[gmx-users] gmx4.5.4 installation help

[Chandan Choudhury]

Hello gmx-users,

I am trying to install gmx-4.5.4 on a HPC Linux cluster x86_64.
1. I installed fftw 3.2.2
 ./configure --prefix /soft/sudip/abc/execs/fftw/
--enable-single --enable-threads
2. Installing Gromacs : CPPFLAGS and LDFLAGS were written in bashrc file
a) ./configure --prefix=/soft/sudip/abc/execs/gromacs/
   execute successfully without any complain.
b) make
 /usr/bin/ld:
/soft/sudip/abc/execs/fftw/lib/libfftw3f.a(apiplan.o): relocation
R_X86_64_32 against `a local symbol' can not be used when making a shared
object; recompile with -fPIC
 /soft/sudip/abc/execs/fftw/lib/libfftw3f.a: could not read
symbols: Bad value
 collect2: ld returned 1 exit status
 make[3]: *** [libmd.la] Error 1
 make[3]: Leaving directory
`/soft/sudip/abc/untar/gromacs-4.5.4/src/mdlib'
 make[2]: *** [all-recursive] Error 1
 make[2]: Leaving directory
`/soft/sudip/abc/untar/gromacs-4.5.4/src'
 make[1]: *** [all] Error 2
 make[1]: Leaving directory
`/soft/sudip/abc/untar/gromacs-4.5.4/src'
 make: *** [all-recursive] Error 1

  shows problem.

Couldnot understand the origin of problem. Kndly let me know if some
information is missing.

Chandan

--
Chandan kumar Choudhury
NCL, Pune
INDIA
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Re: [gmx-users] gmx4.5.4 installation help

[Mark Abraham]

On 2/06/2011 5:03 PM, Chandan Choudhury wrote:

Hello gmx-users,

I am trying to install gmx-4.5.4 on a HPC Linux cluster x86_64.
1. I installed fftw 3.2.2
 ./configure --prefix /soft/sudip/abc/execs/fftw/  
--enable-single --enable-threads

2. Installing Gromacs : CPPFLAGS and LDFLAGS were written in bashrc file
a) ./configure --prefix=/soft/sudip/abc/execs/gromacs/
   execute successfully without any complain.
b) make
 /usr/bin/ld: 
/soft/sudip/abc/execs/fftw/lib/libfftw3f.a(apiplan.o): relocation 
R_X86_64_32 against `a local symbol' can not be used when making a 
shared object; recompile with -fPIC
 /soft/sudip/abc/execs/fftw/lib/libfftw3f.a: could not 
read symbols: Bad value

 collect2: ld returned 1 exit status
 make[3]: *** [libmd.la ] Error 1
 make[3]: Leaving directory 
`/soft/sudip/abc/untar/gromacs-4.5.4/src/mdlib'

 make[2]: *** [all-recursive] Error 1
 make[2]: Leaving directory 
`/soft/sudip/abc/untar/gromacs-4.5.4/src'

 make[1]: *** [all] Error 2
 make[1]: Leaving directory 
`/soft/sudip/abc/untar/gromacs-4.5.4/src'

 make: *** [all-recursive] Error 1

  shows problem.

Couldnot understand the origin of problem. Kndly let me know if some 
information is missing.


See http://www.gromacs.org/Downloads/Installation_Instructions, where 
this problem is discussed.


Mark
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Re: [gmx-users] gmx4.5.4 installation help

[Jianguo Li]

The error message already shows some hints. Try recompile FFTW with -fPIC.
Jianguo 






From: Chandan Choudhury 
To: gmx-users 
Sent: Thursday, 2 June 2011 15:03:03
Subject: [gmx-users] gmx4.5.4 installation help

Hello gmx-users,

I am trying to install gmx-4.5.4 on a HPC Linux cluster x86_64. 
1. I installed fftw 3.2.2
 ./configure --prefix /soft/sudip/abc/execs/fftw/  --enable-single 
--enable-threads
2. Installing Gromacs : CPPFLAGS and LDFLAGS were written in bashrc file
a) ./configure --prefix=/soft/sudip/abc/execs/gromacs/
   execute successfully without any complain.
b) make
 /usr/bin/ld: 
/soft/sudip/abc/execs/fftw/lib/libfftw3f.a(apiplan.o): 
relocation R_X86_64_32 against `a local symbol' can not be used when making a 
shared object; recompile with -fPIC
 /soft/sudip/abc/execs/fftw/lib/libfftw3f.a: could not read 
symbols: 
Bad value
 collect2: ld returned 1 exit status
 make[3]: *** [libmd.la] Error 1
 make[3]: Leaving directory 
`/soft/sudip/abc/untar/gromacs-4.5.4/src/mdlib'
 make[2]: *** [all-recursive] Error 1
 make[2]: Leaving directory 
`/soft/sudip/abc/untar/gromacs-4.5.4/src'
 make[1]: *** [all] Error 2
 make[1]: Leaving directory 
`/soft/sudip/abc/untar/gromacs-4.5.4/src'
 make: *** [all-recursive] Error 1

  shows problem. 

Couldnot understand the origin of problem. Kndly let me know if some 
information 
is missing.

Chandan

--
Chandan kumar Choudhury
NCL, Pune
INDIA
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[gmx-users] g_rdf query

[Anirban Ghosh]

Hi ALL,

I am using in calculating the distribution of a solvent around the COM of a
protein chain using g_rdf. When I plot the output file (attached) I get a
curve which increases first (from 1 to a value of about 2.5) and then
decreases to x-axis values ranging from 1 to 5. If I understand correctly
then x-axis values represent the radius of calculation around the protein.
right? It says "r". Whats its unit? And what does the y-axis values stand
for? Can someone please explain me the g_rdf plot attached here.
Thanks a lot in advance.


Regards,

Anirban
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Re: [gmx-users] g_rdf query

[Mark Abraham]

On 2/06/2011 5:52 PM, Anirban Ghosh wrote:


Hi ALL,

I am using in calculating the distribution of a solvent around the COM
of a protein chain using g_rdf. When I plot the output file (attached)
I get a curve which increases first (from 1 to a value of about 2.5)
and then decreases to x-axis values ranging from 1 to 5. If I
understand correctly then x-axis values represent the radius of
calculation around the protein. right? It says "r". Whats its unit?


See chapter 2 of the manual.


And what does the y-axis values stand for? Can someone please explain
me the g_rdf plot attached here.
Thanks a lot in advance.


It means what the y-axis normally means in a distribution (or frequency) 
plot. The absolute magnitude of the values is unimportant, except 
inasmuch as they determine how the integral is interpreted (and vice-versa).


Mark
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Re: [gmx-users] viscosity

[Dommert Florian]

On Wed, 2011-06-01 at 23:37 +0200, Thomas Koller wrote: 
> Hello,
>  
> I calculate the viscosity with g_energy using option -vis (Gromacs
> 4.0.7):
>  
> g_energy -f file.trr -s file.tpr -vis visc.xvg
>  
> Why do I get viscosity values only until the half of the simulation
> time?

This results from the method an autocorrelation function is averaged.
For an average that is unbiased you need the same number of samples for
every time step. You achieve this by shifting the choice of the value
for t=0 through the trajectory. The maximal length of the average you
can achieve with this is exactly half the simulation time.

/Flo
   
>  
> Thomas
>  
>  
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-- 
Florian Dommert
Dipl. - Phys.

Institute for Computational Physics
University Stuttgart

Pfaffenwaldring 27
70569 Stuttgart

EMail: domm...@icp.uni-stuttgart.de
Homepage: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert

Tel.: +49 - (0)711 - 68563613
Fax.: +49 - (0)711 - 68563658


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[gmx-users] Enthalpy of vaporization

[Fabian Casteblanco]

Hello all,

I am trying to find the enthalpy of vaporization for 7 types of
alcohols to try to compare to experimental values.  I have all of them
simulated to equilibrium and I can use g_energy to view the Total
Energy (both kinetic and potential).  In order for me to find the
enthalpy of vaporization, is it as simple as just running the NPT
script again and changing the temperature to that of its boiling point
and 1 degree K over that?  Would it just be the difference between the
enthalpy at boiling pt and 1 degree past boiling?

If anyone could possibly lead me in the right direction I would
greatly appreciate it.  Thanks for your help.

--
Best regards,

Fabian F. Casteblanco
Rutgers University --
Chemical Engineering PhD Student
C: +908 917 0723
E:  fabian.castebla...@gmail.com


npt.mdp
Description: Binary data


md.mdp
Description: Binary data
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Re: [gmx-users] Enthalpy of vaporization

[Justin A. Lemkul]

Fabian Casteblanco wrote:

Hello all,

I am trying to find the enthalpy of vaporization for 7 types of
alcohols to try to compare to experimental values.  I have all of them
simulated to equilibrium and I can use g_energy to view the Total
Energy (both kinetic and potential).  In order for me to find the
enthalpy of vaporization, is it as simple as just running the NPT
script again and changing the temperature to that of its boiling point
and 1 degree K over that?  Would it just be the difference between the
enthalpy at boiling pt and 1 degree past boiling?

If anyone could possibly lead me in the right direction I would
greatly appreciate it.  Thanks for your help.



Use g_energy -nmol on your liquid state to extract potential energy per mole. 
Simulate one molecule in the gas phase (no PBC, all cutoffs equal to zero) and 
extract its potential energy.  Then:


DHvap =  -  + RT

-Justin


--
Best regards,

Fabian F. Casteblanco
Rutgers University --
Chemical Engineering PhD Student
C: +908 917 0723
E:  fabian.castebla...@gmail.com



--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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] Invitation to connect on LinkedIn

[srajan jain via LinkedIn]

LinkedIn





srajan jain requested to add you as a connection on LinkedIn:
  
--

Chinmay,

I'd like to add you to my professional network on LinkedIn.

