[gmx-users] Error- Atom not found in residue seq nr while adding atom

[aiswarya pawar]

Hi Users,

I did the following step=
 pdb2gmx -ignh -f 1ahw.pdb -o sample.pdb -p sample.top


and received an error= Atom ND1 not found in residue seq.nr. 7 while adding
atom.

I dont understand how do i rectify this.


-- 
Aiswarya
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Re: [gmx-users] Error- Atom not found in residue seq nr while adding atom

[aiswarya pawar]

Hi Javier,

I did tried using the swisspdb for adding missing atoms still am receiving
the same error.


On Wed, Apr 18, 2012 at 3:44 PM, Javier Cerezo j...@um.es wrote:

  Your PDB structure have probably some missing atoms. Check if this is the
 case for residue nr. 7.

 To solve it you can use an external tool to process your PDB file adding
 the missing atoms. I've used SwissPDB and worked fine.

 Javier

 El 18/04/12 11:24, aiswarya pawar escribió:

 Hi Users,

 I did the following step=
  pdb2gmx -ignh -f 1ahw.pdb -o sample.pdb -p sample.top


 and received an error= Atom ND1 not found in residue seq.nr. 7 while
 adding atom.

 I dont understand how do i rectify this.


 --
 Aiswarya



 --
 Javier CEREZO BASTIDA
 PhD Student
 Physical Chemistry
 Universidad de Murcia
 Murcia (Spain)
 Tel: (+34)868887434

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-- 
Aiswarya  B Pawar

Project Assistant,
Bioinformatics Dept,
Indian Institute of Science
Bangalore
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Re: [gmx-users] using more processors for g_mindist

[aiswarya pawar]

Mark,

i want to know which water atoms stay within a cut off to protein atom. ie
i need the duration at which a water resides on the protein atoms. so for
that i need the whole 5ns frames because am looking for water molecules
which reside more than 50% of time.

Thanks

On Wed, Feb 29, 2012 at 12:41 PM, Mark Abraham mark.abra...@anu.edu.auwrote:

  On 29/02/2012 6:01 PM, aiswarya pawar wrote:

 Mark,

 Right now am computing distance between each protein atom against all
 water atoms,


 That's expensive. mdrun goes to great lengths to speed up computing
 billions of distances.

  which is taking too long for 5ns run. i cant reduce the frames


 Yes you can. Even if you think you need data from every frame, you
 probably don't because they're correlated with each other, and at the very
 least you can do a pilot study on a frame every 100ps or every nanosecond
 before committing to one on all the frames.


  either the number of water atoms. So is there any alternate.


 You are not likely to get a better solution if you only describe your
 attempt, rather than describe the objective. Asking how do I hammer
 harder? if you're hammering a screw makes it impossible to get the correct
 solution Use a screwdriver.

 Mark


 Thanks

 On Wed, Feb 29, 2012 at 12:27 PM, Mark Abraham mark.abra...@anu.edu.auwrote:

  On 29/02/2012 5:17 PM, aiswarya pawar wrote:

 Dear all,

 Am running g_mindist on large number of atoms, i would like to know
 whether i can run this on more than one processors say 8 processors to
 speed up the task?


  No. If it will take too long, you need to reduce your number of frames
 (trjconv), or the number of atoms (also trjconv), or some such.

 Mark


  and will this effect the output in anyways.

 Thanks,

 --
 Aiswarya  B Pawar






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 --
 Aiswarya  B Pawar

  Project Assistant,
 Bioinformatics Dept,
 Indian Institute of Science
 Bangalore






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-- 
Aiswarya  B Pawar

Project Assistant,
Bioinformatics Dept,
Indian Institute of Science
Bangalore
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Re: [gmx-users] using more processors for g_mindist

[aiswarya pawar]

Mark,

In the g_mindist output data gives which atom was within cutoff to protein
atom ie the output file of g_mindist

5.00e+02   518 42680
5.01e+02   518 20942
5.02e+02   518 67844
5.03e+02   518  5984
5.04e+02   518 67844
5.05e+02   518  5984
5.06e+02   518 30116
5.07e+02   518 67844
5.08e+02   518 32957
5.09e+02   518 67844
5.10e+02   518 19610
5.11e+02   518 19610
5.12e+02   518 22895
5.13e+02   518 30116
5.14e+02   518 19610
5.15e+02   518 22895
5.16e+02   518 13628
5.17e+02   518  5984

2nd column is the protein atom and the 3rd column the water atom.

if iam doing g_dist how is it possible to know the which water molecule has
to be considered for the distance calculations ie should i compute the
distance between one protein atom against all the water within the cut off
individually?

Thanks

On Wed, Feb 29, 2012 at 2:12 PM, Mark Abraham mark.abra...@anu.edu.auwrote:

  On 29/02/2012 7:21 PM, aiswarya pawar wrote:

 Mark,

 i want to know which water atoms stay within a cut off to protein atom.


 OK, but as you will read in g_mindist -h, it will count such atoms and not
 identify which they were...


  ie i need the duration at which a water resides on the protein atoms.


 ... and identity of the atoms is needed for measuring duration of contact.
 g_dist does something like this, and reading g_mindist -h should have
 prompted you to find this out.

 Otherwise, you will have to construct an index group for each water
 molecule, and script a loop to examine each water molecule separately using
 some tool that observes what you really want to measure.


  so for that i need the whole 5ns frames because am looking for water
 molecules which reside more than 50% of time.


 You also need to be clear about whether you care about continuous contact.
 Does a water molecule that oscillates at a distance around the cutoff
 reside about 50% of the time?

 You still don't need high time resolution for testing whether this
 analysis might give you the information you want. The water molecules that
 are in contact for more than 50% of the time (continuous or not) will show
 up in 5 snapsnots spaced every nanosecond. 5000 snapshots every picosecond
 is better, but not if you can't afford to wait for it.


 Mark


 Thanks

 On Wed, Feb 29, 2012 at 12:41 PM, Mark Abraham mark.abra...@anu.edu.auwrote:

  On 29/02/2012 6:01 PM, aiswarya pawar wrote:

 Mark,

 Right now am computing distance between each protein atom against all
 water atoms,


  That's expensive. mdrun goes to great lengths to speed up computing
 billions of distances.

  which is taking too long for 5ns run. i cant reduce the frames


  Yes you can. Even if you think you need data from every frame, you
 probably don't because they're correlated with each other, and at the very
 least you can do a pilot study on a frame every 100ps or every nanosecond
 before committing to one on all the frames.


  either the number of water atoms. So is there any alternate.


  You are not likely to get a better solution if you only describe your
 attempt, rather than describe the objective. Asking how do I hammer
 harder? if you're hammering a screw makes it impossible to get the correct
 solution Use a screwdriver.

 Mark


 Thanks

 On Wed, Feb 29, 2012 at 12:27 PM, Mark Abraham 
 mark.abra...@anu.edu.auwrote:

  On 29/02/2012 5:17 PM, aiswarya pawar wrote:

 Dear all,

 Am running g_mindist on large number of atoms, i would like to know
 whether i can run this on more than one processors say 8 processors to
 speed up the task?


  No. If it will take too long, you need to reduce your number of frames
 (trjconv), or the number of atoms (also trjconv), or some such.

 Mark


  and will this effect the output in anyways.

 Thanks,

 --
 Aiswarya  B Pawar






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 --
 Aiswarya  B Pawar

  Project Assistant,
 Bioinformatics Dept,
 Indian Institute of Science
 Bangalore






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[gmx-users] using more processors for g_mindist

[aiswarya pawar]

Dear all,

Am running g_mindist on large number of atoms, i would like to know whether
i can run this on more than one processors say 8 processors to speed up the
task? and will this effect the output in anyways.

Thanks,

-- 
Aiswarya  B Pawar
-- 
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Re: [gmx-users] using more processors for g_mindist

[aiswarya pawar]

Mark,

Right now am computing distance between each protein atom against all water
atoms, which is taking too long for 5ns run. i cant reduce the frames
either the number of water atoms. So is there any alternate.

Thanks

On Wed, Feb 29, 2012 at 12:27 PM, Mark Abraham mark.abra...@anu.edu.auwrote:

  On 29/02/2012 5:17 PM, aiswarya pawar wrote:

 Dear all,

 Am running g_mindist on large number of atoms, i would like to know
 whether i can run this on more than one processors say 8 processors to
 speed up the task?


 No. If it will take too long, you need to reduce your number of frames
 (trjconv), or the number of atoms (also trjconv), or some such.

 Mark


  and will this effect the output in anyways.

 Thanks,

 --
 Aiswarya  B Pawar






 --
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-- 
Aiswarya  B Pawar

Project Assistant,
Bioinformatics Dept,
Indian Institute of Science
Bangalore
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[gmx-users] Error energy minimization on protein with implicit water

[aiswarya pawar]

Dear Gromacs users,

I have a MD simulated protein and i take frame from this and remove water
and add water implicit in the interface and want to do energy minimization
but while doing the minimization i get errors. The steps followed are-

pdb2gmx -ignh -f 1OC0.pdb -o 1oco.pdb -p 1oco.top -nocmap
grompp -f minim.mdp -c 1oco.pdb -p 1oco.top -o 1oco.tpr

The minim.mdp file =

; Lines starting with ';' ARE COMMENTS
; Everything following ';' is also comment

title= Energy Minimization; Title of run

; The following line tell the program the standard locations where to find
certain files
cpp= /lib/cpp; Preprocessor

; Define can be used to control processes
define  = -DFLEXIBLE

; Parameters describing what to do, when to stop and what to save
integrator= steep; Algorithm (steep = steepest descent
minimization)
emtol= 1000.0; Stop minimization when the maximum force  1.0
kJ/mol
nsteps= 5000; Maximum number of (minimization) steps to
perform
nstenergy= 1; Write energies to disk every nstenergy steps
energygrps= System; Which energy group(s) to write to disk

; Parameters describing how to find the neighbors of each atom and how to
calculate the interactions
ns_type= simple  ; Method to determine neighbor list (simple,
grid)
coulombtype= cut-off  ; Treatment of long range electrostatic
interactions
rcoulomb= 1.0; long range electrostatic cut-off
rvdw= 1.0; long range Van der Waals cut-off
constraints= none; Bond types to replace by constraints
pbc= no; Periodic Boundary Conditions (yes/no)

I get a note as =
System has non-zero total charge: -4.96e+00

then i tried using genion step as=

genion -s 1oco.tpr -o 1oco.pdb -pname NA -np 5 -p 1oco.top -g ion.log

then again the grompp step and mdrun .
but while doing mdrun i get an error as=

Stepsize too small, or no change in energy.
Converged to machine precision,
but not to the requested precision Fmax  1000


but here i have given nsteps as 5000 so why does it stop.
-- 
Aiswarya  B Pawar

Project Assistant,
Bioinformatics Dept,
Indian Institute of Science
Bangalore
-- 
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[gmx-users] Error energy minimization on protein with implicit water

[aiswarya pawar]

Dear Gromacs users,

I have a MD simulated protein and i take frame from this and remove water
and add water implicit in the interface and want to do energy minimization
but while doing the minimization i get errors. The steps followed are-

pdb2gmx -ignh -f 1OC0.pdb -o 1oco.pdb -p 1oco.top -nocmap
grompp -f minim.mdp -c 1oco.pdb -p 1oco.top -o 1oco.tpr

The minim.mdp file =

; Lines starting with ';' ARE COMMENTS
; Everything following ';' is also comment

title= Energy Minimization; Title of run

; The following line tell the program the standard locations where to find
certain files
cpp= /lib/cpp; Preprocessor

; Define can be used to control processes
define  = -DFLEXIBLE

; Parameters describing what to do, when to stop and what to save
integrator= steep; Algorithm (steep = steepest descent
minimization)
emtol= 1000.0; Stop minimization when the maximum force  1.0
kJ/mol
nsteps= 5000; Maximum number of (minimization) steps to
perform
nstenergy= 1; Write energies to disk every nstenergy steps
energygrps= System; Which energy group(s) to write to disk

; Parameters describing how to find the neighbors of each atom and how to
calculate the interactions
ns_type= simple  ; Method to determine neighbor list (simple,
grid)
coulombtype= cut-off  ; Treatment of long range electrostatic
interactions
rcoulomb= 1.0; long range electrostatic cut-off
rvdw= 1.0; long range Van der Waals cut-off
constraints= none; Bond types to replace by constraints
pbc= no; Periodic Boundary Conditions (yes/no)

I get a note as =
System has non-zero total charge: -4.96e+00

then i tried using genion step as=

genion -s 1oco.tpr -o 1oco.pdb -pname NA -np 5 -p 1oco.top -g ion.log

then again the grompp step and mdrun .
but while doing mdrun i get an error as=

Stepsize too small, or no change in energy.
Converged to machine precision,
but not to the requested precision Fmax  1000


but here i have given nsteps as 5000 so why does it stop.
-- 
Aiswarya  B Pawar

Project Assistant,
Bioinformatics Dept,
Indian Institute of Science
Bangalore





-- 
Aiswarya  B Pawar

Project Assistant,
Bioinformatics Dept,
Indian Institute of Science
Bangalore
-- 
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Re: [gmx-users] Error energy minimization on protein with implicit water

[aiswarya pawar]

By setting the emtol to 1.0, didnt work. Anyother way i could figure out.

