrote:

well, that's one of the log files.
I've tried both

VERSION 4.6-dev-20121004-5d6c49d
VERSION 4.6-beta1
VERSION 4.6-beta2
and the latest 5.0 by git.

the problems are the same.:-(



It seems to me that the system is simply crashing like any other that becomes 
unstable.  Does the simulation run at all on plain CPU?


-Justin





On 12/17/2012 07:56 PM, Mark Abraham wrote:

On Mon, Dec 17, 2012 at 6:01 PM, Albertmailmd2...@gmail.com  wrote:


hello:

  I reduced the GPU to two, and it said:

Back Off! I just backed up nvt.log to ./#nvt.log.1#
Reading file nvt.tpr, VERSION 4.6-dev-20121004-5d6c49d (single precision)


This is a development version from October 1. Please use the mdrun version
you think you're using:-)

Mark
--




--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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[gmx-users] Re: Actual box size

2012-12-17 Thread zugunder

Thank you, Justin, for the prompt answer!


Justin Lemkul wrote
 In almost all cases, a dodecahedral box is the optimal choice.  A cubic
 box with the same periodic distance for an elongated protein would be much
 larger.

OK, got it. 


Justin Lemkul wrote
 In the absence of the actual editconf commands, it's hard to judge the
 utility of each of these setups.
 The box vectors shown are the ones that will be used unless you manipulate
 them in some way.

In this particular case the commands were:

g_editconf -f protein.gro -o protein_box.gro -bt triclinic -d 1.0 -c
and
g_editconf -f protein.gro -o protein_box.gro -bt dodecahedron -d 1.0 -c

and my concern is that the reported box volume in case of dodecahedron is
much bigger than that for a triclinic one (for the same protein). Sure, the
triclinic box volume is calculated from vectors 100% correctly, and I guess
that it is correct for dodecahedron as well 

 And I have one more short question:
 Is it possible somehow to visualize the actual dodecahedral box at this
 stage (i.e. right after adding water, having no trajectory file yet)?



Justin Lemkul wrote
 You need a .tpr file and can re-wrap the periodic image with trjconv -pbc
 mol -ur compact.

So I need to run at least genion first. Got it.

Thank you.




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Re: [gmx-users] Re: Actual box size




On 12/17/12 2:14 PM, zugunder wrote:

Thank you, Justin, for the prompt answer!


Justin Lemkul wrote

In almost all cases, a dodecahedral box is the optimal choice.  A cubic
box with the same periodic distance for an elongated protein would be much
larger.


OK, got it.


Justin Lemkul wrote

In the absence of the actual editconf commands, it's hard to judge the
utility of each of these setups.
The box vectors shown are the ones that will be used unless you manipulate
them in some way.


In this particular case the commands were:

g_editconf -f protein.gro -o protein_box.gro -bt triclinic -d 1.0 -c
and
g_editconf -f protein.gro -o protein_box.gro -bt dodecahedron -d 1.0 -c

and my concern is that the reported box volume in case of dodecahedron is
much bigger than that for a triclinic one (for the same protein). Sure, the
triclinic box volume is calculated from vectors 100% correctly, and I guess
that it is correct for dodecahedron as well



It is calculated correctly, the math is just a bit more complex (see the manual 
for the equations).  The distance to the box edge is defined the same way, but 
the two approaches don't necessarily give equally suitable results.  Consider 
the first case, which produces a rectangular box from an elongated 
configuration.  If your protein rotates 90 degrees about the z-axis, you will 
likely violate the minimum image convention, as the box vector along y is 
insufficient to accommodate the protein.  Problem!  The dodecahedral box is 
pseudo-spherical and thus, regardless of how the protein rotates, the minimum 
image convention is not violated.



And I have one more short question:
Is it possible somehow to visualize the actual dodecahedral box at this
stage (i.e. right after adding water, having no trajectory file yet)?




Justin Lemkul wrote

You need a .tpr file and can re-wrap the periodic image with trjconv -pbc
mol -ur compact.


So I need to run at least genion first. Got it.