- srajan

Accept invitation from srajan jain
http://www.linkedin.com/e/-85v1n9-gofphsu5-3b/Xl9gjr6GAOlB4vIjeR9gqTUPRTlBoITTu0/blk/I2857404434_2/1BpC5vrmRLoRZcjkkZt5YCpnlOt3RApnhMpmdzgmhxrSNBszYOnPgPd3gMd3sRe399bTBlqlB1u3xvbPsSdPAPcPkUc3cLrCBxbOYWrSlI/EML_comm_afe/

View invitation from srajan jain
http://www.linkedin.com/e/-85v1n9-gofphsu5-3b/Xl9gjr6GAOlB4vIjeR9gqTUPRTlBoITTu0/blk/I2857404434_2/39vd3cQd30QdPkUcAALqnpPbOYWrSlI/svi/


 
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[gmx-users] Fatal error: Not enough memory. Failed to realloc

[shivangi nangia]

Dear gmx-users,

I was carrying out a continuation of an NPT equilibration from NVT.

As soon the job started it ran into the following error:

Fatal error:
Not enough memory. Failed to realloc 1488624 bytes for nl->shift,
nl->shift=0x0
(called from file ns.c, line 101)


What is the error about?

I did search few archives, in one someone had suggested to use an upgraded
version.
I am currently using 4.0.5

Is upgrading the solution to this problem?

Thanks in advance,
SN
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Re: [gmx-users] Fatal error: Not enough memory. Failed to realloc

[Justin A. Lemkul]

shivangi nangia wrote:

Dear gmx-users,

I was carrying out a continuation of an NPT equilibration from NVT.

As soon the job started it ran into the following error:

Fatal error:
Not enough memory. Failed to realloc 1488624 bytes for nl->shift, 
nl->shift=0x0

(called from file ns.c, line 101)


What is the error about?

I did search few archives, in one someone had suggested to use an 
upgraded version.

I am currently using 4.0.5

Is upgrading the solution to this problem?



Maybe, try it.  Otherwise:

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

-Justin

--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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] Protein ligand segmentation fault

[גדעון לפידות]

Hi all,
I have been trying to run a protein ligand simulation in water using Gromacs
version 4.0.7 and GROMOS 53a6 ff. My protein is about 250 aa and my ligand
is pip3 (Phosphatidylinositol (3,4,5)-trisphosphate) which I have
constructed using PRODRG (using EM and full charges option). I have tried
running the simulation several times under different conditions and every
time the simulation crashed around the first few ps of MD giving a
segmentation fault. I have tried coupling the temp and pressure of the
ligand to the solvent and other times to the protein, changing the partial
charges of the ligand using common GROMOS FF parametes.
When running the same protein with a similar ligand (pip2) who's topology I
have downloaded from the PDB website everything runs smoothly..
 when running the protein and ligand in separate simulations they both run
fine. I have also tried taking frames from the ligand and protein separate
simulations and then placing them in the same box and still the simulation
crashes. I have gone through Justin's tutorial on protein ligand simulations
but to no avail.
I'll be glad to provide further details to any one who think know what might
be wrong..
Thanks,
Gideon
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Re: [gmx-users] Protein ligand segmentation fault

[Justin A. Lemkul]

גדעון לפידות wrote:

Hi all,
I have been trying to run a protein ligand simulation in water using 
Gromacs version 4.0.7 and GROMOS 53a6 ff. My protein is about 250 aa and 
my ligand is pip3 (Phosphatidylinositol (3,4,5)-trisphosphate) which I 
have constructed using PRODRG (using EM and full charges option). I have 
tried running the simulation several times under different conditions 
and every time the simulation crashed around the first few ps of MD 
giving a segmentation fault. I have tried coupling the temp and pressure 
of the ligand to the solvent and other times to the protein, changing 
the partial charges of the ligand using common GROMOS FF parametes.
When running the same protein with a similar ligand (pip2) who's 
topology I have downloaded from the PDB website everything runs smoothly..
 when running the protein and ligand in separate simulations they both 
run fine. I have also tried taking frames from the ligand and protein 
separate simulations and then placing them in the same box and still the 
simulation crashes. I have gone through Justin's tutorial on protein 
ligand simulations but to no avail.
I'll be glad to provide further details to any one who think know what 
might be wrong..


Please post an .mdp file for a run that is crashing.  Other general advice:

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

Since the simulation runs for a short time, you should be able to watch the 
trajectory and see where it starts to fall apart.


-Justin

--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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] Enthalpy of Vaporization

[Fabian Casteblanco]

Hello Justin,

Thank you for your response.  I just wanted to make sure I understand
what you meant.  I'm assuming that you want the one molecule in the
gas phase at its boiling point and you are doing this because you want
the molecule alone with no intermolecular interactions?  (since heat
of vaporization is the energy required to break those interactions
amoung liquid molecules)  Is that why we ignore kinetic energy?  Is
the liquid alcohol that I already simulated (liquid methanol, 1 bar,
298 K) also suppose to be at the 338 K boiling temperature?  Would I
simply run the npt equilibrium again but simply change the temperature
from 298 to 338 K?

Also, you stated the equation:

DHvap =  -  + RT

The first Epot(gas) would be the potential energy for 1 molecule but
the Epot(liq) would be the potential energy for 1 mole?

Thanks for your help Justin.

-- 
Best regards,

Fabian F. Casteblanco
Rutgers University --
Chemical Engineering PhD Student
C: +908 917 0723
E:  fabian.castebla...@gmail.com
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Re: [gmx-users] Enthalpy of Vaporization

[Justin A. Lemkul]

Fabian Casteblanco wrote:

Hello Justin,

Thank you for your response.  I just wanted to make sure I understand
what you meant.  I'm assuming that you want the one molecule in the
gas phase at its boiling point and you are doing this because you want
the molecule alone with no intermolecular interactions?  (since heat
of vaporization is the energy required to break those interactions
amoung liquid molecules)  Is that why we ignore kinetic energy?  Is
the liquid alcohol that I already simulated (liquid methanol, 1 bar,
298 K) also suppose to be at the 338 K boiling temperature?  Would I
simply run the npt equilibrium again but simply change the temperature
from 298 to 338 K?



No, run both at the same temperature.  Kinetic energy doesn't enter the equation 
here.  Also, you need temperature to be constant in the equation below.  If you 
run two simulations at two different temperatures, which T do you use.  DHvap 
and other thermodynamic quantities are generally obtained at standard state, 
i.e. 298.15 K.



Also, you stated the equation:

DHvap =  -  + RT

The first Epot(gas) would be the potential energy for 1 molecule but
the Epot(liq) would be the potential energy for 1 mole?



No, that's why you use g_energy -nmol for the liquid system.  The output of 
g_energy is in kJ/mol of equivalent systems.  Dividing by the value given in 
-nmol is energy in kJ/mol of molecules.  That way, you compare the same 
quantities.  Otherwise, you've got the energy of one molecule in the gas phase 
(kJ/mol of molecules) minus the energy of one mole of a system of molecules in 
the liquid phase (kJ/mol of systems).  You'd get a nonsensical result.


-Justin

--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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] g_dipoles + tpbconv

[Nilesh Dhumal]

Hello,

I have a system with a glucose molecule.

I want to calculate the dipole moment of a particular OH in glucose
molecule.I made an index file which have a group containing atoms.

[ O8 ]
  8   18

10 is oxygen no. and 20 is hydroen no.



But, if I try to use g_dipoles to get the dipole moment contribution from 
using following command:

g_dipoles -f 6.trr -s 6.tpr  -n index.ndx -corr mol -nonormalize  -c

I get the following error.

Fatal error:
index[1]=8 does not correspond to the first atom of a molecule

I read on gmx-users mailing list.

http://www.mail-archive.com/gmx-users@gromacs.org/msg40091.html

Calculating a dipole moment of a possibly-charged species requires that
there be a reference point, which is conventionally the center of mass of
the molecule. This means all the atoms of the molecule have to be known,
and g_dipoles assumes the index group consists of whole molecules.

So to do the partition you want, you will need to provide the same
molecules, but with zero charges. That will mean making a copy of your
.top and hacking those charges to zero to generate a new such .tpr.

Actually, tpbconv has the ability to set the charges of a group in a .tpr
to zero.

So I tried

tpbconv -f 6.trr -s 6.tpr -n glu-emi-cl-128-no.ndx -e 6.edr  -o zero.tpr

I got the error

segmentataion fault

How can I solve this problem to calcualte the dipole moment of a bond?

I am using gromacs version 4.0.7.

Thanks

Nilesh






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[gmx-users] error: Only triclinic boxes...

[Elisabeth]

Hello all,

I am getting the error below at the very beginning of the simulation (both
serial and parallel). I am sure I did not encounter this problem before with
the same input files. This has just happened now. I really have no clue why
this is happening. could you please help me? Thank you all in advance.


Warning: Only triclinic boxes with the first vector parallel to the x-axis
and the second vector in the xy-plane are supported.
 Box (3x3):
Box[0]={ nan,  0.0e+00,  0.0e+00}
Box[1]={ nan,  nan,  nan}
Box[2]={ nan,  nan,  nan}
 Can not fix pbc.