On Thu, Feb 9, 2012 at 6:32 PM, Justin A. Lemkul jalem...@vt.edu wrote:



 lina wrote:

 On Thu, Feb 9, 2012 at 6:17 PM, aiswarya pawar aiswarya.pa...@gmail.com
 wrote:

 Dear Gromacs users,

 I have a MD simulated protein and i take frame from this and remove water
 and add water implicit in the interface and want to do energy
 minimization
 but while doing the minimization i get errors. The steps followed are-

 pdb2gmx -ignh -f 1OC0.pdb -o 1oco.pdb -p 1oco.top -nocmap
 grompp -f minim.mdp -c 1oco.pdb -p 1oco.top -o 1oco.tpr

 The minim.mdp file =

 ; Lines starting with ';' ARE COMMENTS
 ; Everything following ';' is also comment

 title= Energy Minimization; Title of run

 ; The following line tell the program the standard locations where to
 find
 certain files
 cpp= /lib/cpp; Preprocessor

 ; Define can be used to control processes
 define  = -DFLEXIBLE

 ; Parameters describing what to do, when to stop and what to save
 integrator= steep; Algorithm (steep = steepest descent
 minimization)
 emtol= 1000.0; Stop minimization when the maximum force  1.0

 emtol = 1.0


 If mdrun could not converge to 1000, setting a target of 1 will not solve
 anything.  The OP should refer to:

 http://www.gromacs.org/**Documentation/Errors#Stepsize_**
 too_small.2c_or_no_change_in_**energy._Converged_to_machine_**
 precision.2c_but_not_to_the_**requested_precisionhttp://www.gromacs.org/Documentation/Errors#Stepsize_too_small.2c_or_no_change_in_energy._Converged_to_machine_precision.2c_but_not_to_the_requested_precision

 -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/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

 ==**==

 --
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-- 
Aiswarya  B Pawar

Project Assistant,
Bioinformatics Dept,
Indian Institute of Science
Bangalore
-- 
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[gmx-users] g_analyze doubt

[aiswarya pawar]

Dear Gromacs Users,

i have data for the distance between the protein and water atoms within a
cut off of 8A for 5ns using the g_dist option. Now i want to use g_analyze
on this data. The time frame in the output data is not continuous because
of the cut off provided. So i would like to know how would the g_analyze
would compute the data.


Thanks

-- 
Aiswarya  B Pawar

Project Assistant,
Bioinformatics Dept,
Indian Institute of Science
Bangalore
-- 
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Re: [gmx-users] g_analyze doubt

[aiswarya pawar]

Hi,

I have used the command =

g_dist -f md.xtc -s md.tpr -n index.ndx

which gives an output of data=

  0.0000.62590240.3880.3610001   -0.3329997
   1.0000.67787750.25900030.593   -0.198
   2.0000.67590300.25299980.593   -0.203
   3.0000.64633530.16900010.5680003   -0.257
   4.0000.68088910.2630.605   -0.1669998
   5.0000.68835610.3090.592   -0.1670003
   6.0000.62016600.27699970.513   -0.2090001
   7.0000.68320050.29100010.580   -0.211
   8.0000.64729990.29600020.533   -0.2150002
   9.0000.65426920.1880.540   -0.3180003
  10.0000.67256020.32300020.5780001   -0.118
  11.0000.61387120.34700010.4769998   -0.171
  12.0000.69996450.2860.6150002   -0.172
  13.0000.65045930.1210.6160002   -0.171
  14.0000.64471600.2110.586   -0.1629996
  15.0000.66456100.2040.5710001   -0.2720003
  16.0000.64812760.23300030.5560002   -0.237
  17.0000.6530.22400020.560   -0.243
  18.0000.71192580.26500010.6220002   -0.223
  19.0000.66535630.0920.6170001   -0.230
  20.0000.68816380.25200010.6070004   -0.204
  21.0000.71619440.20900010.6220002   -0.2870002
  22.0000.65877780.1410.6020002   -0.2279997
  23.0000.57986310.01700020.5160003   -0.263
  24.0000.58625640.0390.5239997   -0.258
  25.0000.6923014   -0.12400010.552   -0.3990002
  26.0000.5787479   -0.0870.5050001   -0.2680001
  27.0000.5776323   -0.25899980.473   -0.2070003
  28.0000.5910018   -0.16300010.5250001   -0.217
  29.0000.4448786   -0.15700010.402   -0.1079998
  30.0000.4806164   -0.21600010.401   -0.1560001
  31.0000.5405830   -0.1710.473   -0.198
  32.0000.5614526   -0.10800030.493   -0.2459998
  33.0000.4994450   -0.0730.453   -0.204
  34.0000.5323368   -0.14200020.4830003   -0.1730003


From this the first column is the time and the second is the water protein
atom distance. so when am using the g_analyze i would use the 1st and 2nd
column for the input? More over now this distances are below 0.8 nm . what
would i do if my data in between shows distance more than 0.8nm.

Thanks
On Wed, Feb 1, 2012 at 6:48 PM, Justin A. Lemkul jalem...@vt.edu wrote:



 aiswarya pawar wrote:

 Dear Gromacs Users,

 i have data for the distance between the protein and water atoms within a
 cut off of 8A for 5ns using the g_dist option. Now i want to use g_analyze
 on this data. The time frame in the output data is not continuous because
 of the cut off provided. So i would like to know how would the g_analyze
 would compute the data.



 I'm not clear on what you're trying to do.  g_analyze performs simple
 statistical operations (averages, error estimates) on the input data.  If
 there are discontinuities (which I do not understand the nature of), they
 come from the g_dist data, not what g_analyze is doing.

 Please provide a more clear description of what you are doing, including
 all relevant commands, and examples of the data files, 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/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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-- 
Aiswarya  B Pawar

Project Assistant,
Bioinformatics Dept,
Indian Institute of Science
Bangalore
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Re: [gmx-users] g_analyze doubt

[aiswarya pawar]

If i give command as =

g_dist -f md.xtc -s md.tpr -n index.ndx -dist 0.8

this prints out all the protein water distance within 0.8nm. The data printed 
out is such that=

t: 1466  5369 SOL 20624 OW  0.789894 (nm)
t: 1467  5369 SOL 20624 OW  0.781596 (nm)
t: 1469  5369 SOL 20624 OW  0.785377 (nm)
t: 1473  5369 SOL 20624 OW  0.763485 (nm)
t: 1474  5369 SOL 20624 OW  0.767805 (nm)
t: 1475  5369 SOL 20624 OW  0.736003 (nm)
t: 1476  5369 SOL 20624 OW  0.707953 (nm)
t: 1477  5369 SOL 20624 OW  0.713135 (nm)
t: 1478  5369 SOL 20624 OW  0.694042 (nm)
t: 1480  5369 SOL 20624 OW  0.733907 (nm)
t: 1481  5369 SOL 20624 OW  0.705245 (nm)
t: 1482  5369 SOL 20624 OW  0.678473 (nm)
t: 1483  5369 SOL 20624 OW  0.6288 (nm)
t: 1492  5369 SOL 20624 OW  0.794252 (nm)
t: 1496  5369 SOL 20624 OW  0.753049 (nm)
t: 1497  5369 SOL 20624 OW  0.782796 (nm)
t: 1498  5369 SOL 20624 OW  0.799607 (nm)
t: 1499  5369 SOL 20624 OW  0.69987 (nm)
t: 1500  5369 SOL 20624 OW  0.763511 (nm)
t: 1501  5369 SOL 20624 OW  0.764072 (nm)
t: 1502  5369 SOL 20624 OW  0.739181 (nm)
t: 1503  5369 SOL 20624 OW  0.70336 (nm)


In the above data can be seen that the time frame is not continuos. i.e. only 
the time at which the protein water distance within 0.8nm are shown. So is it 
possible to do g_analyze on this?


On 01-Feb-2012, at 6:48 PM, Justin A. Lemkul wrote:

 
 
 aiswarya pawar wrote:
 Dear Gromacs Users,
 i have data for the distance between the protein and water atoms within a 
 cut off of 8A for 5ns using the g_dist option. Now i want to use g_analyze 
 on this data. The time frame in the output data is not continuous because of 
 the cut off provided. So i would like to know how would the g_analyze would 
 compute the data.
 
 I'm not clear on what you're trying to do.  g_analyze performs simple 
 statistical operations (averages, error estimates) on the input data.  If 
 there are discontinuities (which I do not understand the nature of), they 
 come from the g_dist data, not what g_analyze is doing.
 
 Please provide a more clear description of what you are doing, including all 
 relevant commands, and examples of the data files, 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
 
 
 -- 
 gmx-users mailing listgmx-users@gromacs.org
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 Please don't post (un)subscribe requests to the list. Use the www interface 
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Re: [gmx-users] mdrun-gpu error

[aiswarya pawar]

Has the tesla card got to do anything with the error. Am using Nvidia Tesla
S1070 1U server.


On Thu, Jan 19, 2012 at 8:37 PM, Szilárd Páll szilard.p...@cbr.su.sewrote:

 And sorting out where the /bin/cat error comes from because that is
 surely not a Gromacs message!

 Cheers,
 --
 Szilárd



 On Thu, Jan 19, 2012 at 1:12 PM, Mark Abraham mark.abra...@anu.edu.au
 wrote:
  On 19/01/2012 8:45 PM, aiswarya pawar wrote:
 
  Mark,
 
  THe normal mdrun also hangs thus not generating any output.
 
 
  OK. It's your problem to solve... keep simplifying stuff until you can
  isolate a small number of possible causes. Top of the list is file system
  availability.
 
  Mark
 
 
 
  On Thu, Jan 19, 2012 at 3:09 AM, Mark Abraham mark.abra...@anu.edu.au
  wrote:
 
  On 19/01/2012 2:59 AM, aiswarya.pa...@gmail.com wrote:
 
  Hi,
 
  Its going into the running mode but gets hang there for long hours which
  generating any data in the output file. And am not able to figure out
 the
  error file_doc. Please anyone knows what's going wrong.
 
 
  No, but you should start trying to simplify what you're doing to see
 where
  the problem lies. Does normal mdrun work?
 
  Mark
 
 
  Thanks
  Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go
 for
  it!
 
  -Original Message-
  From: Szilárd Páll szilard.p...@cbr.su.se
  Sender: gmx-users-boun...@gromacs.org
  Date: Wed, 18 Jan 2012 14:47:59
  To: Discussion list for GROMACS usersgmx-users@gromacs.org
  Reply-To: Discussion list for GROMACS users gmx-users@gromacs.org
  Subject: Re: [gmx-users] mdrun-gpu error
 
  Hi,
 
  Most of those are just warnings, the only error I see there comes from
  the shell, probably an error in your script.
 
  Cheers,
  --
  Szilárd
 
 
 
  On Wed, Jan 18, 2012 at 12:27 PM, aiswarya pawar
  aiswarya.pa...@gmail.com wrote:
 
  Hi users,
 
  Am running mdrun on gpu . I receive an error such as=
 
  WARNING: This run will generate roughly 38570 Mb of data
 
 
  WARNING: OpenMM does not support leap-frog, will use velocity-verlet
  integrator.
 
 
  WARNING: OpenMM supports only Andersen thermostat with the
  md/md-vv/md-vv-avek integrators.
 
 
  WARNING: OpenMM supports only Monte Carlo barostat for pressure
 coupling.
 
 
  WARNING: OpenMM provides contraints as a combination of SHAKE, SETTLE
 and
  CCMA. Accuracy is based on the SHAKE tolerance set by the shake_tol
  option.
 
  /bin/cat: file_loc: No such file or directory
 
 
  and the job is running but the nothing written into .xtc, .trr, .edr
 files
  .
  What could have gone wrong?
 
  --
  Aiswarya  B Pawar
 
  Bioinformatics Dept,
  Indian Institute of Science
  Bangalore
 
 
 
  --
  gmx-users mailing listgmx-users@gromacs.org
  http://lists.gromacs.org/mailman/listinfo/gmx-users
  Please search the archive at
  http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
  Please don't post (un)subscribe requests to the list. Use the
  www interface or send it to gmx-users-requ...@gromacs.org.
  Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
 
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  Please search the archive at
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  Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
 
 
 
 
  --
  Aiswarya  B Pawar
 
  Bioinformatics Dept,
  Indian Institute of Science
  Bangalore
 
 
 
 
 
 
  --
  gmx-users mailing listgmx-users@gromacs.org
  http://lists.gromacs.org/mailman/listinfo/gmx-users
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-- 
Aiswarya  B Pawar

Bioinformatics Dept,
Indian Institute of Science
Bangalore
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive

Re: [gmx-users] mdrun-gpu error

[aiswarya pawar]

when i tired running it again, i got an error as

Cuda error in file
'/home/staff/sec/secdpal/software/openmm_tesla/platforms/cuda/./src/kernels//
bbsort.cu' in line 176 : unspecified launch failure.
/bin/cat: file_loc: No such file or directory

On Thu, Jan 19, 2012 at 8:45 PM, aiswarya pawar aiswarya.pa...@gmail.comwrote:

 Has the tesla card got to do anything with the error. Am using Nvidia
 Tesla S1070 1U server.