Not genion, but grompp.

-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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[gmx-users] Re: Actual box size

2012-12-17 Thread zugunder

Justin Lemkul wrote
 It is calculated correctly, the math is just a bit more complex (see the
 manual for the equations).  The distance to the box edge is defined the
 same way, but the two approaches don't necessarily give equally suitable
 results.  Consider the first case, which produces a rectangular box from
 an elongated configuration.  If your protein rotates 90 degrees about the
 z-axis, you will likely violate the minimum image convention, as the box
 vector along y is insufficient to accommodate the protein.  Problem!  The
 dodecahedral box is pseudo-spherical and thus, regardless of how the
 protein rotates, the minimum image convention is not violated.

So, in other words, the safest way for an elongated protein (with no
restrictions on rotation) is either a cube or dodecahedron, because only in
these 2 cases only the longest dimension of the protein is effectively taken
into account - do I understand it correctly? And obviously, this is true for
any almost-spherical protein as well...

And, therefore, any rectangular box, different from a cube will bring to a
violation of the minimum image convention in case of unrestricted rotation
of an elongated protein around its shorter axes assuming we set the same -d
as in case of a cube? So do I get it right that non-cubic rectangular boxes
are used only in such specific cases with restrictions on rotation?

Thank you.



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Re: [gmx-users] Re: Actual box size




On 12/17/12 3:04 PM, zugunder wrote:

Justin Lemkul wrote

It is calculated correctly, the math is just a bit more complex (see the
manual for the equations).  The distance to the box edge is defined the
same way, but the two approaches don't necessarily give equally suitable
results.  Consider the first case, which produces a rectangular box from
an elongated configuration.  If your protein rotates 90 degrees about the
z-axis, you will likely violate the minimum image convention, as the box
vector along y is insufficient to accommodate the protein.  Problem!  The
dodecahedral box is pseudo-spherical and thus, regardless of how the
protein rotates, the minimum image convention is not violated.


So, in other words, the safest way for an elongated protein (with no
restrictions on rotation) is either a cube or dodecahedron, because only in
these 2 cases only the longest dimension of the protein is effectively taken
into account - do I understand it correctly? And obviously, this is true for
any almost-spherical protein as well...



Yes, it's a reflection on the inherent rotational symmetry of the molecule.  A 
dodecahedron can give you the same periodic distance as a cube, but is much more 
efficient since there are fewer waters.



And, therefore, any rectangular box, different from a cube will bring to a
violation of the minimum image convention in case of unrestricted rotation
of an elongated protein around its shorter axes assuming we set the same -d
as in case of a cube? So do I get it right that non-cubic rectangular boxes
are used only in such specific cases with restrictions on rotation?



Or in cases where a rectangle is suitable, i.e. for surfaces or membranes.

-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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[gmx-users] Re: gmx-users Digest, Vol 104, Issue 73

2012-12-17 Thread fatemeh ramezani



 Dear Justin 

According to papers, I expect gold atom interacts with the sulfur atom of amino 
acid cysteine covalently. But in last email you said  in the case of protein-Au 
This will not be true to add these parameters
 in topology file. Then in which file should I add the parameters between gold 
and sulfur?

What do you suggest? How do I define for the program that can be established 
between these two atoms covalent bond ?

many thanks


Fatemeh Ramezani



 From: gmx-users-requ...@gromacs.org gmx-users-requ...@gromacs.org
To: gmx-users@gromacs.org 
Sent: Monday, 17 December 2012, 1:47
Subject: gmx-users Digest, Vol 104, Issue 73
 
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Today's Topics:

   1. Re: Parametrisation of the cyclic nucleotides in Gromos    force
      fields (James Starlight)
   2. Re: Parametrisation of the cyclic nucleotides in Gromos    force
      fields (Justin Lemkul)
   3. Re: gold-S simulation (fatemeh ramezani)
   4. Re: gold-S simulation (fatemeh ramezani)
   5. Re: gold-S simulation (francesco oteri)
   6. Box Pressure on individual box walls (John Doe)
   7. Re: Box Pressure on individual box walls (David van der Spoel)
   8. Re: gold-S simulation (Justin Lemkul)