;Run control
integrator  =  md
dt  =  0.002
nsteps  =  100 ;5000
nstcomm =  100

;Output control
nstenergy   =  100
nstxout =  100
nstvout =  0
nstfout =  0
nstlog  =  1000
nstxtcout  =  1000

;Neighbor searching
nstlist =  10
ns_type =  grid

;Electrostatics/VdW
coulombtype =  Shift
vdw-type=  Shift
rcoulomb-switch =  0
rvdw-switch =  0.9 ;0

;Cut-offs
rlist   =  1.25
rcoulomb=  1.0
rvdw=  1.0

;Temperature coupling
Tcoupl  =  v-rescale
tc-grps =  System
tau_t   =  0.1
ref_t   =  300

;Pressure coupling
Pcoupl  =  Parrinello-Rahman
Pcoupltype  =  isotropic
tau_p   =  1
compressibility =  3.5e-5
ref_p   =  10

;Velocity generation
gen_vel =  yes
gen_temp=  300.0
gen_seed=  173529

;Bonds
constraints = all-bonds
constraint-algorithm = lincs
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Re: [gmx-users] error: Only triclinic boxes...

[Justin A. Lemkul]

Elisabeth wrote:

Hello all,

I am getting the error below at the very beginning of the simulation 
(both serial and parallel). I am sure I did not encounter this problem 
before with the same input files. This has just happened now. I really 
have no clue why this is happening. could you please help me? Thank you 
all in advance.



Warning: Only triclinic boxes with the first vector parallel to the 
x-axis and the second vector in the xy-plane are supported.

 Box (3x3):
Box[0]={ nan,  0.0e+00,  0.0e+00}
Box[1]={ nan,  nan,  nan}
Box[2]={ nan,  nan,  nan}
 Can not fix pbc.



Your system is probably blowing up.  "Nan" means "not a number," so the box 
vectors have become either infinitely large or small.  Either the input 
coordinate file contained a malformed or non-existent box, or the simulation is 
collapsing along the way somewhere.  Does the simulation run for a while before 
printing this, or is it right away?


You can check the starting box vectors in the .tpr file with gmxdump to verify 
that they are sensible.


-Justin



  
;Run control   
integrator  =  md
dt  =  0.002   
nsteps  =  100 ;5000 
nstcomm =  100   


;Output control
nstenergy   =  100
nstxout =  100 
nstvout =  0

nstfout =  0
nstlog  =  1000   
nstxtcout  =  1000 


;Neighbor searching
nstlist =  10   
ns_type =  grid   


;Electrostatics/VdW
coulombtype =  Shift
vdw-type=  Shift 
rcoulomb-switch =  0   
rvdw-switch =  0.9 ;0   


;Cut-offs
rlist   =  1.25 
rcoulomb=  1.0
rvdw=  1.0   

;Temperature coupling   
Tcoupl  =  v-rescale 
tc-grps =  System 
tau_t   =  0.1
ref_t   =  300
   
;Pressure coupling
Pcoupl  =  Parrinello-Rahman
Pcoupltype  =  isotropic   
tau_p   =  1   
compressibility =  3.5e-5  
ref_p   =  10

;Velocity generation   
gen_vel =  yes 
gen_temp=  300.0   
gen_seed=  173529 


;Bonds
constraints = all-bonds  
constraint-algorithm = lincs





--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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] g_dipoles + tpbconv

[Justin A. Lemkul]

Nilesh Dhumal wrote:

Hello,

I have a system with a glucose molecule.

I want to calculate the dipole moment of a particular OH in glucose
molecule.I made an index file which have a group containing atoms.

[ O8 ]
  8   18

10 is oxygen no. and 20 is hydroen no.




I'm assuming you mean 8 is O and 18 is H?



But, if I try to use g_dipoles to get the dipole moment contribution from 
using following command:


g_dipoles -f 6.trr -s 6.tpr  -n index.ndx -corr mol -nonormalize  -c

I get the following error.

Fatal error:
index[1]=8 does not correspond to the first atom of a molecule

I read on gmx-users mailing list.

http://www.mail-archive.com/gmx-users@gromacs.org/msg40091.html

Calculating a dipole moment of a possibly-charged species requires that
there be a reference point, which is conventionally the center of mass of
the molecule. This means all the atoms of the molecule have to be known,
and g_dipoles assumes the index group consists of whole molecules.

So to do the partition you want, you will need to provide the same
molecules, but with zero charges. That will mean making a copy of your
.top and hacking those charges to zero to generate a new such .tpr.

Actually, tpbconv has the ability to set the charges of a group in a .tpr
to zero.

So I tried

tpbconv -f 6.trr -s 6.tpr -n glu-emi-cl-128-no.ndx -e 6.edr  -o zero.tpr



This command doesn't accomplish anything.  If you're trying to zero out the 
charges, you need to use the -zeroq option.  But then, if you have two atoms 
with zero charge, then the dipole will of course be zero!



I got the error

segmentataion fault

How can I solve this problem to calcualte the dipole moment of a bond?



I doubt you can do it with g_dipoles.  You've been told already that the group 
analyzed has to have a net charge of zero.  An OH group will not satisfy that 
need, nor does assigning each of the atoms zero charge.  You're better off using 
g_dist (or maybe g_bond) to find the distance between the O and H atoms over 
time and plug that into an equation using the partial charges on the atoms to 
calculate the dipole yourself.  The charges are fixed, so the only thing that 
changes (in the absence of constraints) is the distance between them.


-Justin


I am using gromacs version 4.0.7.

Thanks

Nilesh








--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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: Re: question about trjcat command: Merge files

[Miguel Quiliano Meza]

Dear community.

Thanks to all, finally I could resolve my problem, with the option
"-setttime", it was vital, then "c" (continue).

Now I have two questions,

1) In which case the option "l" could be useful? I did not understand very
well the aplicability.

2) Could you please recommend me an article (Most cited maybe) or tutorial
that analyze changes in protein folding due to single mutation? I  would
like to study its methodology.

Thanks in advance.

Miguel.
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[gmx-users] Enthalpy of Vaporization

[Fabian Casteblanco]

Thanks Justin.  That clarified a lot.  I'm having trouble simulating
the 1 molecule of gas methanol.  I took the original energy minimized
molecule and I'm trying to start it off on NVT using the following
*.mdp file.  I got rid of PBC (ns_type=simple) and I set
rlist=infinite.  After correcting some errors, "Can not have
dispersion correction with pbc=no", (set dispcorr=no), and setting
nstlist=0 since Gromacs says simulating without cut-offs is usually
faster with nstlist=0, I now keep getting an error saying "Can not
have nstlist<=0 with twin-range interactions".   Should nstlist be =0
as it says in the Gromacs manual when simulating with no cut-offs for
pbc=no?  It says I can not have Ewald with pbc=no which makes sense
but I don't know what to replace it with.

Thanks Justin. I appreciate your help.

-- 
Best regards,

Fabian F. Casteblanco
Rutgers University --
Chemical Engineering PhD Student
C: +908 917 0723
E:  fabian.castebla...@gmail.com


nvt.mdp
Description: Binary data
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Re: [gmx-users] Enthalpy of Vaporization

[Justin A. Lemkul]

Fabian Casteblanco wrote:

Thanks Justin.  That clarified a lot.  I'm having trouble simulating
the 1 molecule of gas methanol.  I took the original energy minimized
molecule and I'm trying to start it off on NVT using the following
*.mdp file.  I got rid of PBC (ns_type=simple) and I set
rlist=infinite.  After correcting some errors, "Can not have
dispersion correction with pbc=no", (set dispcorr=no), and setting
nstlist=0 since Gromacs says simulating without cut-offs is usually
faster with nstlist=0, I now keep getting an error saying "Can not
have nstlist<=0 with twin-range interactions".   Should nstlist be =0
as it says in the Gromacs manual when simulating with no cut-offs for
pbc=no?  It says I can not have Ewald with pbc=no which makes sense
but I don't know what to replace it with.



A few things:

1. "rlist = infinite" is not an option.  The value of rlist is a floating-point 
number.  To achieve infinite cutoffs, set rlist=rvdw=rcoulomb=0.


2. Don't use PME.  Set "coulombtype = cutoff."  There are no cutoff artifacts 
here, since with rcoulomb=0, all interactions are calculated.


-Justin

--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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] Switching from v4.0.7 to v 4.5.3 - being able to get the correct terms from a edr file when continuing a simulation

[Anna Duncan]

Hi,

I'm doing a coarse-grained simulation, using the MARTINI forcefield,  
of a protein in a lipid bilayer.  I carried out the equilibration  
stages using Gromacs 4.0.7.  Equilibration was done in several stages  
but the last stage was with a Nosé-Hoover thermostat for temperature  
coupling and Parrinello-Rahman thermostat for pressure coupling.  The  
next stage I carried out was a simulation of system with nothing  
except the backbone of the protein restrained, to relax the  
sidechains.  For this stage I used a newer, faster server which has  
Gromacs 4.5.3 installed on it.  The mdp file is below.

I used the command:
g_grompp -f ../md_T296.mdp -p ../prot_memb_system2.top -c npt_bPR.gro - 
e npt_bPR.edr -t npt_bPR.trr -n prot_bilayer.ndx -o md_schain


I got the error message:
---
Program g_grompp, VERSION 4.5.3
Source code file: /builddir/build/BUILD/gromacs-4.5.3/src/gmxlib/ 
enxio.c, line: 1056


Fatal error:
Could not find energy term named 'Xi-0-Protein'
For more information and tips for troubleshooting, please check the  
GROMACS

website at http://www.gromacs.org/Documentation/Errors
---


I assumed that this was something to do with my switching between  
versions, maybe that the .edr file that's written by version 4.0.7  
doesn't have the terms that are required by version 4.5.3, so I  
removed the -e option from the command line and ran the simulation  
using the commands:
g_grompp -f ../md_T296.mdp -p ../prot_memb_system2.top -c npt_bPR.gro - 
t npt_bPR.trr -n prot_bilayer.ndx -o md_schain

g_mdrun -v -nt 1 -deffnm md_schain

For the next stage, I want to simulate the whole system, for which I  
use the mdp file below except with no -DPOSREBB defined (line 10) and  
with nsteps = 1000, and version 4.5.3 again.