 On Thu, Jan 19, 2012 at 8:37 PM, Szilárd Páll szilard.p...@cbr.su.sewrote:

 And sorting out where the /bin/cat error comes from because that is
 surely not a Gromacs message!

 Cheers,
 --
 Szilárd



 On Thu, Jan 19, 2012 at 1:12 PM, Mark Abraham mark.abra...@anu.edu.au
 wrote:
  On 19/01/2012 8:45 PM, aiswarya pawar wrote:
 
  Mark,
 
  THe normal mdrun also hangs thus not generating any output.
 
 
  OK. It's your problem to solve... keep simplifying stuff until you can
  isolate a small number of possible causes. Top of the list is file
 system
  availability.
 
  Mark
 
 
 
  On Thu, Jan 19, 2012 at 3:09 AM, Mark Abraham mark.abra...@anu.edu.au
  wrote:
 
  On 19/01/2012 2:59 AM, aiswarya.pa...@gmail.com wrote:
 
  Hi,
 
  Its going into the running mode but gets hang there for long hours
 which
  generating any data in the output file. And am not able to figure out
 the
  error file_doc. Please anyone knows what's going wrong.
 
 
  No, but you should start trying to simplify what you're doing to see
 where
  the problem lies. Does normal mdrun work?
 
  Mark
 
 
  Thanks
  Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go
 for
  it!
 
  -Original Message-
  From: Szilárd Páll szilard.p...@cbr.su.se
  Sender: gmx-users-boun...@gromacs.org
  Date: Wed, 18 Jan 2012 14:47:59
  To: Discussion list for GROMACS usersgmx-users@gromacs.org
  Reply-To: Discussion list for GROMACS users gmx-users@gromacs.org
  Subject: Re: [gmx-users] mdrun-gpu error
 
  Hi,
 
  Most of those are just warnings, the only error I see there comes from
  the shell, probably an error in your script.
 
  Cheers,
  --
  Szilárd
 
 
 
  On Wed, Jan 18, 2012 at 12:27 PM, aiswarya pawar
  aiswarya.pa...@gmail.com wrote:
 
  Hi users,
 
  Am running mdrun on gpu . I receive an error such as=
 
  WARNING: This run will generate roughly 38570 Mb of data
 
 
  WARNING: OpenMM does not support leap-frog, will use velocity-verlet
  integrator.
 
 
  WARNING: OpenMM supports only Andersen thermostat with the
  md/md-vv/md-vv-avek integrators.
 
 
  WARNING: OpenMM supports only Monte Carlo barostat for pressure
 coupling.
 
 
  WARNING: OpenMM provides contraints as a combination of SHAKE, SETTLE
 and
  CCMA. Accuracy is based on the SHAKE tolerance set by the shake_tol
  option.
 
  /bin/cat: file_loc: No such file or directory
 
 
  and the job is running but the nothing written into .xtc, .trr, .edr
 files
  .
  What could have gone wrong?
 
  --
  Aiswarya  B Pawar
 
  Bioinformatics Dept,
  Indian Institute of Science
  Bangalore
 
 
 
  --
  gmx-users mailing listgmx-users@gromacs.org
  http://lists.gromacs.org/mailman/listinfo/gmx-users
  Please search the archive at
  http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
  Please don't post (un)subscribe requests to the list. Use the
  www interface or send it to gmx-users-requ...@gromacs.org.
  Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
 
  --
  gmx-users mailing listgmx-users@gromacs.org
  http://lists.gromacs.org/mailman/listinfo/gmx-users
  Please search the archive at
  http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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  www interface or send it to gmx-users-requ...@gromacs.org.
  Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
 
 
 
 
 
  --
  gmx-users mailing listgmx-users@gromacs.org
  http://lists.gromacs.org/mailman/listinfo/gmx-users
  Please search the archive at
  http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
  Please don't post (un)subscribe requests to the list. Use the
  www interface or send it to gmx-users-requ...@gromacs.org.
  Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
 
 
 
 
  --
  Aiswarya  B Pawar
 
  Bioinformatics Dept,
  Indian Institute of Science
  Bangalore
 
 
 
 
 
 
  --
  gmx-users mailing listgmx-users@gromacs.org
  http://lists.gromacs.org/mailman/listinfo/gmx-users
  Please search the archive at
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 Please don't post (un)subscribe requests to the list. Use the
 www

Re: [gmx-users] mdrun-gpu error

[aiswarya pawar]

Szilárd,

I did a memory test run yesterday and it went fine but today received an
error. So you mean to say the tesla card version nothing to do with this
right.

Thanks

On Thu, Jan 19, 2012 at 11:09 PM, Szilárd Páll szilard.p...@cbr.su.sewrote:

 That's a generic GPU kernel launch failure which can mean anything,
 from faulty hardware to bad driver to messed up installation.

 Does the memory test run? Try to compile/install again and see if it works.

 --
 Szilárd



 On Thu, Jan 19, 2012 at 4:18 PM, aiswarya pawar
 aiswarya.pa...@gmail.com wrote:
  when i tired running it again, i got an error as
 
  Cuda error in file
 
 '/home/staff/sec/secdpal/software/openmm_tesla/platforms/cuda/./src/kernels//
 bbsort.cu'
  in line 176 : unspecified launch failure.
 
  /bin/cat: file_loc: No such file or directory
 
 
  On Thu, Jan 19, 2012 at 8:45 PM, aiswarya pawar 
 aiswarya.pa...@gmail.com
  wrote:
 
  Has the tesla card got to do anything with the error. Am using Nvidia
  Tesla S1070 1U server.
 
 
  On Thu, Jan 19, 2012 at 8:37 PM, Szilárd Páll szilard.p...@cbr.su.se
  wrote:
 
  And sorting out where the /bin/cat error comes from because that is
  surely not a Gromacs message!
 
  Cheers,
  --
  Szilárd
 
 
 
  On Thu, Jan 19, 2012 at 1:12 PM, Mark Abraham mark.abra...@anu.edu.au
 
  wrote:
   On 19/01/2012 8:45 PM, aiswarya pawar wrote:
  
   Mark,
  
   THe normal mdrun also hangs thus not generating any output.
  
  
   OK. It's your problem to solve... keep simplifying stuff until you
 can
   isolate a small number of possible causes. Top of the list is file
   system
   availability.
  
   Mark
  
  
  
   On Thu, Jan 19, 2012 at 3:09 AM, Mark Abraham 
 mark.abra...@anu.edu.au
   wrote:
  
   On 19/01/2012 2:59 AM, aiswarya.pa...@gmail.com wrote:
  
   Hi,
  
   Its going into the running mode but gets hang there for long hours
   which
   generating any data in the output file. And am not able to figure
 out
   the
   error file_doc. Please anyone knows what's going wrong.
  
  
   No, but you should start trying to simplify what you're doing to see
   where
   the problem lies. Does normal mdrun work?
  
   Mark
  
  
   Thanks
   Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network.
 Go
   for
   it!
  
   -Original Message-
   From: Szilárd Páll szilard.p...@cbr.su.se
   Sender: gmx-users-boun...@gromacs.org
   Date: Wed, 18 Jan 2012 14:47:59
   To: Discussion list for GROMACS usersgmx-users@gromacs.org
   Reply-To: Discussion list for GROMACS users gmx-users@gromacs.org
   Subject: Re: [gmx-users] mdrun-gpu error
  
   Hi,
  
   Most of those are just warnings, the only error I see there comes
 from
   the shell, probably an error in your script.
  
   Cheers,
   --
   Szilárd
  
  
  
   On Wed, Jan 18, 2012 at 12:27 PM, aiswarya pawar
   aiswarya.pa...@gmail.com wrote:
  
   Hi users,
  
   Am running mdrun on gpu . I receive an error such as=
  
   WARNING: This run will generate roughly 38570 Mb of data
  
  
   WARNING: OpenMM does not support leap-frog, will use velocity-verlet
   integrator.
  
  
   WARNING: OpenMM supports only Andersen thermostat with the
   md/md-vv/md-vv-avek integrators.
  
  
   WARNING: OpenMM supports only Monte Carlo barostat for pressure
   coupling.
  
  
   WARNING: OpenMM provides contraints as a combination of SHAKE,
 SETTLE
   and
   CCMA. Accuracy is based on the SHAKE tolerance set by the
 shake_tol
   option.
  
   /bin/cat: file_loc: No such file or directory
  
  
   and the job is running but the nothing written into .xtc, .trr, .edr
   files
   .
   What could have gone wrong?
  
   --
   Aiswarya  B Pawar
  
   Bioinformatics Dept,
   Indian Institute of Science
   Bangalore
  
  
  
   --
   gmx-users mailing listgmx-users@gromacs.org
   http://lists.gromacs.org/mailman/listinfo/gmx-users
   Please search the archive at
   http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
   Please don't post (un)subscribe requests to the list. Use the
   www interface or send it to gmx-users-requ...@gromacs.org.
   Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
  
   --
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   www interface or send it to gmx-users-requ...@gromacs.org.
   Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
  
  
  
  
  
   --
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   Please search the archive at
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Re: [gmx-users] mdrun-gpu error

[aiswarya pawar]

Justin,

Sorry for not giving the correct information.

Gromacs version 4.5.5
Tesla card- Nvidia Tesla S1070 (Tesla T10 Processor)
Cuda version 3.1
CMake 2.8

I installed the OpenMM from the source using commands=

ccmake -i .
make
make test
make install

everything went fine and set the paths

export OPENMM_ROOT_DIR=path_to_custom_openmm_installation
cmake -DGMX_OPENMM=ON

then
make
make install

The submission script used is=

#!/bin/csh
#PBS -l gpu=1
#PBS -l ncpus=1
#PBS -o /global/utemp/cuda-out2.out
#PBS -e /global/utemp/cuda-err2.out
/home/staff/software/gromacs_gpu_t/bin/mdrun-gpu -device
OpenMM:platform=Cuda,DeviceID=0,Memtest=15,**,force-device=yes  -v
-deffnm /global/utemp/md

for this i receive an error such as
Cuda error in file
'/home/staff/software/openmm_tesla/platforms/cuda/./src/kernels//bbsort.cu'
in line 176 : unspecified launch failure.
/bin/cat: file_loc: No such file or directory




On Thu, Jan 19, 2012 at 11:41 PM, Justin A. Lemkul jalem...@vt.edu wrote:



 aiswarya pawar wrote:

 Szilárd,

 I did a memory test run yesterday and it went fine but today received an
 error. So you mean to say the tesla card version nothing to do with this
 right.


 You're trying to solve multiple problems at once.  You told Mark that the
 normal mdrun executable (which works independently of any GPU components)
 also hangs, so either your filesystem is faulty or your installation
 procedure produced nonfunctional executables.

 You're posting bits and pieces of information, which makes it incredibly
 hard for anyone to help you.  Let's recap and try again.  Please provide:

 1. The Gromacs version you're using
 2. Description of the hardware (GPU and non-GPU components)
 3. Installation procedure for Gromacs and any of the prerequisite software
 and libraries that were required, including versions
 4. The exact command(s) you're issuing, including the full script that is
 causing a problem

 -Justin

  Thanks


 On Thu, Jan 19, 2012 at 11:09 PM, Szilárd Páll 
 szilard.p...@cbr.su.semailto:
 szilard.p...@cbr.su.se** wrote:

That's a generic GPU kernel launch failure which can mean anything,
from faulty hardware to bad driver to messed up installation.

Does the memory test run? Try to compile/install again and see if it
works.

--
Szilárd



On Thu, Jan 19, 2012 at 4:18 PM, aiswarya pawar
aiswarya.pa...@gmail.com 
 mailto:aiswarya.pawar@gmail.**comaiswarya.pa...@gmail.com
 wrote:
  when i tired running it again, i got an error as
 
  Cuda error in file
 
'/home/staff/sec/secdpal/**software/openmm_tesla/**
 platforms/cuda/./src/kernels//**bbsort.cu http://bbsort.cu
http://bbsort.cu'

  in line 176 : unspecified launch failure.
 
  /bin/cat: file_loc: No such file or directory
 
 
  On Thu, Jan 19, 2012 at 8:45 PM, aiswarya pawar
aiswarya.pa...@gmail.com 
 mailto:aiswarya.pawar@gmail.**comaiswarya.pa...@gmail.com
 

  wrote:
 
  Has the tesla card got to do anything with the error. Am
using Nvidia
  Tesla S1070 1U server.
 