--

Message: 1
Date: Sun, 16 Dec 2012 19:34:57 +0400
From: James Starlight jmsstarli...@gmail.com
Subject: Re: [gmx-users] Parametrisation of the cyclic nucleotides in
    Gromos    force fields
To: Discussion list for GROMACS users gmx-users@gromacs.org
Message-ID:
    CAALQopzp6xCweeYWRcmMsZNYDnEvg_=gjpqofrlazphv5dd...@mail.gmail.com
Content-Type: text/plain; charset=ISO-8859-1

Justin,  thanks again for explanation.
So the first 5 atoms in cmap.it correspond to the starting sequence of
the backbone atoms of the amino acid doesnt it ? So what is the  24 24
numbers at the end of each cmap line ?
E.g in the  C NH1 CT1 C NC=O 1 24 24\ the first C B CA C N atoms would
be assigned as the backbone. That lines were added after grompp
produce error about unknown cmap for that 5 atoms of the chromophore.
Should the 24 24 \ be removed from each line of the chromophore cmap ?


James


--

Message: 2
Date: Sun, 16 Dec 2012 11:12:35 -0500
From: Justin Lemkul jalem...@vt.edu
Subject: Re: [gmx-users] Parametrisation of the cyclic nucleotides in
    Gromos    force fields
To: Discussion list for GROMACS users gmx-users@gromacs.org
Message-ID: 50cdf2f3.4030...@vt.edu
Content-Type: text/plain; charset=ISO-8859-1; format=flowed



On 12/16/12 10:34 AM, James Starlight wrote:
 Justin,  thanks again for explanation.
 So the first 5 atoms in cmap.it correspond to the starting sequence of
 the backbone atoms of the amino acid doesnt it ? So what is the  24 24
 numbers at the end of each cmap line ?

Probably something related to how Gromacs tools read in the CMAP data.  I don't 
have time to go through the code to find exactly how it's used.

 E.g in the  C NH1 CT1 C NC=O 1 24 24\ the first C B CA C N atoms would
 be assigned as the backbone. That lines were added after grompp
 produce error about unknown cmap for that 5 atoms of the chromophore.
 Should the 24 24 \ be removed from each line of the chromophore cmap ?


You shouldn't be modifying anything about cmap.itp, nor should those numbers be 
present in your .rtp file.  Your [cmap] directive in the .rtp entry should 
contain a sequence of 5 atom names to which the CMAP corrections are applied.

-Justin

-- 


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin




--

Message: 3
Date: Sun, 16 Dec 2012 09:58:16 -0800 (PST)
From: fatemeh ramezani fr_...@yahoo.com
Subject: Re: [gmx-users] gold-S simulation
To: gmx-users-requ...@gromacs.org gmx-users-requ...@gromacs.org,
    gmx-users@gromacs.org gmx-users@gromacs.org,
    gmx-users-ow...@gromacs.org gmx-users-ow...@gromacs.org
Message-ID:
    1355680696.17757.yahoomail...@web113504.mail.gq1.yahoo.com
Content-Type: text/plain; charset=iso-8859-1



Dear francesco 
I extract gold parameter from papers that I attached them for you. But  for 
gold and other atom parameters, you should calculate them using common 
combination rule. 


Fatemeh Ramezani




--

Message: 4
Date: Sun, 16

Re: [gmx-users] Re: gold-S simulation




On 12/17/12 4:01 PM, fatemeh ramezani wrote:



  Dear Justin

According to papers, I expect gold atom interacts with the sulfur atom of amino 
acid cysteine covalently. But in last email you said  in the case of protein-Au 
This will not be true to add these parameters
  in topology file. Then in which file should I add the parameters between gold 
and sulfur?

What do you suggest? How do I define for the program that can be established 
between these two atoms covalent bond ?



Bonds do not break and form in standard MD.  For that, you need QM or QM/MM type 
calculations.