When I use the command:
g_grompp -f ../md_T296.mdp -p ../prot_memb_system2.top -c  
md_schain.gro -e md_schain.edr -t md_schain.trr -n prot_bilayer.ndx -o  
md1_t296


I again get the error message:
---
Program g_grompp, VERSION 4.5.3
Source code file: /builddir/build/BUILD/gromacs-4.5.3/src/gmxlib/ 
enxio.c, line: 1056


Fatal error:
Could not find energy term named 'Xi-0-Protein'
For more information and tips for troubleshooting, please check the  
GROMACS

website at http://www.gromacs.org/Documentation/Errors
---


Can you help me with exactly what's going wrong?  I'm not sure if I  
should be carrying out the simulation without being able to pass on  
the information from the .edr file of the sidechain-relaxing  
simulation?  If not, what can I do to pass on the information  
necessary from the .edr file?


Many thanks in advance,

Anna

***
mdp file
***
;
; STANDARD MD INPUT OPTIONS FOR MARTINI 2.0
;
; for use with GROMACS 3.3
;

; VARIOUS PREPROCESSING OPTIONS =
title= Martini
cpp  = /usr/bin/cpp
define   = -DPOSREBB

; RUN CONTROL PARAMETERS =
; MARTINI - Most simulations are stable with dt=40 fs,
; some (especially rings) require 20-30 fs.
; The range of time steps used for parametrization
; is 20-40 fs, using smaller time steps is therefore not recommended.

integrator   = md
; start time and timestep in ps
tinit= 0.0
dt   = 0.030
nsteps   = 100
; number of steps for center of mass motion removal =
nstcomm  = 1
comm-mode= Linear
comm-grps= Protein_Lipids W

; OUTPUT CONTROL OPTIONS =
; Output frequency for coords (x), velocities (v) and forces (f) =
nstxout  = 5000
nstvout  = 5000
nstfout  = 0
; Output frequency for energies to log file and energy file =
nstlog   = 1000
nstenergy= 1000
; Output frequency and precision for xtc file =
nstxtcout= 1000
xtc_precision= 100
; This selects the subset of atoms for the xtc file. You can =
; select multiple groups. By default all atoms will be written. =
xtc-grps =
; Selection of energy groups =
energygrps   =

; NEIGHBORSEARCHING PARAMETERS =
; MARTINI - no need for more frequent updates
; or larger neighborlist cut-off due
; to the use of shifted potential energy functions.

; nblist update frequency =
nstlist  = 10
; ns algorithm (simple or grid) =
ns_type  = grid
; Periodic boundary conditions: xyz or none =
pbc  = xyz
; nblist cut-off =
rlist= 1.2

; OPTIONS FOR ELECTROSTATICS AND VDW =
; MARTINI - vdw and electrostatic interactions are used
; in their shifted forms. Changing to other types of
; electrostatics will affect 

Re: [gmx-users] Switching from v4.0.7 to v 4.5.3 - being able to get the correct terms from a edr file when continuing a simulation

[Justin A. Lemkul]

Anna Duncan wrote:


Hi,

I'm doing a coarse-grained simulation, using the MARTINI forcefield, of 
a protein in a lipid bilayer.  I carried out the equilibration stages 
using Gromacs 4.0.7.  Equilibration was done in several stages but the 
last stage was with a Nosé-Hoover thermostat for temperature coupling 
and Parrinello-Rahman thermostat for pressure coupling.  The next stage 
I carried out was a simulation of system with nothing except the 
backbone of the protein restrained, to relax the sidechains.  For this 
stage I used a newer, faster server which has Gromacs 4.5.3 installed on 
it.  The mdp file is below.

I used the command:
g_grompp -f ../md_T296.mdp -p ../prot_memb_system2.top -c npt_bPR.gro -e 
npt_bPR.edr -t npt_bPR.trr -n prot_bilayer.ndx -o md_schain


I got the error message:
---
Program g_grompp, VERSION 4.5.3
Source code file: 
/builddir/build/BUILD/gromacs-4.5.3/src/gmxlib/enxio.c, line: 1056


Fatal error:
Could not find energy term named 'Xi-0-Protein'
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---


I assumed that this was something to do with my switching between 
versions, maybe that the .edr file that's written by version 4.0.7 
doesn't have the terms that are required by version 4.5.3, so I removed 
the -e option from the command line and ran the simulation using the 
commands:
g_grompp -f ../md_T296.mdp -p ../prot_memb_system2.top -c npt_bPR.gro -t 
npt_bPR.trr -n prot_bilayer.ndx -o md_schain

g_mdrun -v -nt 1 -deffnm md_schain

For the next stage, I want to simulate the whole system, for which I use 
the mdp file below except with no -DPOSREBB defined (line 10) and with 
nsteps = 1000, and version 4.5.3 again.

When I use the command:
g_grompp -f ../md_T296.mdp -p ../prot_memb_system2.top -c md_schain.gro 
-e md_schain.edr -t md_schain.trr -n prot_bilayer.ndx -o md1_t296


I again get the error message:
---
Program g_grompp, VERSION 4.5.3
Source code file: 
/builddir/build/BUILD/gromacs-4.5.3/src/gmxlib/enxio.c, line: 1056


Fatal error:
Could not find energy term named 'Xi-0-Protein'
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---



What does g_energy tell you is in the .edr file?  If g_energy says Xi-0-Protein 
is present, but grompp can't find it, then perhaps there's a grompp-specific 
problem reading the energy file.  It would also be interesting to know if the 
problem persists in 4.5.4, as I know there has been some debugging of .edr 
files, but I can't find anything specific in the release history that might be 
pertinent here.




Can you help me with exactly what's going wrong?  I'm not sure if I 
should be carrying out the simulation without being able to pass on the 
information from the .edr file of the sidechain-relaxing simulation?  If 
not, what can I do to pass on the information necessary from the .edr file?




Forget about passing .trr and .edr files to grompp.  It's more accurate to 
simply pass a checkpoint file to grompp -t.  Checkpoints contain all the 
necessary state information for the system.


-Justin


Many thanks in advance,

Anna

***
mdp file
***
;
; STANDARD MD INPUT OPTIONS FOR MARTINI 2.0
;
; for use with GROMACS 3.3
;

; VARIOUS PREPROCESSING OPTIONS =
title= Martini
cpp  = /usr/bin/cpp
define = -DPOSREBB

; RUN CONTROL PARAMETERS =
; MARTINI - Most simulations are stable with dt=40 fs,
; some (especially rings) require 20-30 fs.
; The range of time steps used for parametrization
; is 20-40 fs, using smaller time steps is therefore not recommended.

integrator   = md
; start time and timestep in ps
tinit= 0.0
dt   = 0.030
nsteps   = 100
; number of steps for center of mass motion removal =
nstcomm  = 1
comm-mode = Linear
comm-grps = Protein_Lipids W

; OUTPUT CONTROL OPTIONS =
; Output frequency for coords (x), velocities (v) and forces (f) =
nstxout  = 5000
nstvout  = 5000
nstfout  = 0
; Output frequency for energies to log file and energy file =
nstlog   = 1000
nstenergy= 1000
; Output frequency and precision for xtc file =
nstxtcout= 1000
xtc_precision= 100
; This selects the subset of atoms for the xtc file. You can =
; select multiple groups. By default all atoms will be written. =
xtc-grps =
; Selection of energy groups =
energygrps   =

; NEIGHBORSEA

Re: [gmx-users] Switching from v4.0.7 to v 4.5.3 - being able to get the correct terms from a edr file when continuing a simulation

[Anna Duncan]

Hi Justin,

Thanks for your speedy response.  I've set off the simulation with the  
checkpoint file rather than the trajectory and energy files and that  
seems to be going fine now.


v4.5.3 g_energy showed the .edr file from the backbone-restrained run  
to have no Xi-0-Protein term present, although the .edr file from the  
equilibration run has a term called 'Xi-Protein'


Best wishes,

Anna



On 2 Jun 2011, at 18:36, Justin A. Lemkul wrote:




Anna Duncan wrote:

Hi,
I'm doing a coarse-grained simulation, using the MARTINI  
forcefield, of a protein in a lipid bilayer.  I carried out the  
equilibration stages using Gromacs 4.0.7.  Equilibration was done  
in several stages but the last stage was with a Nosé-Hoover  
thermostat for temperature coupling and Parrinello-Rahman  
thermostat for pressure coupling.  The next stage I carried out was  
a simulation of system with nothing except the backbone of the  
protein restrained, to relax the sidechains.  For this stage I used  
a newer, faster server which has Gromacs 4.5.3 installed on it.   
The mdp file is below.