 
  On Thu, Jan 19, 2012 at 8:37 PM, Szilárd Páll
szilard.p...@cbr.su.se mailto:szilard.p...@cbr.su.se**

  wrote:
 
  And sorting out where the /bin/cat error comes from because that
 is
  surely not a Gromacs message!
 
  Cheers,
  --
  Szilárd
 
 
 
  On Thu, Jan 19, 2012 at 1:12 PM, Mark Abraham
mark.abra...@anu.edu.au 
 mailto:mark.abra...@anu.edu.**aumark.abra...@anu.edu.au
 

  wrote:
   On 19/01/2012 8:45 PM, aiswarya pawar wrote:
  
   Mark,
  
   THe normal mdrun also hangs thus not generating any output.
  
  
   OK. It's your problem to solve... keep simplifying stuff
until you can
   isolate a small number of possible causes. Top of the list is
file
   system
   availability.
  
   Mark
  
  
  
   On Thu, Jan 19, 2012 at 3:09 AM, Mark Abraham
mark.abra...@anu.edu.au 
 mailto:mark.abra...@anu.edu.**aumark.abra...@anu.edu.au
 

   wrote:
  
   On 19/01/2012 2:59 AM, aiswarya.pa...@gmail.com
mailto:aiswarya.pawar@gmail.**com aiswarya.pa...@gmail.com wrote:
  
   Hi,
  
   Its going into the running mode but gets hang there for long
hours
   which
   generating any data in the output file. And am not able to
figure out
   the
   error file_doc. Please anyone knows what's going wrong.
  
  
   No, but you should start trying to simplify what you're
doing to see
   where
   the problem lies. Does normal mdrun work?
  
   Mark
  
  
   Thanks
   Sent from my BlackBerryŽ on Reliance Mobile, India's No. 1

Network. Go
   for
   it!
  
   -Original Message-
   From: Szilárd Páll szilard.p...@cbr.su.se
mailto:szilard.p...@cbr.su.se**
   Sender: gmx-users-boun...@gromacs.org

[gmx-users] mdrun-gpu error

[aiswarya pawar]

Hi users,

Am running mdrun on gpu . I receive an error such as=

WARNING: This run will generate roughly 38570 Mb of data


WARNING: OpenMM does not support leap-frog, will use velocity-verlet
integrator.


WARNING: OpenMM supports only Andersen thermostat with the
md/md-vv/md-vv-avek integrators.


WARNING: OpenMM supports only Monte Carlo barostat for pressure coupling.


WARNING: OpenMM provides contraints as a combination of SHAKE, SETTLE and
CCMA. Accuracy is based on the SHAKE tolerance set by the shake_tol
option.

/bin/cat: file_loc: No such file or directory


and the job is running but the nothing written into .xtc, .trr, .edr files
. What could have gone wrong?

-- 
Aiswarya  B Pawar

Bioinformatics Dept,
Indian Institute of Science
Bangalore
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Re: [gmx-users] mdrun-gpu error

[aiswarya . pawar]

Hi, 

Its going into the running mode but gets hang there for long hours which 
generating any data in the output file. And am not able to figure out the error 
file_doc. Please anyone knows what's going wrong.

Thanks
Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for it!

-Original Message-
From: Szilárd Páll szilard.p...@cbr.su.se
Sender: gmx-users-boun...@gromacs.org
Date: Wed, 18 Jan 2012 14:47:59 
To: Discussion list for GROMACS usersgmx-users@gromacs.org
Reply-To: Discussion list for GROMACS users gmx-users@gromacs.org
Subject: Re: [gmx-users] mdrun-gpu error

Hi,

Most of those are just warnings, the only error I see there comes from
the shell, probably an error in your script.

Cheers,
--
Szilárd



On Wed, Jan 18, 2012 at 12:27 PM, aiswarya pawar
aiswarya.pa...@gmail.com wrote:
 Hi users,

 Am running mdrun on gpu . I receive an error such as=

 WARNING: This run will generate roughly 38570 Mb of data


 WARNING: OpenMM does not support leap-frog, will use velocity-verlet
 integrator.


 WARNING: OpenMM supports only Andersen thermostat with the
 md/md-vv/md-vv-avek integrators.


 WARNING: OpenMM supports only Monte Carlo barostat for pressure coupling.


 WARNING: OpenMM provides contraints as a combination of SHAKE, SETTLE and
 CCMA. Accuracy is based on the SHAKE tolerance set by the shake_tol
 option.

 /bin/cat: file_loc: No such file or directory


 and the job is running but the nothing written into .xtc, .trr, .edr files .
 What could have gone wrong?

 --
 Aiswarya  B Pawar

 Bioinformatics Dept,
 Indian Institute of Science
 Bangalore



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[gmx-users] Invalid T coupling input: 1 groups, 2 ref_t values and 2 tau_t values

[aiswarya pawar]

Hi users,

Am trying to run the grimaces gpu version. I receive an error while doing
the nvt step . my nvt.mdp file goes like this=

; VARIOUS PREPROCESSING OPTIONS
title= NVT simulation (constant number, volume and
temperature)
cpp  = /lib/cpp

; RUN CONTROL PARAMETERS
integrator   = md
dt   = 0.002
nsteps   = 1250

; OUTPUT CONTROL OPTIONS
nstxout  = 0; No output, except for
last frame (coordinates)
nstvout  = 0; No output, except for
last frame (velocities)
nstfout  = 0; No output, except for
last frame (forces)
nstlog   = 1; Write every step to the
log
nstenergy= 5; Write energies at every
step
nstxtcout= 0; Do not write a compressed
trajectory
energygrps   = System   ; Write energy information
separately for these groups

; NEIGHBORSEARCHING PARAMETERS
nstlist  = 5
ns-type  = Grid
pbc  = xyz
rlist= 0.9

; OPTIONS FOR ELECTROSTATICS AND VDW
coulombtype  = PME
rcoulomb = 0.9
epsilon_rf   = 54
vdw-type = Cut-off
rvdw = 1.4

; Temperature coupling
tcoupl   = Berendsen
tc-grps  = System
tau_t= 0.1  0.1
ref_t= 300  300

; Pressure coupling
pcoupl   = no

; OPTIONS FOR BONDS
constraints  = hbonds


i get an error as Invalid T coupling input: 1 groups, 2 ref_t values and 2
tau_t values

please tell me whats wrong.

Thanks
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Re: [gmx-users] Invalid T coupling input: 1 groups, 2 ref_t values and 2 tau_t values

[aiswarya pawar]

Yes it worked. Thanks :)

On Tue, Jan 17, 2012 at 10:26 PM, Justin A. Lemkul jalem...@vt.edu wrote:



 aiswarya pawar wrote:

 Hi users,

 Am trying to run the grimaces gpu version. I receive an error while doing
 the nvt step . my nvt.mdp file goes like this=

 ; VARIOUS PREPROCESSING OPTIONS
 title= NVT simulation (constant number, volume and
 temperature)
 cpp  = /lib/cpp

 ; RUN CONTROL PARAMETERS
 integrator   = md
 dt   = 0.002
 nsteps   = 1250

 ; OUTPUT CONTROL OPTIONS
 nstxout  = 0; No output, except for
 last frame (coordinates)
 nstvout  = 0; No output, except for
 last frame (velocities)
 nstfout  = 0; No output, except for
 last frame (forces)
 nstlog   = 1; Write every step to the
 log nstenergy= 5; Write energies at
 every step
 nstxtcout= 0; Do not write a
 compressed trajectory
 energygrps   = System   ; Write energy
 information separately for these groups

 ; NEIGHBORSEARCHING PARAMETERS
 nstlist  = 5
 ns-type  = Grid
 pbc  = xyz
 rlist= 0.9

 ; OPTIONS FOR ELECTROSTATICS AND VDW
 coulombtype  = PME
 rcoulomb = 0.9
 epsilon_rf   = 54
 vdw-type = Cut-off
 rvdw = 1.4

 ; Temperature coupling  tcoupl   = Berendsen
 tc-grps  = System
 tau_t= 0.1  0.1
 ref_t= 300  300

 ; Pressure coupling pcoupl   = no

 ; OPTIONS FOR BONDSconstraints  = hbonds


 i get an error as Invalid T coupling input: 1 groups, 2 ref_t values and
 2 tau_t values

 please tell me whats wrong.


 Precisely what it says.  You specify one group to be coupled (System), but
 then provide coupling information for two groups.

 -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/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

 ==**==
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Re: [gmx-users] Regarding trajectory file

[aiswarya pawar]

You can write this on VMD forum. Anyways you can try by doing this in the
Tcl console-

set sel [atomselect top solvent]
$sel get {x y z}

This would give you the coordinates of the solvent, for your purpose you
got to iterate so as to get  for each time step.


Aiswarya
SERC Dept, IISc
Bangalore



On Wed, Jan 18, 2012 at 12:06 PM, Mark Abraham mark.abra...@anu.edu.auwrote:

 On 18/01/2012 5:31 PM, Ravi Kumar Venkatraman wrote:


 Dear All,
 I have ran a 10 ns production run for chloranil in 500
 methanol solvent box. I want to get the coordinates of solvent and solute
 at different time steps from the trajectory file (*.xtc). Can anybody tell
 me how to extract the details using VMD or any other viewer.


 You're unlikely to get help for non-GROMACS software on this mailing list.
 Check out manual section 7.4 for clues on what GROMACS tools might help,
 and then section 8 and appendix D for more details.

 Mark
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[gmx-users] no output in atm-pair.out

[aiswarya pawar]

Dear Users,

Am running a shell script for the command g_mindist=

#!/bin/bash

groups=`grep ^\[  -o index.ndx | wc -l`

for ((i=0; i$groups; i++))
do
  echo $((i++)) 3393 | g_mindist -f md.xtc -s md.tpr -od $i.xvg -o
atm-pair$i.out -d 0.8  -e 5000 -n index.ndx

done


here the index file has 3393 groups, the script reads each group against
the final group ie 3393 (1-3393,2-3393,3-3393etc), the .xvg file has been
created successfully but the .out file is empty. Please tell me why its so.

Thanks,
Aiswarya
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Re: [gmx-users] Re: LINCS error

[aiswarya . pawar]

I did few changes ie decreased the time step/ increased the equilibration 
steps/ omitted the generation of velocity in production run / did 2 steps of 
equilibration / checked the starting structure for steric clashes. 

I don't understand what else should I try to fix the lincs warnings.


Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for it!

-Original Message-
From: Mark Abraham mark.abra...@anu.edu.au
Sender: gmx-users-boun...@gromacs.org
Date: Wed, 21 Dec 2011 00:15:15 
To: Discussion list for GROMACS usersgmx-users@gromacs.org
Reply-To: Discussion list for GROMACS users gmx-users@gromacs.org
Subject: Re: [gmx-users] Re: LINCS error

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[gmx-users] Re: LINCS error

[aiswarya pawar]

i went through the mailing list, but i dont understand when i run the same
protein on my computer it runs correctly without any LINCS warning. On the
cluster with 64 processors the job runs but crashes in between and shows
the LINCS warning.


Please anyone tell me what could be the reason. Is anything wrong with my
protein.


On Sun, Dec 18, 2011 at 7:35 PM, aiswarya pawar aiswarya.pa...@gmail.comwrote:

 Hi users,

 I did energy minimization of a protein complex using the following
 minimization mdp file.