If there should be a bond between Cys and Au, you need to write that into the 
topology or use the specbond.dat mechanism.  pdb2gmx will not create bonds 
between Au and Cys otherwise.  The other modifications you have made, as far as 
I can tell, are fine.


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] question of improper dihedral of opls aa




On 12/17/12 5:51 PM, Tom wrote:

Dear Gromacs Users,

I created a new residue on aminoacids.rtp file
and assigned improper dihedral after [ bonds ], for example

[ impropers ]
   C2H  C3 S1

Then I want to add the parameters of this dihedral angle potential
onto ffbonded.itp

I know how to assign dihedral. Dihedral can be assigned with
these 4 atom types with the format as the follow
   Br C  CB CT  3  0.0   0.0   0.0   0.0
   0.0   0.0 ; acyl halide



That's a proper dihedral, using a Ryckaert-Bellemans function.


*But the format of improper dihedral potential is not clear to me.*
*Can anyone help with the format? How to type these parameters
on ffbonded.itp ?*



Check the existing entries in ffbonded.itp.  It's the next [dihedraltypes] block 
with #define statements for the impropers.


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] Error in energy minimization




On 12/17/12 7:17 PM, Kieu Thu Nguyen wrote:

Dear All,

When i do step EM, the output file .gro is separated into many step.pdb
files .  And many errors Water molecule starting at atom XXX can not be
settled  appears. And the potential energy is positive !

What should i do to solve it ?



Please consult the list archive and Gromacs website first.  This is an error 
that is posted probably every other day.  Likely some of the thousands of posts 
in the archive will help, as well as 
http://www.gromacs.org/Documentation/Errors#LINCS.2fSETTLE.2fSHAKE_warnings.


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] Error in energy minimization

Thank Justin !


On Tue, Dec 18, 2012 at 7:20 AM, Justin Lemkul jalem...@vt.edu wrote:



 On 12/17/12 7:17 PM, Kieu Thu Nguyen wrote:

 Dear All,

 When i do step EM, the output file .gro is separated into many step.pdb
 files .  And many errors Water molecule starting at atom XXX can not be
 settled  appears. And the potential energy is positive !

 What should i do to solve it ?


 Please consult the list archive and Gromacs website first.  This is an
 error that is posted probably every other day.  Likely some of the
 thousands of posts in the archive will help, as well as
 http://www.gromacs.org/**Documentation/Errors#LINCS.**
 2fSETTLE.2fSHAKE_warningshttp://www.gromacs.org/Documentation/Errors#LINCS.2fSETTLE.2fSHAKE_warnings
 .

 -Justin

 --
 ==**==

 Justin A. Lemkul, Ph.D.
 Research Scientist
 Department of Biochemistry
 Virginia Tech
 Blacksburg, VA
 jalemkul[at]vt.edu | (540) 231-9080
 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

 ==**==
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Re: [gmx-users] error while running mdrun

2012-12-17 Thread Christopher Samuel

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1

On 17/12/12 21:57, ananyachatterjee wrote:

 [ganga:04205] *** Process received signal *** [ganga:04205] Signal:
 Segmentation fault (11) [ganga:04205] Signal code: Address not
 mapped (1) [ganga:04205] Failing at address: 0x201a01c20

Segmentation faults are usually bugs in the program where it is trying
to access memory it shouldn't be.  Very occasionally they can be
caused by hardware issues corrupting pointers, but usually it's just a
bug.

If, as Justin suggests, it's a problem in your simulation then I would
suggest that the program should detect it and tell you, not got off
into the weeds and trigger a condition that causes the OS kernel to
kill it with a SEGV.

Might be worth reporting a bug and seeing what the maintainers say.

cheers!
Chris (a sysadmin, not a scientist)
- -- 
 Christopher SamuelSenior Systems Administrator
 VLSCI - Victorian Life Sciences Computation Initiative
 Email: sam...@unimelb.edu.au Phone: +61 (0)3 903 55545
 http://www.vlsci.org.au/  http://twitter.com/vlsci

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Re: [gmx-users] error while running mdrun