I used the command:
g_grompp -f ../md_T296.mdp -p ../prot_memb_system2.top -c  
npt_bPR.gro -e npt_bPR.edr -t npt_bPR.trr -n prot_bilayer.ndx -o  
md_schain

I got the error message:
---
Program g_grompp, VERSION 4.5.3
Source code file: /builddir/build/BUILD/gromacs-4.5.3/src/gmxlib/ 
enxio.c, line: 1056

Fatal error:
Could not find energy term named 'Xi-0-Protein'
For more information and tips for troubleshooting, please check the  
GROMACS

website at http://www.gromacs.org/Documentation/Errors
---
I assumed that this was something to do with my switching between  
versions, maybe that the .edr file that's written by version 4.0.7  
doesn't have the terms that are required by version 4.5.3, so I  
removed the -e option from the command line and ran the simulation  
using the commands:
g_grompp -f ../md_T296.mdp -p ../prot_memb_system2.top -c  
npt_bPR.gro -t npt_bPR.trr -n prot_bilayer.ndx -o md_schain

g_mdrun -v -nt 1 -deffnm md_schain
For the next stage, I want to simulate the whole system, for which  
I use the mdp file below except with no -DPOSREBB defined (line 10)  
and with nsteps = 1000, and version 4.5.3 again.

When I use the command:
g_grompp -f ../md_T296.mdp -p ../prot_memb_system2.top -c  
md_schain.gro -e md_schain.edr -t md_schain.trr -n prot_bilayer.ndx  
-o md1_t296

I again get the error message:
---
Program g_grompp, VERSION 4.5.3
Source code file: /builddir/build/BUILD/gromacs-4.5.3/src/gmxlib/ 
enxio.c, line: 1056

Fatal error:
Could not find energy term named 'Xi-0-Protein'
For more information and tips for troubleshooting, please check the  
GROMACS

website at http://www.gromacs.org/Documentation/Errors
---


What does g_energy tell you is in the .edr file?  If g_energy says  
Xi-0-Protein is present, but grompp can't find it, then perhaps  
there's a grompp-specific problem reading the energy file.  It would  
also be interesting to know if the problem persists in 4.5.4, as I  
know there has been some debugging of .edr files, but I can't find  
anything specific in the release history that might be pertinent here.


Can you help me with exactly what's going wrong?  I'm not sure if I  
should be carrying out the simulation without being able to pass on  
the information from the .edr file of the sidechain-relaxing  
simulation?  If not, what can I do to pass on the information  
necessary from the .edr file?


Forget about passing .trr and .edr files to grompp.  It's more  
accurate to simply pass a checkpoint file to grompp -t.  Checkpoints  
contain all the necessary state information for the system.


-Justin


Many thanks in advance,
Anna
***
mdp file
***
;
; STANDARD MD INPUT OPTIONS FOR MARTINI 2.0
;
; for use with GROMACS 3.3
;
; VARIOUS PREPROCESSING OPTIONS =
title= Martini
cpp  = /usr/bin/cpp
define = -DPOSREBB
; RUN CONTROL PARAMETERS =
; MARTINI - Most simulations are stable with dt=40 fs,
; some (especially rings) require 20-30 fs.
; The range of time steps used for parametrization
; is 20-40 fs, using smaller time steps is therefore not recommended.
integrator   = md
; start time and timestep in ps
tinit= 0.0
dt   = 0.030
nsteps   = 100
; number of steps for center of mass motion removal =
nstcomm  = 1
comm-mode = Linear
comm-grps = Protein_Lipids W
; OUTPUT CONTROL OPTIONS =
; Output frequency for coords (x), velocities (v) and forces (f) =
nstxout  = 5000
nstvout  = 5000
nstfout 

[gmx-users] Enthalpy of Vaporization

[Fabian Casteblanco]

Thanks Justin. It worked and it is only off by 3% from experimental
value so that is great.   Thanks for your help!

-- 
Best regards,

Fabian F. Casteblanco
Rutgers University --
Chemical Engineering PhD Student
C: +908 917 0723
E:  fabian.castebla...@gmail.com
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Re: [gmx-users] error: Only triclinic boxes...

[Elisabeth]

Hello Justin,

Thank you. I am using
gmxdump -s *.tpr   -om to produce mdout.mdp file but I dont see box vector
information. This error happens at the very beginning. I see no steps are
calculated.



On 2 June 2011 13:11, Justin A. Lemkul  wrote:

>
>
> Elisabeth wrote:
>
>> Hello all,
>>
>> I am getting the error below at the very beginning of the simulation (both
>> serial and parallel). I am sure I did not encounter this problem before with
>> the same input files. This has just happened now. I really have no clue why
>> this is happening. could you please help me? Thank you all in advance.
>>
>>
>> Warning: Only triclinic boxes with the first vector parallel to the x-axis
>> and the second vector in the xy-plane are supported.
>> Box (3x3):
>>Box[0]={ nan,  0.0e+00,  0.0e+00}
>>Box[1]={ nan,  nan,  nan}
>>Box[2]={ nan,  nan,  nan}
>> Can not fix pbc.
>>
>>
> Your system is probably blowing up.  "Nan" means "not a number," so the box
> vectors have become either infinitely large or small.  Either the input
> coordinate file contained a malformed or non-existent box, or the simulation
> is collapsing along the way somewhere.  Does the simulation run for a while
> before printing this, or is it right away?
>
> You can check the starting box vectors in the .tpr file with gmxdump to
> verify that they are sensible.
>
> -Justin
>
>
>>  ;Run control   integrator  =  md
>>dt  =  0.002   nsteps  =
>>  100 ;5000 nstcomm =  100
>> ;Output control
>> nstenergy   =  100nstxout =  100
>>   nstvout =  0
>> nstfout =  0
>> nstlog  =  1000   nstxtcout  =  1000
>>
>> ;Neighbor searching
>> nstlist =  10   ns_type =  grid
>>
>> ;Electrostatics/VdW
>> coulombtype =  Shiftvdw-type=
>>  Shift rcoulomb-switch =  0   rvdw-switch
>>   =  0.9 ;0
>> ;Cut-offs
>> rlist   =  1.25 rcoulomb=  1.0
>>rvdw=  1.0
>> ;Temperature coupling   Tcoupl  =  v-rescale
>>   tc-grps =  System tau_t   =  0.1
>>  ref_t   =  300   ;Pressure coupling
>> Pcoupl  =  Parrinello-RahmanPcoupltype
>>  =  isotropic   tau_p   =  1
>> compressibility =  3.5e-5  ref_p   =  10
>>
>> ;Velocity generation   gen_vel =  yes
>> gen_temp=  300.0   gen_seed=
>>  173529
>> ;Bonds
>> constraints = all-bonds  constraint-algorithm =
>> lincs
>>
>>
>>
> --
> 
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> 
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
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Re: [gmx-users] Switching from v4.0.7 to v 4.5.3 - being able to get the correct terms from a edr file when continuing a simulation

[Justin A. Lemkul]

Anna Duncan wrote:


Hi Justin,

Thanks for your speedy response.  I've set off the simulation with the 
checkpoint file rather than the trajectory and energy files and that 
seems to be going fine now. 

v4.5.3 g_energy showed the .edr file from the backbone-restrained run to 
have no Xi-0-Protein term present, although the .edr file from the 
equilibration run has a term called 'Xi-Protein'




It looks like there may be a bug in the code, related to the nhchainlength 
parameter.  The energy term names are now prefixed not by "Xi-" but "Xi-(chain 
index)," for which the only value can be zero, as I understand the code in its 
present form.


I'll look into this a bit more and file a bug report, if necessary.

-Justin

--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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: Only triclinic boxes...

[Justin A. Lemkul]

Elisabeth wrote:

Hello Justin,

Thank you. I am using
gmxdump -s *.tpr   -om to produce mdout.mdp file but I dont see box 


You don't need an mdout.mdp file, nor would box vectors be present in one.  What 
you're looking for is the box information present in the .tpr file.  Run:


gmxdump -s topol.tpr > out

Then search in the "out" file for the box information.

vector information. This error happens at the very beginning. I see no 
steps are calculated.




Then the input box information is likely corrupt, or the simulation blows up at 
the very start of the simulation (i.e. step 0).


-Justin




On 2 June 2011 13:11, Justin A. Lemkul > wrote:




Elisabeth wrote:

Hello all,

I am getting the error below at the very beginning of the
simulation (both serial and parallel). I am sure I did not
encounter this problem before with the same input files. This
has just happened now. I really have no clue why this is
happening. could you please help me? Thank you all in advance.


Warning: Only triclinic boxes with the first vector parallel to
the x-axis and the second vector in the xy-plane are supported.
Box (3x3):
   Box[0]={ nan,  0.0e+00,  0.0e+00}
   Box[1]={ nan,  nan,  nan}
   Box[2]={ nan,  nan,  nan}
Can not fix pbc.


Your system is probably blowing up.  "Nan" means "not a number," so
the box vectors have become either infinitely large or small.
 Either the input coordinate file contained a malformed or
non-existent box, or the simulation is collapsing along the way
somewhere.  Does the simulation run for a while before printing
this, or is it right away?

You can check the starting box vectors in the .tpr file with gmxdump
to verify that they are sensible.