 ; Lines starting with ';' ARE COMMENTS
 ; Everything following ';' is also comment

 title = Energy Minimization ; Title of run

 ; The following line tell the program the standard locations where to find
 certain files
 cpp = /lib/cpp ; Preprocessor


 ; Define can be used to control processes
 define  = -DFLEXIBLE

 ; Parameters describing what to do, when to stop and what to save
 integrator = steep ; Algorithm (steep = steepest descent minimization)
 emtol = 1000.0   ; Stop minimization when the maximum force  1.0 kJ/mol
 emstep  = 0.01
 nsteps = 5000 ; Maximum number of (minimization) steps to perform
 nstenergy = 10 ; Write energies to disk every nstenergy steps
 energygrps = Protein ; Which energy group(s) to write to disk

 ; Parameters describing how to find the neighbors of each atom and how to
 calculate the interactions
 nstlist = 10 ; Frequency to update the neighbor list and long range forces
 ns_type = grid   ; Method to determine neighbor list (simple, grid)
 rlist = 1.0 ; Cut-off for making neighbor list (short range forces)
 coulombtype = PME   ; Treatment of long range electrostatic interactions
 rcoulomb = 1.0 ; long range electrostatic cut-off
 rvdw = 1.4 ; long range Van der Waals cut-off
 constraints = none ; Bond types to replace by constraints
 pbc= xyz ; Periodic Boundary Conditions (yes/no)


 and the pr.mdp =

 ; VARIOUS PREPROCESSING OPTIONS
 title= Position Restrained Molecular Dynamics
 define   = -DPOSRES

 constraints  = all-bonds
 integrator   = md
 dt   = 0.001 ; ps !
 nsteps   = 25000 ; total 50 ps.
 nstcomm  = 10
 nstxout  = 500 ; collect data every 1 ps
 nstxtcout= 500
 nstvout  = 0
 nstfout  = 0
 nstlist  = 10
 ns_type  = grid
 rlist= 1.0
 coulombtype  = PME
 rcoulomb = 1.0
 vdwtype  = cut-off
 rvdw = 1.4
 pme_order= 4
 ewald_rtol   = 1e-5
 optimize_fft = yes
 DispCorr = no
 ; Berendsen temperature coupling is on
 Tcoupl   = v-rescale
 tau_t= 0.1 0.1
 tc-grps = protein non-protein
 ref_t= 300 300
 ; Pressure coupling is on
 Pcoupl   = parrinello-rahman
 Pcoupltype   = isotropic
 tau_p= 1.0
 compressibility  = 4.5e-5
 ref_p= 1.0
 ; Generate velocites is on at 300 K.
 gen_vel  = yes
 gen_temp = 300.0
 gen_seed = -1

 and md.mdp file =

 ; VARIOUS PREPROCESSING OPTIONS
 title= Position Restrained Molecular Dynamics


 ; RUN CONTROL PARAMETERS
 constraints = all-bonds
 integrator = md
 dt = 0.002 ; 2fs !
 nsteps = 250 ; total 5000 ps.
 nstcomm = 10
 nstxout = 500 ; collect data every 1 ps
 nstxtcout = 0
 nstvout = 0
 nstfout = 0
 nstlist = 10
 ns_type = grid
 rlist = 1.0
 coulombtype = PME
 rcoulomb = 1.0
 vdwtype = cut-off
 rvdw = 1.4
 pme_order = 4
 ewald_rtol = 1e-5
 optimize_fft = yes
 DispCorr = no
 ; Berendsen temperature coupling is on
 Tcoupl = v-rescale
 tau_t = 0.1 0.1
 tc-grps = protein non-protein
 ref_t = 300 300
 ; Pressure coupling is on
 Pcoupl = parrinello-rahman
 Pcoupltype = isotropic
 tau_p = 1.0
 compressibility = 4.5e-5
 ref_p = 1.0
 ; Generate velocites is on at 300 K.
 gen_vel = yes
 gen_temp = 300.0
 gen_seed = -1


 The minimization step went well. but while doing the final mdrun am
 getting LINCS error. i read through the numerous mailing list on grimaces
 but still couldn't understand how would i fix this. am getting this error
 for all the 10 protein complex i did minimization for. Please help.


 Thanks,
 Aiswarya


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Re: [gmx-users] LINCS error

[aiswarya pawar]

I get an error like this=
Step 43230, time 86.46 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.033583, max 1.621884 (between atoms 2032 and 2030)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
   2032   2030   90.00.4449   0.2622  0.1000
   2031   2030   90.00.1949   0.1264  0.1000
Wrote pdb files with previous and current coordinates

Step 43231, time 86.462 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.066301, max 3.173023 (between atoms 2032 and 2030)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
   2032   2030   90.00.2622   0.4173  0.1000
   2031   2030   89.90.1264   0.1675  0.1000

---
Program mdrun, VERSION 4.5.3
Source code file: constr.c, line: 176

Fatal error:
Too many LINCS warnings (1001)
If you know what you are doing you can adjust the lincs warning threshold
in your mdp file
or set the environment variable GMX_MAXCONSTRWARN to -1,
but normally it is better to fix the problem
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---


and my md.mdp file i altered goes like this=
; VARIOUS PREPROCESSING OPTIONS
title= Production Simulation
cpp  = /lib/cpp

; RUN CONTROL PARAMETERS
integrator   = md
tinit= 0   ; Starting time
dt   = 0.002   ; 2 femtosecond time step for integration
nsteps   = 250; Make it 10 ns

; OUTPUT CONTROL OPTIONS
nstxout  = 500 ; Writing full precision coordinates every
nanosecond
nstvout  = 500 ; Writing velocities every nanosecond
nstfout  = 0 ; Not writing forces
nstlog   = 2500  ; Writing to the log file every step
nstenergy= 2500  ; Writing out energy information every step
nstxtcout= 500  ; Writing coordinates every 5 ps
energygrps   = Protein Non-Protein

; NEIGHBORSEARCHING PARAMETERS
nstlist  = 5
ns-type  = Grid
pbc  = xyz
rlist= 0.9

; OPTIONS FOR ELECTROSTATICS AND VDW
coulombtype  = Reaction-Field
rcoulomb = 1.4
epsilon_rf   = 78
epsilon_r= 1
vdw-type = Cut-off
rvdw = 1.4

; Temperature coupling
Tcoupl   = Berendsen
tc-grps  = Protein  Non-Protein
tau_t= 0.1  0.1
ref_t= 300  300
; Pressure coupling
Pcoupl   = Berendsen
Pcoupltype   = Isotropic
tau_p= 1.0
compressibility  = 4.5e-5
ref_p= 1.0

; GENERATE VELOCITIES FOR STARTUP RUN
gen_vel  = no
; OPTIONS FOR BONDS
constraints  = all-bonds
constraint-algorithm = Lincs
unconstrained-start  = yes
lincs-order  = 4
lincs-iter   = 1
lincs-warnangle  = 30


how should i rectify this. Please help


On Sun, Dec 18, 2011 at 8:12 PM, Mark Abraham mark.abra...@anu.edu.auwrote:

  On 19/12/2011 1:05 AM, aiswarya pawar wrote:

 Hi users,

  I did energy minimization of a protein complex using the following
 minimization mdp file.


 See
 http://www.gromacs.org/Documentation/How-tos/Steps_to_Perform_a_Simulationfor 
 general advice.



  ; Lines starting with ';' ARE COMMENTS
 ; Everything following ';' is also comment

  title = Energy Minimization ; Title of run

  ; The following line tell the program the standard locations where to
 find certain files
 cpp = /lib/cpp ; Preprocessor


  ; Define can be used to control processes
 define  = -DFLEXIBLE

  ; Parameters describing what to do, when to stop and what to save
 integrator = steep ; Algorithm (steep = steepest descent minimization)
 emtol = 1000.0   ; Stop minimization when the maximum force  1.0 kJ/mol
 emstep  = 0.01
 nsteps = 5000 ; Maximum number of (minimization) steps to perform
 nstenergy = 10 ; Write energies to disk every nstenergy steps
 energygrps = Protein ; Which energy group(s) to write to disk

  ; Parameters describing how to find the neighbors of each atom and how
 to calculate the interactions
 nstlist = 10 ; Frequency to update the neighbor list and long range forces
 ns_type = grid   ; Method to determine neighbor list (simple, grid)
 rlist = 1.0 ; Cut-off for making neighbor list (short range forces)
 coulombtype = PME   ; Treatment of long range electrostatic interactions
 rcoulomb = 1.0 ; long range electrostatic cut-off
 rvdw = 1.4 ; long range Van der Waals cut-off
 constraints = none ; Bond types to replace by constraints
 pbc= xyz ; Periodic

[gmx-users] LINCS error

[aiswarya pawar]

Hi users,

I did energy minimization of a protein complex using the following
minimization mdp file.

; Lines starting with ';' ARE COMMENTS
; Everything following ';' is also comment

title = Energy Minimization ; Title of run

; The following line tell the program the standard locations where to find
certain files
cpp = /lib/cpp ; Preprocessor


; Define can be used to control processes
define  = -DFLEXIBLE

; Parameters describing what to do, when to stop and what to save
integrator = steep ; Algorithm (steep = steepest descent minimization)
emtol = 1000.0   ; Stop minimization when the maximum force  1.0 kJ/mol
emstep  = 0.01
nsteps = 5000 ; Maximum number of (minimization) steps to perform
nstenergy = 10 ; Write energies to disk every nstenergy steps
energygrps = Protein ; Which energy group(s) to write to disk

; Parameters describing how to find the neighbors of each atom and how to
calculate the interactions
nstlist = 10 ; Frequency to update the neighbor list and long range forces
ns_type = grid   ; Method to determine neighbor list (simple, grid)
rlist = 1.0 ; Cut-off for making neighbor list (short range forces)
coulombtype = PME   ; Treatment of long range electrostatic interactions
rcoulomb = 1.0 ; long range electrostatic cut-off
rvdw = 1.4 ; long range Van der Waals cut-off
constraints = none ; Bond types to replace by constraints
pbc= xyz ; Periodic Boundary Conditions (yes/no)


and the pr.mdp =

; VARIOUS PREPROCESSING OPTIONS
title= Position Restrained Molecular Dynamics
define   = -DPOSRES

constraints  = all-bonds
integrator   = md
dt   = 0.001 ; ps !
nsteps   = 25000 ; total 50 ps.
nstcomm  = 10
nstxout  = 500 ; collect data every 1 ps
nstxtcout= 500
nstvout  = 0
nstfout  = 0
nstlist  = 10
ns_type  = grid
rlist= 1.0
coulombtype  = PME
rcoulomb = 1.0
vdwtype  = cut-off
rvdw = 1.4
pme_order= 4
ewald_rtol   = 1e-5
optimize_fft = yes
DispCorr = no
; Berendsen temperature coupling is on
Tcoupl   = v-rescale
tau_t= 0.1 0.1
tc-grps = protein non-protein
ref_t= 300 300
; Pressure coupling is on
Pcoupl   = parrinello-rahman
Pcoupltype   = isotropic
tau_p= 1.0
compressibility  = 4.5e-5
ref_p= 1.0
; Generate velocites is on at 300 K.
gen_vel  = yes
gen_temp = 300.0
gen_seed = -1

and md.mdp file =

; VARIOUS PREPROCESSING OPTIONS
title= Position Restrained Molecular Dynamics


; RUN CONTROL PARAMETERS
constraints = all-bonds
integrator = md
dt = 0.002 ; 2fs !
nsteps = 250 ; total 5000 ps.
nstcomm = 10
nstxout = 500 ; collect data every 1 ps
nstxtcout = 0
nstvout = 0
nstfout = 0
nstlist = 10
ns_type = grid
rlist = 1.0
coulombtype = PME
rcoulomb = 1.0
vdwtype = cut-off
rvdw = 1.4
pme_order = 4
ewald_rtol = 1e-5
optimize_fft = yes
DispCorr = no
; Berendsen temperature coupling is on
Tcoupl = v-rescale
tau_t = 0.1 0.1
tc-grps = protein non-protein
ref_t = 300 300
; Pressure coupling is on
Pcoupl = parrinello-rahman
Pcoupltype = isotropic
tau_p = 1.0
compressibility = 4.5e-5
ref_p = 1.0
; Generate velocites is on at 300 K.
gen_vel = yes
gen_temp = 300.0
gen_seed = -1


The minimization step went well. but while doing the final mdrun am getting
LINCS error. i read through the numerous mailing list on grimaces but still
couldn't understand how would i fix this. am getting this error for all the
10 protein complex i did minimization for. Please help.


Thanks,
Aiswarya
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Re: [gmx-users] compatible gromacs

[aiswarya pawar]

I did the openmpi installation on IBM cluster, when i try to run the md.tpr
is read but gets abort and leaves and error saying=

p4_error: interrupt SIGx:4

Anyone knows the solution to this.

Thanks,
Aiswarya

On Fri, Dec 16, 2011 at 2:28 PM, Mark Abraham mark.abra...@anu.edu.auwrote:

 On 16/12/2011 4:55 PM, aiswarya pawar wrote:

 Hi users,

 i would like to know which version of gromacs would be compatible with
 the cluster architecture =

 Linux cnode39 2.6.5-7.244-pseries64 #1 SMP Mon Dec 12 18:32:25 UTC 2005
 ppc64 ppc64 ppc64 GNU/Linux


 Any.



 And which gromacs version would be compatible with the mpi version =
 mpich-1.2.7


 Don't know - use of MPICH is discouraged because of some historical
 problems. Knowledge that a particular version works well with modern
 version of GROMACS would be a useful addition to the installation guide.

 Mark
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Fw: [gmx-users] Re: submission error

[aiswarya . pawar]

Lina,

I used the same script for mpi ie other than usr/bin/poe I have given 
usr/bin/mpirun I still receive the same errorOn 15/12/2011 4:51 PM, aiswarya pawar wrote:

 Hi,


 When i tried running mdrun without mip i received the same error ie

 when i gave mdrun -deffnm md

 i got=
 Back Off! I just backed up md.log to ./#md.log.1#
 Getting Loaded...
 Reading file md.tpr, VERSION 4.5.4 (single precision)
 Loaded with Money

 p0_23443:  p4_error: interrupt SIGx: 4

The job you ran below with poe did not have the MPI suffix, so I am not 
convinced you are doing appropriate things with appropriate executables. 
Above, a p4_error is consistent with an MPI-enabled executable.

Get an MPI hello world program and get it running before worrying 
about GROMACS. Follow the user guide for your cluster. Get your 
MPI-enabled mdrun suffixed with _mpi like the installation guides recommend.