-Justin


 ;Run control   integrator
 =  mddt  =  0.002  
nsteps  =  100 ;5000 nstcomm
=  100  
;Output control

nstenergy   =  100nstxout =
 100 nstvout =  0
nstfout =  0
nstlog  =  1000   nstxtcout  =  1000
   
;Neighbor searching

nstlist =  10   ns_type =
 grid  
;Electrostatics/VdW
coulombtype =  Shiftvdw-type
   =  Shift rcoulomb-switch =  0
  rvdw-switch =  0.9 ;0  
;Cut-offs
rlist   =  1.25 rcoulomb  
 =  1.0rvdw=  1.0  
;Temperature coupling   Tcoupl  =  v-rescale

tc-grps =  System tau_t
  =  0.1ref_t   =  300  
;Pressure coupling
Pcoupl  =  Parrinello-Rahman  
 Pcoupltype  =  isotropic   tau_p  
=  1   compressibility =  3.5e-5
 ref_p   =  10
;Velocity generation   gen_vel =
 yes gen_temp=  300.0  
gen_seed=  173529
;Bonds
constraints = all-bonds
 constraint-algorithm = lincs




-- 



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.bi

[gmx-users] Solvating dodecahedron

[shivangi nangia]

Hello All,


I am trying to solvate a protein sitting in a dodecahedron using genbox.
It gets solvated but a box of solvent is created around the protein.
I want the protein to be sitting in a dodecahedron filed with solvent.


I used the following commands:

editconf -f onlyhis.gro -bt dodecahedron -box 9 -d 1 -o dodec.gro
genbox -cp dodec.gro -cs mix.gro -o solv.gro


I have never used this utility of creating a docecahedron nor I could find a
way to view the dodecahedron shae in VMD.
Am I going wrong?


Thanks,
SN
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Re: [gmx-users] error: Only triclinic boxes...

[Elisabeth]

Dear Justin,

I find:


box (3x3):
   box[0]={ 1.6e+01,  0.0e+00,  0.0e+00}
   box[1]={ 0.0e+00,  1.6e+01,  0.0e+00}
   box[2]={ 0.0e+00,  0.0e+00,  1.6e+01}
box_rel (3x3):
   box_rel[0]={ 0.0e+00,  0.0e+00,  0.0e+00}
   box_rel[1]={ 0.0e+00,  1.0e+00,  0.0e+00}
   box_rel[2]={ 0.0e+00,  0.0e+00,  1.0e+00}
boxv (3x3):
   boxv[0]={ 0.0e+00,  0.0e+00,  0.0e+00}
   boxv[1]={ 0.0e+00,  0.0e+00,  0.0e+00}
   boxv[2]={ 0.0e+00,  0.0e+00,  0.0e+00}
pres_prev (3x3):
   pres_prev[0]={ 0.0e+00,  0.0e+00,  0.0e+00}
   pres_prev[1]={ 0.0e+00,  0.0e+00,  0.0e+00}
   pres_prev[2]={ 0.0e+00,  0.0e+00,  0.0e+00}
svir_prev (3x3):
   svir_prev[0]={ 0.0e+00,  0.0e+00,  0.0e+00}
   svir_prev[1]={ 0.0e+00,  0.0e+00,  0.0e+00}
   svir_prev[2]={ 0.0e+00,  0.0e+00,  0.0e+00}
fvir_prev (3x3):
   fvir_prev[0]={ 0.0e+00,  0.0e+00,  0.0e+00}
   fvir_prev[1]={ 0.0e+00,  0.0e+00,  0.0e+00}
   fvir_prev[2]={ 0.0e+00,  0.0e+00,  0.0e+00}
nosehoover_xi: not available
x (2896x3):
   x[0]={-7.49400e+00,  4.57000e-01,  5.0e-01}
   x[1]={-7.58200e+00,  5.21000e-01,  5.0e-01}
   x[2]={-7.49600e+00,  3.94000e-01,  4.11000e-01}
   x[3]={-7.49600e+00,  3.94000e-01,  5.89000e-01}
   x[4]={-7.36800e+00,  5.43000e-01,  5.0e-01}
   x[5]={-7.36800e+00,  6.06000e-01,  5.89000e-01}
   x[6]={-7.36800e+00,  6.06000e-01,  4.11000e-01}
   x[7]={-7.24200e+00,  4.57000e-01,  5.0e-01}
   x[8]={-7.24200e+00,  3.94000e-01,  4.11000e-01}
   x[9]={-7.24200e+00,  3.94000e-01,  5.89000e-01}
   x[   10]={-7.11700e+00,  5.43000e-01,  5.0e-01}
   x[   11]={-7.11700e+00,  6.06000e-01,  5.89000e-01}
   x[   12]={-7.11700e+00,  6.06000e-01,  4.11000e-01}
   x[   13]={-6.99100e+00,  4.57000e-01,  5.0e-01}

I made box bigger to remove bad contacts in initial configuration (although
I have been using the same gro file before and never got such error). Do you
recommend I reinstall 4.5.4 ?

Appreciate any help...

Regards,



On 2 June 2011 14:47, Justin A. Lemkul  wrote:

>
>
> Elisabeth wrote:
>
>> Hello Justin,
>>
>> Thank you. I am using
>> gmxdump -s *.tpr   -om to produce mdout.mdp file but I dont see box
>>
>
> You don't need an mdout.mdp file, nor would box vectors be present in one.
>  What you're looking for is the box information present in the .tpr file.
>  Run:
>
> gmxdump -s topol.tpr > out
>
> Then search in the "out" file for the box information.
>
>
>  vector information. This error happens at the very beginning. I see no
>> steps are calculated.
>>
>>
> Then the input box information is likely corrupt, or the simulation blows
> up at the very start of the simulation (i.e. step 0).
>
> -Justin
>
>
>>
>> On 2 June 2011 13:11, Justin A. Lemkul > jalem...@vt.edu>> wrote:
>>
>>
>>
>>Elisabeth wrote:
>>
>>Hello all,
>>
>>I am getting the error below at the very beginning of the
>>simulation (both serial and parallel). I am sure I did not
>>encounter this problem before with the same input files. This
>>has just happened now. I really have no clue why this is
>>happening. could you please help me? Thank you all in advance.
>>
>>
>>Warning: Only triclinic boxes with the first vector parallel to
>>the x-axis and the second vector in the xy-plane are supported.
>>Box (3x3):
>>   Box[0]={ nan,  0.0e+00,  0.0e+00}
>>   Box[1]={ nan,  nan,  nan}
>>   Box[2]={ nan,  nan,  nan}
>>Can not fix pbc.
>>
>>
>>Your system is probably blowing up.  "Nan" means "not a number," so
>>the box vectors have become either infinitely large or small.
>> Either the input coordinate file contained a malformed or
>>non-existent box, or the simulation is collapsing along the way
>>somewhere.  Does the simulation run for a while before printing
>>this, or is it right away?
>>
>>You can check the starting box vectors in the .tpr file with gmxdump
>>to verify that they are sensible.
>>
>>-Justin
>>
>>
>> ;Run control   integrator
>> =  mddt  =  0.002
>>  nsteps  =  100 ;5000 nstcomm=
>>  100  ;Output control
>>nstenergy   =  100nstxout =
>> 100 nstvout =  0
>>nstfout =  0
>>nstlog  =  1000   nstxtcout  =  1000
>>   ;Neighbor searching
>>nstlist =  10   ns_type

[gmx-users] g_rdf: how to change grid spacing for structure factor

[Sanku M]

Hi,
  I am using gromacs_4.0.7 to calculate the Scattering Intensity as a function 
of scattering vectors(q) using g_rdf -sq command .
But, I found that there is no way that one can increase/decrease the grid 
spacing  for structure factor calculation. I tried using -bin option , but that 
does not change anything as that only works for changing bin-width for Radial 
distribution function calculation. 
If some one can point me out any way out of changing the grid spacing for 
structure factor, that will be very helpful.

Sanku-- 
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Re: [gmx-users] error: Only triclinic boxes...

[Justin A. Lemkul]

Elisabeth wrote:

Dear Justin,

I find:


box (3x3):
   box[0]={ 1.6e+01,  0.0e+00,  0.0e+00}
   box[1]={ 0.0e+00,  1.6e+01,  0.0e+00}
   box[2]={ 0.0e+00,  0.0e+00,  1.6e+01}
box_rel (3x3):
   box_rel[0]={ 0.0e+00,  0.0e+00,  0.0e+00}
   box_rel[1]={ 0.0e+00,  1.0e+00,  0.0e+00}
   box_rel[2]={ 0.0e+00,  0.0e+00,  1.0e+00}
boxv (3x3):
   boxv[0]={ 0.0e+00,  0.0e+00,  0.0e+00}
   boxv[1]={ 0.0e+00,  0.0e+00,  0.0e+00}
   boxv[2]={ 0.0e+00,  0.0e+00,  0.0e+00}
pres_prev (3x3):
   pres_prev[0]={ 0.0e+00,  0.0e+00,  0.0e+00}
   pres_prev[1]={ 0.0e+00,  0.0e+00,  0.0e+00}
   pres_prev[2]={ 0.0e+00,  0.0e+00,  0.0e+00}
svir_prev (3x3):
   svir_prev[0]={ 0.0e+00,  0.0e+00,  0.0e+00}
   svir_prev[1]={ 0.0e+00,  0.0e+00,  0.0e+00}
   svir_prev[2]={ 0.0e+00,  0.0e+00,  0.0e+00}
fvir_prev (3x3):
   fvir_prev[0]={ 0.0e+00,  0.0e+00,  0.0e+00}
   fvir_prev[1]={ 0.0e+00,  0.0e+00,  0.0e+00}
   fvir_prev[2]={ 0.0e+00,  0.0e+00,  0.0e+00}
nosehoover_xi: not available
x (2896x3):
   x[0]={-7.49400e+00,  4.57000e-01,  5.0e-01}
   x[1]={-7.58200e+00,  5.21000e-01,  5.0e-01}
   x[2]={-7.49600e+00,  3.94000e-01,  4.11000e-01}
   x[3]={-7.49600e+00,  3.94000e-01,  5.89000e-01}
   x[4]={-7.36800e+00,  5.43000e-01,  5.0e-01}
   x[5]={-7.36800e+00,  6.06000e-01,  5.89000e-01}
   x[6]={-7.36800e+00,  6.06000e-01,  4.11000e-01}
   x[7]={-7.24200e+00,  4.57000e-01,  5.0e-01}
   x[8]={-7.24200e+00,  3.94000e-01,  4.11000e-01}
   x[9]={-7.24200e+00,  3.94000e-01,  5.89000e-01}
   x[   10]={-7.11700e+00,  5.43000e-01,  5.0e-01}
   x[   11]={-7.11700e+00,  6.06000e-01,  5.89000e-01}
   x[   12]={-7.11700e+00,  6.06000e-01,  4.11000e-01}
   x[   13]={-6.99100e+00,  4.57000e-01,  5.0e-01}

I made box bigger to remove bad contacts in initial configuration 
(although I have been using the same gro file before and never got such 
error). Do you recommend I reinstall 4.5.4 ?




Simply increasing a box size may not alleviate bad contacts in and of itself. 
Plus, you're applying high pressure (10 bar), which is probably just causing the 
box to rapidly collapse in on itself due to void space.


I doubt reinstalling would do any good.  If your installation was severely 
broken, nothing would be working.


-Justin

--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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] Solvating dodecahedron

[Justin A. Lemkul]

shivangi nangia wrote:

Hello All,


I am trying to solvate a protein sitting in a dodecahedron using genbox.
It gets solvated but a box of solvent is created around the protein.
I want the protein to be sitting in a dodecahedron filed with solvent.


I used the following commands:

editconf -f onlyhis.gro -bt dodecahedron -box 9 -d 1 -o dodec.gro
genbox -cp dodec.gro -cs mix.gro -o solv.gro


I have never used this utility of creating a docecahedron nor I could 
find a way to view the dodecahedron shae in VMD.

Am I going wrong?



Nothing is wrong.  The unit cell will always be in a triclinic representation. 
You can see a dodecahedron using trjconv -pbc mol -ur compact.  Note that the 
pseudo-sphere representation is for visualization purposes only; the triclinic 
cell should be the input for any simulation.


-Justin

--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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] Liquid/Gas Systems

[Fabian Casteblanco]

Hi Justin,

You had helped me earlier on calculating the heat of vaporization of
methanol and it worked great.  I'm just trying hard to understand
conceptually what is the difference between simulating a liquid phase
and a gas phase in Gromacs.  I mean technically if we throw in 1000
molecules of component A, would it only be a gas if we made the box
super huge?  If we run NPT on a system, is that technically when we
are compounding it together to find a liquid density?  I'm just a bit
confused on the difference.  I've been simulating liquids up to this
point so when I ran only NVT on a single gas molecule, I was trying to
understand why we only run NVT on it (0 pressure so no pressure
coupling).

Thanks for your expertise.

-- 
Best regards,

Fabian F. Casteblanco
Rutgers University --
Chemical Engineering PhD Student
C: +908 917 0723
E:  fabian.castebla...@gmail.com
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Re: [gmx-users] Liquid/Gas Systems

[Justin A. Lemkul]

Fabian Casteblanco wrote:

Hi Justin,

You had helped me earlier on calculating the heat of vaporization of
methanol and it worked great.  I'm just trying hard to understand
conceptually what is the difference between simulating a liquid phase
and a gas phase in Gromacs.  I mean technically if we throw in 1000
molecules of component A, would it only be a gas if we made the box
super huge?  If we run NPT on a system, is that technically when we
are compounding it together to find a liquid density?  I'm just a bit
confused on the difference.  I've been simulating liquids up to this
point so when I ran only NVT on a single gas molecule, I was trying to
understand why we only run NVT on it (0 pressure so no pressure
coupling).


The basic premise is that, in the gas phase, the gaseous species (atoms or 
molecules) do not interact (assuming an ideal gas), so yes, you absolutely could 
build a huge box that has N molecules in it to match your condensed phase 
system.  What tends to happen is that molecules will eventually find one another 
and form clusters, which really (I think) is just an artifact of using 
condensed-phase parameters to simulate a gas.  If the atoms/molecules find each 
other, they condense.  This type of simulation would have to be done under NVT 
conditions, since gases fill the volume of their container, right?  NPT would 
indeed just compress all of your particles together into a liquid.


The purpose of simulating just a single molecule in isolation is that it easily 
satisfies all the requirements of the ideal state.  The molecule is completely 
isolated and there are no periodicity artifacts.


-Justin

--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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] selecting atoms---MD analysis

[Mr Bernard Ramos]

Hi everyone!
 
I have already have the MD data, I need to select certain atoms/residues with 
their XYZ coordinates in each time frame. I have problems in using the g_select 
if this is the proper tool to use for this. Thanks. -- 
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Re: [gmx-users] selecting atoms---MD analysis

[Justin A. Lemkul]

Mr Bernard Ramos wrote:

Hi everyone!
 
I have already have the MD data, I need to select certain 
atoms/residues with their XYZ coordinates in each time frame. I have 
problems in using the g_select if this is the proper tool to use for 
this. Thanks.




g_select allows you to create dynamic indices, but the other analysis tools 
cannot yet make full use of the resulting index files.  If the information you 
wish to extract is for a fixed set of atoms/residues, then use make_ndx and 
extract the desired coordinate information with g_traj.  If this is not the 
case, then please provide additional details of what you wish to do and what 
exactly isn't working.


-Justin

--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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] Liquid/Gas Systems

[Jussi Lehtola]

On Thu, 02 Jun 2011 17:20:35 -0400
"Justin A. Lemkul"  wrote:
> Fabian Casteblanco wrote:
> > Hi Justin,
> > 
> > You had helped me earlier on calculating the heat of vaporization of
> > methanol and it worked great.  I'm just trying hard to understand
> > conceptually what is the difference between simulating a liquid
> > phase and a gas phase in Gromacs.  I mean technically if we throw
> > in 1000 molecules of component A, would it only be a gas if we made
> > the box super huge?  If we run NPT on a system, is that technically
> > when we are compounding it together to find a liquid density?

This all depends on the temperature (and pressure). If the temperature
is low, the system might be in a liquid (or solid) state even if
the box is *huge*. The matter would then be in small droplets,
i.e. clusters.

Whether or not the clusters will merge at some point depends on the
system and the temperature. The interaction between clusters might be
so weak that compounding does not occur.

> > I'm just a bit confused on the difference.  I've been simulating
> > liquids up to this point so when I ran only NVT on a single gas
> > molecule, I was trying to understand why we only run NVT on it (0
> > pressure so no pressure coupling).

NPT for a single molecule would not make sense, since pressure is a
macroscopic quantity and so you need a lot more molecules than one to
define a pressure. This is also a numeric difficulty, since the
(instantaneous) pressure fluctuates a lot even in "reasonably sized"
systems.

> The basic premise is that, in the gas phase, the gaseous species
> (atoms or molecules) do not interact (assuming an ideal gas), so yes,
> you absolutely could build a huge box that has N molecules in it to
> match your condensed phase system.

But they *do* interact in the gaseous state. The point is that the
interaction is weak compared to the kinetic energy, i.e.  << .
Only an ideal gas has no interactions between molecules.

> What tends to happen is that molecules will eventually find one
> another and form clusters, which really (I think) is just an artifact
> of using condensed-phase parameters to simulate a gas.

Clusters *are* physical entities and can be found in gases. The
question about the validity of extending condensed-phase parameters to
the gaseous state is, of course, very important, so at a given
temperature (and pressure) you might end up with a wrong amount of
clusters.

>  If the atoms/molecules find each other, they condense.  This type of
> simulation would have to be done under NVT conditions, since gases
> fill the volume of their container, right?  NPT would indeed just
> compress all of your particles together into a liquid.

As I stated above, I'd say you can still have the "flying ice cube"
effect in NVT.

NPT won't compress the system into a liquid if the temperature is high
enough (and the pressure low enough).
-- 
--
Mr. Jussi Lehtola, M. Sc., Doctoral Student
Department of Physics, University of Helsinki, Finland
jussi.leht...@helsinki.fi
--
Jussi Lehtola, FM, Tohtorikoulutettava
Fysiikan laitos, Helsingin Yliopisto
jussi.leht...@helsinki.fi, p. 191 50632
--
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Re: [gmx-users] Re: compression to study pressure effect

[Vitaly Chaban]

Hey Eli:

What is the correlation observed between you and Moeed?

I suppose you eventually compressed your system so much, that it
became very distorted. Check your GRO file. I believe it is not
healthy inside.

Regards.