Mark



 Thanks,
 Aiswarya

 On Wed, Dec 14, 2011 at 5:00 PM, aiswarya pawar 
 aiswarya.pa...@gmail.com mailto:aiswarya.pa...@gmail.com wrote:

 Hi users,

 I have a submission script for gromacs mdrun to be used on IBM
 cluster, but i get an error while running it. the script goes like
 this=

 #!/bin/sh
 # @ error   = job1.$(Host).$(Cluster).$(Process).err
 # @ output  = job1.$(Host).$(Cluster).$(Process).out
 # @ class = ptask32
 # @ job_type = parallel
 # @ node = 1
 # @ tasks_per_node = 4
 # @ queue

 echo _
 echo LOADL_STEP_ID=$LOADL_STEP_ID
 echo _

 machine_file=/tmp/machinelist.$LOADL_STEP_ID
 rm -f $machine_file
 for node in $LOADL_PROCESSOR_LIST
 do
 echo $node  $machine_file
 done
 machine_count=`cat /tmp/machinelist.$LOADL_STEP_ID|wc -l`
 echo $machine_count
 echo MachineList:
 cat /tmp/machinelist.$LOADL_STEP_ID
 echo _
 unset LOADLBATCH
 env  |grep LOADLBATCH
 cd /home/staff/1adf/
 /usr/bin/poe /home/gromacs-4.5.5/bin/mdrun -deffnm
 /home/staff/1adf/md -procs $machine_count -hostfile
 /tmp/machinelist.$LOADL_STEP_ID
 rm /tmp/machinelist.$LOADL_STEP_ID


 i get an out file as=
 _
 LOADL_STEP_ID=cnode39.97541.0
 _
 4
 MachineList:
 cnode62
 cnode7
 cnode4
 cnode8
 _
 p0_25108:  p4_error: interrupt SIGx: 4
 p0_2890:  p4_error: interrupt SIGx: 4
 p0_2901:  p4_error: interrupt SIGx: 15
 p0_22760:  p4_error: interrupt SIGx: 15


 an error file =

 Reading file /home/staff/1adf/md.tpr, VERSION 4.5.4 (single precision)
 Sorry couldn't backup /home/staff/1adf/md.log to
 /home/staff/1adf/#md.log.14#

 Back Off! I just backed up /home/staff/1adf/md.log to
 /home/staff/1adf/#md.log.14#
 ERROR: 0031-300  Forcing all remote tasks to exit due to exit code
 1 in task 0

 Please anyone can help with this error.

 Thanks









Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for it!

-Original Message-
From: Mark Abraham mark.abra...@anu.edu.au
Sender: gmx-users-boun...@gromacs.org
Date: Thu, 15 Dec 2011 17:03:12 
To: Discussion list for GROMACS usersgmx-users@gromacs.org
Reply-To: Discussion list for GROMACS users gmx-users@gromacs.org
Subject: Re: [gmx-users] Re: submission error

-- 
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[gmx-users] compatible gromacs

[aiswarya pawar]

Hi users,

i would like to know which version of gromacs would be compatible with the
cluster architecture =

Linux cnode39 2.6.5-7.244-pseries64 #1 SMP Mon Dec 12 18:32:25 UTC 2005
ppc64 ppc64 ppc64 GNU/Linux

And which gromacs version would be compatible with the mpi version =
mpich-1.2.7


Thanks,
Aiswarya
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[gmx-users] submission error

[aiswarya pawar]

Hi users,

I have a submission script for gromacs mdrun to be used on IBM cluster, but
i get an error while running it. the script goes like this=

#!/bin/sh
# @ error   = job1.$(Host).$(Cluster).$(Process).err
# @ output  = job1.$(Host).$(Cluster).$(Process).out
# @ class = ptask32
# @ job_type = parallel
# @ node = 1
# @ tasks_per_node = 4
# @ queue

echo _
echo LOADL_STEP_ID=$LOADL_STEP_ID
echo _

machine_file=/tmp/machinelist.$LOADL_STEP_ID
rm -f $machine_file
for node in $LOADL_PROCESSOR_LIST
do
echo $node  $machine_file
done
machine_count=`cat /tmp/machinelist.$LOADL_STEP_ID|wc -l`
echo $machine_count
echo MachineList:
cat /tmp/machinelist.$LOADL_STEP_ID
echo _
unset LOADLBATCH
env  |grep LOADLBATCH
cd /home/staff/1adf/
/usr/bin/poe /home/gromacs-4.5.5/bin/mdrun -deffnm /home/staff/1adf/md
-procs $machine_count -hostfile /tmp/machinelist.$LOADL_STEP_ID
rm /tmp/machinelist.$LOADL_STEP_ID


i get an out file as=
_
LOADL_STEP_ID=cnode39.97541.0
_
4
MachineList:
cnode62
cnode7
cnode4
cnode8
_
p0_25108:  p4_error: interrupt SIGx: 4
p0_2890:  p4_error: interrupt SIGx: 4
p0_2901:  p4_error: interrupt SIGx: 15
p0_22760:  p4_error: interrupt SIGx: 15


an error file =

Reading file /home/staff/1adf/md.tpr, VERSION 4.5.4 (single precision)
Sorry couldn't backup /home/staff/1adf/md.log to
/home/staff/1adf/#md.log.14#

Back Off! I just backed up /home/staff/1adf/md.log to
/home/staff/1adf/#md.log.14#
ERROR: 0031-300  Forcing all remote tasks to exit due to exit code 1 in
task 0

Please anyone can help with this error.

Thanks
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Re: [gmx-users] submission error

[aiswarya . pawar]

Mark,

I still the same error. 


Thanks
Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for it!

-Original Message-
From: Mark Abraham mark.abra...@anu.edu.au
Sender: gmx-users-boun...@gromacs.org
Date: Wed, 14 Dec 2011 23:03:59 
To: Discussion list for GROMACS usersgmx-users@gromacs.org
Reply-To: Discussion list for GROMACS users gmx-users@gromacs.org
Subject: Re: [gmx-users] submission error

On 14/12/2011 10:30 PM, aiswarya pawar wrote:
 Hi users,

 I have a submission script for gromacs mdrun to be used on IBM 
 cluster, but i get an error while running it. the script goes like this=

 #!/bin/sh
 # @ error   = job1.$(Host).$(Cluster).$(Process).err
 # @ output  = job1.$(Host).$(Cluster).$(Process).out
 # @ class = ptask32
 # @ job_type = parallel
 # @ node = 1
 # @ tasks_per_node = 4
 # @ queue

 echo _
 echo LOADL_STEP_ID=$LOADL_STEP_ID
 echo _

 machine_file=/tmp/machinelist.$LOADL_STEP_ID
 rm -f $machine_file
 for node in $LOADL_PROCESSOR_LIST
 do
 echo $node  $machine_file
 done
 machine_count=`cat /tmp/machinelist.$LOADL_STEP_ID|wc -l`
 echo $machine_count
 echo MachineList:
 cat /tmp/machinelist.$LOADL_STEP_ID
 echo _
 unset LOADLBATCH
 env  |grep LOADLBATCH
 cd /home/staff/1adf/
 /usr/bin/poe /home/gromacs-4.5.5/bin/mdrun -deffnm /home/staff/1adf/md 
 -procs $machine_count -hostfile /tmp/machinelist.$LOADL_STEP_ID
 rm /tmp/machinelist.$LOADL_STEP_ID


 i get an out file as=
 _
 LOADL_STEP_ID=cnode39.97541.0
 _
 4
 MachineList:
 cnode62
 cnode7
 cnode4
 cnode8
 _
 p0_25108:  p4_error: interrupt SIGx: 4
 p0_2890:  p4_error: interrupt SIGx: 4
 p0_2901:  p4_error: interrupt SIGx: 15
 p0_22760:  p4_error: interrupt SIGx: 15


 an error file =

 Reading file /home/staff/1adf/md.tpr, VERSION 4.5.4 (single precision)
 Sorry couldn't backup /home/staff/1adf/md.log to 
 /home/staff/1adf/#md.log.14#

 Back Off! I just backed up /home/staff/1adf/md.log to 
 /home/staff/1adf/#md.log.14#
 ERROR: 0031-300  Forcing all remote tasks to exit due to exit code 1 
 in task 0

Looks like a problem with file writing privileges or maybe disk quota. 
Either make a new run directory or clean up before using this job 
script, and see how you go.

Mark
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Re: [gmx-users] submission error

[aiswarya . pawar]

Am using mipch2-1.2.7. Is this the problem?


Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for it!

-Original Message-
From: aiswarya.pa...@gmail.com
Date: Wed, 14 Dec 2011 13:09:19 
To: Gromacs mailgmx-users@gromacs.org
Reply-To: aiswarya.pa...@gmail.com
Subject: Re: [gmx-users] submission error

Mark,

I still the same error. 


Thanks
Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for it!

-Original Message-
From: Mark Abraham mark.abra...@anu.edu.au
Sender: gmx-users-boun...@gromacs.org
Date: Wed, 14 Dec 2011 23:03:59 
To: Discussion list for GROMACS usersgmx-users@gromacs.org
Reply-To: Discussion list for GROMACS users gmx-users@gromacs.org
Subject: Re: [gmx-users] submission error

On 14/12/2011 10:30 PM, aiswarya pawar wrote:
 Hi users,

 I have a submission script for gromacs mdrun to be used on IBM 
 cluster, but i get an error while running it. the script goes like this=

 #!/bin/sh
 # @ error   = job1.$(Host).$(Cluster).$(Process).err
 # @ output  = job1.$(Host).$(Cluster).$(Process).out
 # @ class = ptask32
 # @ job_type = parallel
 # @ node = 1
 # @ tasks_per_node = 4
 # @ queue

 echo _
 echo LOADL_STEP_ID=$LOADL_STEP_ID
 echo _

 machine_file=/tmp/machinelist.$LOADL_STEP_ID
 rm -f $machine_file
 for node in $LOADL_PROCESSOR_LIST
 do
 echo $node  $machine_file
 done
 machine_count=`cat /tmp/machinelist.$LOADL_STEP_ID|wc -l`
 echo $machine_count
 echo MachineList:
 cat /tmp/machinelist.$LOADL_STEP_ID
 echo _
 unset LOADLBATCH
 env  |grep LOADLBATCH
 cd /home/staff/1adf/
 /usr/bin/poe /home/gromacs-4.5.5/bin/mdrun -deffnm /home/staff/1adf/md 
 -procs $machine_count -hostfile /tmp/machinelist.$LOADL_STEP_ID
 rm /tmp/machinelist.$LOADL_STEP_ID


 i get an out file as=
 _
 LOADL_STEP_ID=cnode39.97541.0
 _
 4
 MachineList:
 cnode62
 cnode7
 cnode4
 cnode8
 _
 p0_25108:  p4_error: interrupt SIGx: 4
 p0_2890:  p4_error: interrupt SIGx: 4
 p0_2901:  p4_error: interrupt SIGx: 15
 p0_22760:  p4_error: interrupt SIGx: 15


 an error file =

 Reading file /home/staff/1adf/md.tpr, VERSION 4.5.4 (single precision)
 Sorry couldn't backup /home/staff/1adf/md.log to 
 /home/staff/1adf/#md.log.14#

 Back Off! I just backed up /home/staff/1adf/md.log to 
 /home/staff/1adf/#md.log.14#
 ERROR: 0031-300  Forcing all remote tasks to exit due to exit code 1 
 in task 0

Looks like a problem with file writing privileges or maybe disk quota. 
Either make a new run directory or clean up before using this job 
script, and see how you go.

Mark
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
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[gmx-users] Re: submission error

[aiswarya pawar]

Hi,


When i tried running mdrun without mip i received the same error ie

when i gave mdrun -deffnm md

i got=
Back Off! I just backed up md.log to ./#md.log.1#
Getting Loaded...
Reading file md.tpr, VERSION 4.5.4 (single precision)
Loaded with Money

p0_23443:  p4_error: interrupt SIGx: 4


Thanks,
Aiswarya

On Wed, Dec 14, 2011 at 5:00 PM, aiswarya pawar aiswarya.pa...@gmail.comwrote:

 Hi users,

 I have a submission script for gromacs mdrun to be used on IBM cluster,
 but i get an error while running it. the script goes like this=

 #!/bin/sh
 # @ error   = job1.$(Host).$(Cluster).$(Process).err
 # @ output  = job1.$(Host).$(Cluster).$(Process).out
 # @ class = ptask32
 # @ job_type = parallel
 # @ node = 1
 # @ tasks_per_node = 4
 # @ queue

 echo _
 echo LOADL_STEP_ID=$LOADL_STEP_ID
 echo _

 machine_file=/tmp/machinelist.$LOADL_STEP_ID
 rm -f $machine_file
 for node in $LOADL_PROCESSOR_LIST
 do
 echo $node  $machine_file
 done
 machine_count=`cat /tmp/machinelist.$LOADL_STEP_ID|wc -l`
 echo $machine_count
 echo MachineList:
 cat /tmp/machinelist.$LOADL_STEP_ID
 echo _
 unset LOADLBATCH
 env  |grep LOADLBATCH
 cd /home/staff/1adf/
 /usr/bin/poe /home/gromacs-4.5.5/bin/mdrun -deffnm /home/staff/1adf/md
 -procs $machine_count -hostfile /tmp/machinelist.$LOADL_STEP_ID
 rm /tmp/machinelist.$LOADL_STEP_ID


 i get an out file as=
 _
 LOADL_STEP_ID=cnode39.97541.0
 _
 4
 MachineList:
 cnode62
 cnode7
 cnode4
 cnode8
 _
 p0_25108:  p4_error: interrupt SIGx: 4
 p0_2890:  p4_error: interrupt SIGx: 4
 p0_2901:  p4_error: interrupt SIGx: 15
 p0_22760:  p4_error: interrupt SIGx: 15


 an error file =

 Reading file /home/staff/1adf/md.tpr, VERSION 4.5.4 (single precision)
 Sorry couldn't backup /home/staff/1adf/md.log to
 /home/staff/1adf/#md.log.14#

 Back Off! I just backed up /home/staff/1adf/md.log to
 /home/staff/1adf/#md.log.14#
 ERROR: 0031-300  Forcing all remote tasks to exit due to exit code 1 in
 task 0

 Please anyone can help with this error.