Dr. Vitaly V. Chaban, Department of Chemistry
University of Rochester, Rochester, New York 14627-0216




On Thu, Jun 2, 2011 at 6:53 PM, Moeed  wrote:
> Dear Dr.Chaban,
>
> I am so sorry to send you this message. Thank you for your comments. I have
> encountered a problem that no one on the list could help much. I am very
> hopeful you can assist me especially because I have noticed you respond to
> messages dealing with compression or NPT runs. I am really confused since I
> have been using the same input files (gro. top and mdp) and have been
> collecting without any problem. Since yesterday I am getting a weird message
> that is printed continuously until I kill mdrun.
>
>
> arning: Only triclinic boxes with the first vector parallel to the x-axis
> and the second vector in the xy-plane are supported.
>  Box (3x3):
>     Box[    0]={ nan,  nan,  nan}
>     Box[    1]={ nan,  nan,  nan}
>     Box[    2]={ nan,  nan,  nan}
>
> I have only polyethylene chains in my system. I really appreciate if you
> could help me or could kindly take a very brief look at my system. I can
> send you top and gro files. I assure you top file is generated properly. I
> have done many runs using that. Please let me know if you are interested.
>
> I thank you so much
>
> Waiting for your reply.
>
> Best regards,
> Eli.
>
>
> ;        Run control
> integrator  =  md
> dt  =  0.002
> nsteps  =  100 ;5000
> nstcomm =  100
>
> ;        Output control
> nstenergy   =  100
> nstxout =  100
> nstvout =  0
> nstfout =  0
> nstlog  =  1000
> nstxtcout          =  1000
>
> ;        Neighbor searching
> nstlist =  10
> ns_type =  grid
>
> ;        Electrostatics/VdW
> coulombtype =  Shift
> vdw-type        =  Shift
> rcoulomb-switch =  0
> rvdw-switch =  0.9 ;0
>
> ;        Cut-offs
> rlist   =  1.25
> rcoulomb    =  1.0 ;1.1
> rvdw    =  1.0
>
> ;        Temperature coupling
> Tcoupl  =  v-rescale
> tc-grps =  System  ;HEX
> tau_t   =  0.1 ;0.1
> ref_t   =  300 ;300
>
> ;        Pressure coupling
> Pcoupl  = Parrinello-Rahman
> Pcoupltype          =  isotropic
> tau_p   =  1            ;0.5
> compressibility =  4.5e-5 4.5e-5
> ref_p   =  10    30
>
> ;        Velocity generation
> gen_vel =  yes
> gen_temp    =  300.0
> gen_seed    =  173529
>
> ;        Bonds
> constraints         = all-bonds
> constraint-algorithm = lincs
>
>
>
>
>
>
> On 1 June 2011 14:59, Vitaly Chaban  wrote:
>>
>> Either a tighter pressure coupling time...
>>
>>
>>
>>
>> On Wed, Jun 1, 2011 at 2:57 PM, Vitaly Chaban  wrote:
>> > Hmm...
>> >
>> >
>> > 1. The background of the task is not quite clear for me.
>> >
>> > 2. Evidently, the fluctuations are higher than the difference for your
>> > pressures.
>> >
>> > 3. Why not to use significantly larger systems and significantly
>> > larger difference between pressures?
>> >
>> >
>> >
>> > --
>> > Dr. Vitaly V. Chaban, Department of Chemistry
>> > University of Rochester, Rochester, New York 14627-0216
>> >
>> >
>> >
>> >
>> >>
>> >> I am trying to study the effect of pressure on total potential of my
>> >> system
>> >> (8 polymer chains). My problem is that I dont see a systematic effect
>> >> of
>> >> pressure on potentials and I cant judge if different pressures increase
>> >> or
>> >> decrease potential. This is the critical observable in my system and
>> >> with
>> >> high fluctuations I am getting I cant make comment on pressure effect.
>> >> Total
>> >> drift is high in most potential functions..I start my runs from a frame
>> >> which is the output of an older NPT run (I use cpt file) that has a
>> >> close
>> >> density to what I want. In the production runs (NPT for 12 27 70 bar).
>> >>
>> >> Below is the settings I am using and I really appreciate it if you
>> >> could
>> >> comment on the most important factors for such a study. I tried
>> >> different
>> >> cutoffs as well...I though maybe increasing cutoffs invloves more
>> >> interactions and can represent better the pressure effect...
>> >>
>> >> Thanks so much!
>> >>
>> >>
>> >> ;        Run control
>> >> integrator          =  md
>> >> dt                  =  0.002
>> >> nsteps              =  100 ;5000
>> >> nstcomm             =  100
>> >>
>> >> ;        Output control
>> >> nstenergy           =  100
>> >> nstxout             =  100
>> >> nstvout             =  0
>> >> nstfout             =  0
>> >> nstlog   

[gmx-users] Re: Liquid/Gas Systems

[Vitaly Chaban]

>
> You had helped me earlier on calculating the heat of vaporization of
> methanol and it worked great.  I'm just trying hard to understand
> conceptually what is the difference between simulating a liquid phase
> and a gas phase in Gromacs.  I mean technically if we throw in 1000
> molecules of component A, would it only be a gas if we made the box
> super huge?  If we run NPT on a system, is that technically when we
> are compounding it together to find a liquid density?  I'm just a bit
> confused on the difference.  I've been simulating liquids up to this
> point so when I ran only NVT on a single gas molecule, I was trying to
> understand why we only run NVT on it (0 pressure so no pressure
> coupling).


I would say the things are much easier than you try to understand
them. There is no difference between simulating different phases in MD
at all. Generally, you may try NPT to simulate gaseous phase. BUT: you
should start from already equilibrated  gas phase, since barostats do
not perform adequately if the pressure/volume drift a lot during MD.
This is not a problem of MD itself.


Dr. Vitaly V. Chaban, Department of Chemistry
University of Rochester, Rochester, New York 14627-0216
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Re: [gmx-users] Re: compression to study pressure effect

[Justin A. Lemkul]

Elisabeth wrote:

Hello Dr. Vitaly Chaban,

Thank you. I asked a friend in our Dept. for help who is working on 
different aspects of the more or less similar system. The message below 
was sent on behalf of me. I apologize if I should not have done this. We 
thought maybe it does not matter under which name messages are sent on 
the gmx list and the idea of using mailing list is to share knowledge 
regardless of names. I hope this has not offended you and other users.


I am also asking Justin to let me know if I have violated mailing list 
rules. I make sure this will not happen again.




http://www.gromacs.org/Support/Mailing_Lists#Mailing_List_Etiquette

Having others send information around haphazardly to different individuals and 
from colleagues or aliases just slows down your overall progress, since we don't 
know who's getting (or providing) what information, or if the discussions are 
even connected.  Keep everything on the list and reply directly to questions 
posed to you with as much detail as you can.


It's also not a good idea for anyone to complain that "no one on the list could 
help much."  I had been trying to extract the necessary diagnostic information 
from you, but perhaps not at the pace you'd like.  Problems aren't solved 
instantly, especially via email by people who have only a very vague idea of 
what you're doing.


-Justin


Thank you,
Best regards,


On 2 June 2011 21:03, Vitaly Chaban > wrote:


Hey Eli:

What is the correlation observed between you and Moeed?

I suppose you eventually compressed your system so much, that it
became very distorted. Check your GRO file. I believe it is not
healthy inside.

Regards.

Dr. Vitaly V. Chaban, Department of Chemistry
University of Rochester, Rochester, New York 14627-0216




On Thu, Jun 2, 2011 at 6:53 PM, Moeed mailto:lecie...@googlemail.com>> wrote:
 > Dear Dr.Chaban,
 >
 > I am so sorry to send you this message. Thank you for your
comments. I have
 > encountered a problem that no one on the list could help much. I
am very
 > hopeful you can assist me especially because I have noticed you
respond to
 > messages dealing with compression or NPT runs. I am really
confused since I
 > have been using the same input files (gro. top and mdp) and have been
 > collecting without any problem. Since yesterday I am getting a
weird message
 > that is printed continuously until I kill mdrun.
 >
 >
 > arning: Only triclinic boxes with the first vector parallel to
the x-axis
 > and the second vector in the xy-plane are supported.
 >  Box (3x3):
 > Box[0]={ nan,  nan,  nan}
 > Box[1]={ nan,  nan,  nan}
 > Box[2]={ nan,  nan,  nan}
 >
 > I have only polyethylene chains in my system. I really appreciate
if you
 > could help me or could kindly take a very brief look at my
system. I can
 > send you top and gro files. I assure you top file is generated
properly. I
 > have done many runs using that. Please let me know if you are
interested.
 >
 > I thank you so much
 >
 > Waiting for your reply.
 >
 > Best regards,
 > Eli.
 >
 >
 > ;Run control
 > integrator  =  md
 > dt  =  0.002
 > nsteps  =  100 ;5000
 > nstcomm =  100
 >
 > ;Output control
 > nstenergy   =  100
 > nstxout =  100
 > nstvout =  0
 > nstfout =  0
 > nstlog  =  1000
 > nstxtcout  =  1000
 >
 > ;Neighbor searching
 > nstlist =  10
 > ns_type =  grid
 >
 > ;Electrostatics/VdW
 > coulombtype =  Shift
 > vdw-type=  Shift
 > rcoulomb-switch =  0
 > rvdw-switch =  0.9 ;0
 >
 > ;Cut-offs
 > rlist   =  1.25
 > rcoulomb=  1.0 ;1.1
 > rvdw=  1.0
 >
 > ;Temperature coupling
 > Tcoupl  =  v-rescale
 > tc-grps =  System  ;HEX
 > tau_t   =  0.1 ;0.1
 > ref_t   =  300 ;300
 >
 > ;Pressure coupling
 > Pcoupl  = Parrinello-Rahman
 > Pcoupltype  =  isotropic
 > tau_p   =  1;0.5
 > compressibility =  4.5e-5 4.5e-5
 > ref_p   =  1030
 >
 > ;Velocity generation
 > gen_vel =  yes
 > gen_temp=  300.0
 > gen_seed=  173529
 >
 > ;Bonds
 > constraints = all-bonds
 > constraint-algorithm = lincs
 >
 >
 >

[gmx-users] option -pbc in trjconv

[Kavyashree M]

Dear users,

 I wanted to ensure that the option of -pbc in trjconv is only for
visualization,
and if I do all possible calculations with the original .xtc file there wont
be any
problem.

Thank you
With regards
M. Kavyashree
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