 Thanks




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[gmx-users] Gromacs Installation error

[aiswarya pawar]

Hi gromacs users,

Iam trying to install gromacs on IBM cluster. I have successfully installed
installed fftw-3.3 version with commands=

./configure --enable-threads --enable-float
make
make install

the set the enviroment=

setenv CPPFLAGS -I/home/fftw/include
setenv LDFLAGS -L/home/fftw/lib

Then the gromacs installation=

./configure --prefix=/home/gromacs --host=ppc --build=ppc64
--enable-mpi --with-fft=fftw3 MPICC=mpCC CC=xlC_r -q64 CFLAGS=-O3
-qarch=ppc64 -qtune=auto CXX=xlC_r -q64 CXXFLAGS=-O3 -qarch=ppc64
-qtune=auto F77=mpixlf_r FFLAGS=-O3 -qarch=ppc64 -qtune=auto

the configure did well but while doing make mdrun i started getting
error such as=

source='vmdio.c' object='vmdio.lo' libtool=yes \
DEPDIR=.deps depmode=none /bin/sh ../../config/depcomp \
/bin/sh ../../libtool --tag=CC   --mode=compile mpCC -DHAVE_CONFIG_H
-I. -I../../src  -I../../include
-DGMXLIBDIR=\/home/gromacs/share/top\ -I/home/include  -O3
-qarch=ppc64 -qtune=auto -c -o vmdio.lo vmdio.c
 mpCC -DHAVE_CONFIG_H -I. -I../../src -I../../include
-DGMXLIBDIR=\/home/gromacs/share/top\ -I/home/include -O3
-qarch=ppc64 -qtune=auto -c vmdio.c -o vmdio.o
1506-503 (W) Option -qlongdouble / -qldbl128 is not supported for
LINUX for Power.
/usr/include/glob.h, line 166.34: 1506-276 (S) Syntax error:
possible missing identifier?
/usr/include/glob.h, line 166.12: 1506-033 (S) Function
__REDIRECT_NTH is not valid. Function cannot return a function.
/usr/include/glob.h, line 166.12: 1506-282 (S) The type of the
parameters must be specified in a prototype.
/usr/include/glob.h, line 169.35: 1506-334 (S) Identifier glob_t has
already been defined on line 113 of /usr/include/glob.h.
/usr/include/glob.h, line 169.42: 1506-277 (S) Syntax error:
possible missing ';' or ','?
/usr/include/glob.h, line 171.39: 1506-276 (S) Syntax error:
possible missing identifier?
/usr/include/glob.h, line 171.13: 1506-282 (S) The type of the
parameters must be specified in a prototype.
/usr/include/glob.h, line 171.13: 1506-343 (S) Redeclaration of
__REDIRECT_NTH differs from previous declaration on line 166 of
/usr/include/glob.h.
/usr/include/glob.h, line 171.13: 1506-050 (I) Return type void in
redeclaration is not compatible with the previous return type
int(const char*,int).
/usr/include/glob.h, line 171.58: 1506-160 (S) Object globfree64
cannot be declared as type void.
/usr/include/glob.h, line 175.12: 1506-343 (S) Redeclaration of
glob64 differs from previous declaration on line 169 of
/usr/include/glob.h.
/usr/include/glob.h, line 175.12: 1506-382 (I) The type int(const
char* restrict,int,int(*)(const char*,int),struct {...}* restrict) of
identifier glob64 differs from previous type int.
make[2]: *** [vmdio.lo] Error 1
make[2]: Leaving directory `/home/gromacs-4.5.5/src/gmxlib'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/home/gromacs-4.5.5/src/gmxlib'
(cd ./src/mdlib  make ; exit 0)
make[1]: Entering directory `/home/gromacs-4.5.5/src/mdlib'
make[1]: *** No rule to make target `../gmxlib/libgmx_mpi.la', needed
by `libmd_mpi.la'.  Stop.
make[1]: Leaving directory `/home/gromacs-4.5.5/src/mdlib'
(cd ./src/kernel  make mdrun ; exit 0)
make[1]: Entering directory `/home/gromacs-4.5.5/src/kernel'
/bin/sh ../../libtool --tag=CC   --mode=link mpCC  -O3 -qarch=ppc64
-qtune=auto -no-undefined -version-info 6:0:0
-L/home/staff/sec/secdpal/soft/lib  -o libgmxpreprocess_mpi.la -rpath
/home/gromacs/lib add_par.lo compute_io.lo convparm.lo fflibutil.lo
gen_ad.lo gen_vsite.lo genhydro.lo gpp_atomtype.lo
gpp_bond_atomtype.lo h_db.lo hackblock.lo hizzie.lo pdb2top.lo
pgutil.lo readir.lo readpull.lo resall.lo sorting.lo specbond.lo
ter_db.lo tomorse.lo topdirs.lo topexcl.lo topio.lo toppush.lo
topshake.lo toputil.lo tpbcmp.lo vsite_parm.lo xlate.lo
../mdlib/libmd_mpi.la -lnsl -lm
libtool: link: cannot find the library `../mdlib/libmd_mpi.la' or
unhandled argument `../mdlib/libmd_mpi.la'
make[1]: *** [libgmxpreprocess_mpi.la] Error 1
make[1]: Leaving directory `/home/gromacs-4.5.5/src/kernel'

please help!

Aiswarya
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Re: [gmx-users] mdrun_mpi error

[aiswarya pawar]

i used the option still i get the error as=

/bin/sh ../../libtool --tag=CC   --mode=compile mpCC -DHAVE_CONFIG_H -I.
-I../../src  -I../../include
-DGMXLIBDIR=\/home/staff/sec/secdpal/soft/gromacs/share/top\
-I/home/staff/sec/secdpal/soft/include  -O3 -qarch=ppc64 -qtune=pwr5 -c -o
vmdio.lo vmdio.c
 mpCC -DHAVE_CONFIG_H -I. -I../../src -I../../include
-DGMXLIBDIR=\/home/staff/sec/secdpal/soft/gromacs/share/top\
-I/home/staff/sec/secdpal/soft/include -O3 -qarch=ppc64 -qtune=pwr5 -c
vmdio.c -o vmdio.o
1506-503 (W) Option -qlongdouble / -qldbl128 is not supported for LINUX
for Power.
/usr/include/glob.h, line 166.34: 1506-276 (S) Syntax error: possible
missing identifier?
/usr/include/glob.h, line 166.12: 1506-033 (S) Function __REDIRECT_NTH is
not valid. Function cannot return a function.
/usr/include/glob.h, line 166.12: 1506-282 (S) The type of the parameters
must be specified in a prototype.
/usr/include/glob.h, line 169.35: 1506-334 (S) Identifier glob_t has
already been defined on line 113 of /usr/include/glob.h.
/usr/include/glob.h, line 169.42: 1506-277 (S) Syntax error: possible
missing ';' or ','?
/usr/include/glob.h, line 171.39: 1506-276 (S) Syntax error: possible
missing identifier?
/usr/include/glob.h, line 171.13: 1506-282 (S) The type of the parameters
must be specified in a prototype.
/usr/include/glob.h, line 171.13: 1506-343 (S) Redeclaration of
__REDIRECT_NTH differs from previous declaration on line 166 of
/usr/include/glob.h.
/usr/include/glob.h, line 171.13: 1506-050 (I) Return type void in
redeclaration is not compatible with the previous return type int(const
char*,int).
/usr/include/glob.h, line 171.58: 1506-160 (S) Object globfree64 cannot
be declared as type void.
/usr/include/glob.h, line 175.12: 1506-343 (S) Redeclaration of glob64
differs from previous declaration on line 169 of /usr/include/glob.h.
/usr/include/glob.h, line 175.12: 1506-382 (I) The type int(const char*
restrict,int,int(*)(const char*,int),struct {...}* restrict) of identifier
glob64 differs from previous type int.
make[2]: *** [vmdio.lo] Error 1
make[2]: Leaving directory
`/home/staff/sec/secdpal/soft/gromacs-4.5.5/src/gmxlib'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory
`/home/staff/sec/secdpal/soft/gromacs-4.5.5/src/gmxlib'
(cd ./src/mdlib  make ; exit 0)
make[1]: Entering directory
`/home/staff/sec/secdpal/soft/gromacs-4.5.5/src/mdlib'
make[1]: Warning: File `Makefile' has modification time 8.8e+02 s in the
future
make[1]: *** No rule to make target `../gmxlib/libgmx_mpi.la', needed by `
libmd_mpi.la'.  Stop.
make[1]: Leaving directory
`/home/staff/sec/secdpal/soft/gromacs-4.5.5/src/mdlib'
(cd ./src/kernel  make mdrun ; exit 0)
make[1]: Entering directory
`/home/staff/sec/secdpal/soft/gromacs-4.5.5/src/kernel'
make[1]: Warning: File `Makefile' has modification time 8.8e+02 s in the
future
/bin/sh ../../libtool --tag=CC   --mode=link mpCC  -O3 -qarch=ppc64
-qtune=pwr5 -no-undefined -version-info 6:0:0
-L/home/staff/sec/secdpal/soft/lib  -o libgmxpreprocess_mpi.la -rpath
/home/staff/sec/secdpal/soft/gromacs/lib add_par.lo compute_io.lo
convparm.lo fflibutil.lo gen_ad.lo gen_vsite.lo genhydro.lo gpp_atomtype.lo
gpp_bond_atomtype.lo h_db.lo hackblock.lo hizzie.lo pdb2top.lo pgutil.lo
readir.lo readpull.lo resall.lo sorting.lo specbond.lo ter_db.lo tomorse.lo
topdirs.lo topexcl.lo topio.lo toppush.lo topshake.lo toputil.lo tpbcmp.lo
vsite_parm.lo xlate.lo ../mdlib/libmd_mpi.la -lnsl -lm
libtool: link: cannot find the library `../mdlib/libmd_mpi.la' or unhandled
argument `../mdlib/libmd_mpi.la'
make[1]: *** [libgmxpreprocess_mpi.la] Error 1
make[1]: Leaving directory
`/home/staff/sec/secdpal/soft/gromacs-4.5.5/src/kernel'
make: warning:  Clock skew detected.  Your build may be incomplete.


On Sat, Dec 10, 2011 at 1:05 PM, Mark Abraham mark.abra...@anu.edu.auwrote:

  On 10/12/2011 6:31 PM, aiswarya pawar wrote:


 Hi,

 I tried giving this-


 ./configure --prefix=/home/soft/gromacs --host=ppc --build=ppc64
 --enable-mpi --with-fft=fftw3 MPICC=mpcc CC=xlc CFLAGS=-O3 -qarch=450d
 -qtune=450 CXX=mpixlC_r CXXFLAGS=-O3 -qarch=450d -qtune=450

 and the configure process ran well.

 but when i gave make mdrun, i get an error which says=

 make[2]: *** [vmdio.lo] Error 1


 The first error happened above this line, so we can't tell what is wrong.
 As a wild guess, use --without-dlopen with configure.

 Mark


 make[2]: Leaving directory `/home/soft/gromacs-4.5.5/src/
 gmxlib'
 make[1]: *** [all-recursive] Error 1
 make[1]: Leaving directory `/home/soft/gromacs-4.5.5/src/gmxlib'
 (cd ./src/mdlib  make ; exit 0)
 make[1]: Entering directory `/home/soft/gromacs-4.5.5/src/mdlib'
 make[1]: Warning: File `Makefile' has modification time 7.6e+02 s in the
 future
 make[1]: *** No rule to make target `../gmxlib/libgmx_mpi.la', needed by `
 libmd_mpi.la'.  Stop.
 make[1]: Leaving directory `/home/soft/gromacs-4.5.5/src/mdlib'
 (cd ./src/kernel  make mdrun ; exit 0)
 make[1]: Entering directory `/home/gromacs

Re: [gmx-users] mdrun_mpi error

[aiswarya pawar]

Hi,

I tried giving this-


./configure --prefix=/home/soft/gromacs --host=ppc --build=ppc64
--enable-mpi --with-fft=fftw3 MPICC=mpcc CC=xlc CFLAGS=-O3 -qarch=450d
-qtune=450 CXX=mpixlC_r CXXFLAGS=-O3 -qarch=450d -qtune=450

and the configure process ran well.

but when i gave make mdrun, i get an error which says=

make[2]: *** [vmdio.lo] Error 1
make[2]: Leaving directory `/home/soft/gromacs-4.5.5/src/gmxlib'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/home/soft/gromacs-4.5.5/src/gmxlib'
(cd ./src/mdlib  make ; exit 0)
make[1]: Entering directory `/home/soft/gromacs-4.5.5/src/mdlib'
make[1]: Warning: File `Makefile' has modification time 7.6e+02 s in the
future
make[1]: *** No rule to make target `../gmxlib/libgmx_mpi.la', needed by `
libmd_mpi.la'.  Stop.
make[1]: Leaving directory `/home/soft/gromacs-4.5.5/src/mdlib'
(cd ./src/kernel  make mdrun ; exit 0)
make[1]: Entering directory `/home/gromacs-4.5.5/src/kernel'
make[1]: Warning: File `Makefile' has modification time 7.5e+02 s in the
future
/bin/sh ../../libtool --tag=CC   --mode=link mpcc  -O3 -qarch=450d
-qtune=450 -no-undefined -version-info 6:0:0
-L/home/staff/sec/secdpal/soft/lib  -o libgmxpreprocess_mpi.la -rpath
/home/staff/sec/secdpal/soft/gromacs/lib add_par.lo compute_io.lo
convparm.lo fflibutil.lo gen_ad.lo gen_vsite.lo genhydro.lo gpp_atomtype.lo
gpp_bond_atomtype.lo h_db.lo hackblock.lo hizzie.lo pdb2top.lo pgutil.lo
readir.lo readpull.lo resall.lo sorting.lo specbond.lo ter_db.lo tomorse.lo
topdirs.lo topexcl.lo topio.lo toppush.lo topshake.lo toputil.lo tpbcmp.lo
vsite_parm.lo xlate.lo ../mdlib/libmd_mpi.la -lnsl -lm
libtool: link: cannot find the library `../mdlib/libmd_mpi.la' or unhandled
argument `../mdlib/libmd_mpi.la'
make[1]: *** [libgmxpreprocess_mpi.la] Error 1


On Thu, Dec 8, 2011 at 5:32 PM, Mark Abraham mark.abra...@anu.edu.auwrote:

 On 8/12/2011 6:35 PM, aiswarya pawar wrote:

 Hi users,

 Am running the mdrun_mpi on cluster with the md.mdp parameters as-

 ; VARIOUS PREPROCESSING OPTIONS
 title= Position Restrained Molecular Dynamics


 ; RUN CONTROL PARAMETERS
 constraints = all-bonds
 integrator = md
 dt = 0.002 ; 2fs !
 nsteps = 250 ; total 5000 ps.
 nstcomm = 10
 nstxout = 500 ; collect data every 1 ps
 nstxtcout = 500
 nstvout = 0
 nstfout = 0
 nstlist = 10
 ns_type = grid
 rlist = 1.0
 coulombtype = PME
 rcoulomb = 1.0
 vdwtype = cut-off
 rvdw = 1.4
 pme_order = 4
 ewald_rtol = 1e-5
 optimize_fft = yes
 DispCorr = no
 ; Berendsen temperature coupling is on
 Tcoupl = v-rescale
 tau_t = 0.1 0.1
 tc-grps = protein non-protein
 ref_t = 300 300
 ; Pressure coupling is on
 Pcoupl = parrinello-rahman
 Pcoupltype = isotropic
 tau_p = 1.0
 compressibility = 4.5e-5
 ref_p = 1.0
 ; Generate velocites is on at 300 K.
 gen_vel = yes
 gen_temp = 300.0
 gen_seed = -1


 The grompp runs fine. but when i run the mdrun_mpi i get an error such as-

 Child exited abnormally!
 Killing remote processes...DONE


 There's no information here upon which one can diagnose anything. Look at
 the stderr, stdout and .log files and consult the errors page on the
 GROMACS website for clues.

 Mark
 --
 gmx-users mailing listgmx-users@gromacs.org
 http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users
 Please search the archive at http://www.gromacs.org/**
 Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore
  posting!
 Please don't post (un)subscribe requests to the list. Use the www
 interface or send it to gmx-users-requ...@gromacs.org.
 Can't post? Read 
 http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists

-- 
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http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] mdrun_mpi error

[aiswarya pawar]

Hi,

I tried giving this-


./configure --prefix=/home/soft/gromacs --host=ppc --build=ppc64
--enable-mpi --with-fft=fftw3 MPICC=mpcc CC=xlc CFLAGS=-O3 -qarch=450d
-qtune=450 CXX=mpixlC_r CXXFLAGS=-O3 -qarch=450d -qtune=450

and the configure process ran well.

but when i gave make mdrun, i get an error which says=

make[2]: *** [vmdio.lo] Error 1
make[2]: Leaving directory `/home/soft/gromacs-4.5.5/src/
gmxlib'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/home/soft/gromacs-4.5.5/src/gmxlib'
(cd ./src/mdlib  make ; exit 0)
make[1]: Entering directory `/home/soft/gromacs-4.5.5/src/mdlib'
make[1]: Warning: File `Makefile' has modification time 7.6e+02 s in the
future
make[1]: *** No rule to make target `../gmxlib/libgmx_mpi.la', needed by `
libmd_mpi.la'.  Stop.
make[1]: Leaving directory `/home/soft/gromacs-4.5.5/src/mdlib'
(cd ./src/kernel  make mdrun ; exit 0)
make[1]: Entering directory `/home/gromacs-4.5.5/src/kernel'
make[1]: Warning: File `Makefile' has modification time 7.5e+02 s in the
future
/bin/sh ../../libtool --tag=CC   --mode=link mpcc  -O3 -qarch=450d
-qtune=450 -no-undefined -version-info 6:0:0  -L/home/soft/lib  -o
libgmxpreprocess_mpi.la -rpath /home/soft/gromacs/lib add_par.lo
compute_io.lo convparm.lo fflibutil.lo gen_ad.lo gen_vsite.lo genhydro.lo
gpp_atomtype.lo gpp_bond_atomtype.lo h_db.lo hackblock.lo hizzie.lo
pdb2top.lo pgutil.lo readir.lo readpull.lo resall.lo sorting.lo specbond.lo
ter_db.lo tomorse.lo topdirs.lo topexcl.lo topio.lo toppush.lo topshake.lo
toputil.lo tpbcmp.lo vsite_parm.lo xlate.lo ../mdlib/libmd_mpi.la -lnsl
-lm
libtool: link: cannot find the library `../mdlib/libmd_mpi.la' or unhandled
argument `../mdlib/libmd_mpi.la'
make[1]: *** [libgmxpreprocess_mpi.la] Error 1

On Sat, Dec 10, 2011 at 1:01 PM, aiswarya pawar aiswarya.pa...@gmail.comwrote:

 Hi,

 I tried giving this-


 ./configure --prefix=/home/soft/gromacs --host=ppc --build=ppc64
 --enable-mpi --with-fft=fftw3 MPICC=mpcc CC=xlc CFLAGS=-O3 -qarch=450d
 -qtune=450 CXX=mpixlC_r CXXFLAGS=-O3 -qarch=450d -qtune=450

 and the configure process ran well.

 but when i gave make mdrun, i get an error which says=

 make[2]: *** [vmdio.lo] Error 1
 make[2]: Leaving directory `/home/soft/gromacs-4.5.5/src/gmxlib'
 make[1]: *** [all-recursive] Error 1
 make[1]: Leaving directory `/home/soft/gromacs-4.5.5/src/gmxlib'
 (cd ./src/mdlib  make ; exit 0)
 make[1]: Entering directory `/home/soft/gromacs-4.5.5/src/mdlib'
 make[1]: Warning: File `Makefile' has modification time 7.6e+02 s in the
 future
 make[1]: *** No rule to make target `../gmxlib/libgmx_mpi.la', needed by `
 libmd_mpi.la'.  Stop.
 make[1]: Leaving directory `/home/soft/gromacs-4.5.5/src/mdlib'
 (cd ./src/kernel  make mdrun ; exit 0)
 make[1]: Entering directory `/home/gromacs-4.5.5/src/kernel'
 make[1]: Warning: File `Makefile' has modification time 7.5e+02 s in the
 future
 /bin/sh ../../libtool --tag=CC   --mode=link mpcc  -O3 -qarch=450d
 -qtune=450 -no-undefined -version-info 6:0:0
 -L/home/staff/sec/secdpal/soft/lib  -o libgmxpreprocess_mpi.la -rpath
 /home/staff/sec/secdpal/soft/gromacs/lib add_par.lo compute_io.lo
 convparm.lo fflibutil.lo gen_ad.lo gen_vsite.lo genhydro.lo gpp_atomtype.lo
 gpp_bond_atomtype.lo h_db.lo hackblock.lo hizzie.lo pdb2top.lo pgutil.lo
 readir.lo readpull.lo resall.lo sorting.lo specbond.lo ter_db.lo tomorse.lo
 topdirs.lo topexcl.lo topio.lo toppush.lo topshake.lo toputil.lo tpbcmp.lo
 vsite_parm.lo xlate.lo ../mdlib/libmd_mpi.la -lnsl -lm
 libtool: link: cannot find the library `../mdlib/libmd_mpi.la' or
 unhandled argument `../mdlib/libmd_mpi.la'
 make[1]: *** [libgmxpreprocess_mpi.la] Error 1



 On Thu, Dec 8, 2011 at 5:32 PM, Mark Abraham mark.abra...@anu.edu.auwrote:

 On 8/12/2011 6:35 PM, aiswarya pawar wrote:

 Hi users,

 Am running the mdrun_mpi on cluster with the md.mdp parameters as-

 ; VARIOUS PREPROCESSING OPTIONS
 title= Position Restrained Molecular Dynamics


 ; RUN CONTROL PARAMETERS
 constraints = all-bonds
 integrator = md
 dt = 0.002 ; 2fs !
 nsteps = 250 ; total 5000 ps.
 nstcomm = 10
 nstxout = 500 ; collect data every 1 ps
 nstxtcout = 500
 nstvout = 0
 nstfout = 0
 nstlist = 10
 ns_type = grid
 rlist = 1.0
 coulombtype = PME
 rcoulomb = 1.0
 vdwtype = cut-off
 rvdw = 1.4
 pme_order = 4
 ewald_rtol = 1e-5
 optimize_fft = yes
 DispCorr = no
 ; Berendsen temperature coupling is on
 Tcoupl = v-rescale
 tau_t = 0.1 0.1
 tc-grps = protein non-protein
 ref_t = 300 300
 ; Pressure coupling is on
 Pcoupl = parrinello-rahman
 Pcoupltype = isotropic
 tau_p = 1.0
 compressibility = 4.5e-5
 ref_p = 1.0
 ; Generate velocites is on at 300 K.
 gen_vel = yes
 gen_temp = 300.0
 gen_seed = -1


 The grompp runs fine. but when i run the mdrun_mpi i get an error such
 as-

 Child exited abnormally!
 Killing remote processes...DONE


 There's no information here upon which one can diagnose anything. Look at
 the stderr, stdout and .log files and consult the errors page

Re: [gmx-users] gromacs installation error

[aiswarya pawar]

when i gave following command for gromacs=

./configure  --with-fft=fftw3 --enable-float --disable-threads

it installed gromacs successfully, but i require a mpi mdrun. when i give
enable mpi it gives me same error as fftw3 library not found.

Thanks


On Wed, Dec 7, 2011 at 2:21 PM, Javier Cerezo j...@um.es wrote:

  You mean that

 $ ls /home/fftw

 gives you the content of the installed fftw library (i.e. bin/  include/
 lib/  share/)?

 El 06/12/11 16:21, aiswarya.pa...@gmail.com escribió:

 Hi,

 Thanks for the reply, I check the path and everything still I get this error.


 Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for it!

 -Original Message-
 From: Javier Cerezo j...@um.es j...@um.es
 Sender: gmx-users-boun...@gromacs.org
 Date: Tue, 06 Dec 2011 13:30:55
 To: Discussion list for GROMACS usersgmx-users@gromacs.org 
 gmx-users@gromacs.org
 Reply-To: Discussion list for GROMACS users gmx-users@gromacs.org 
 gmx-users@gromacs.org
 Subject: Re: [gmx-users] gromacs installation error





 --
 Javier CEREZO BASTIDA
 PhD Student
 Physical Chemistry
 Universidad de Murcia
 Murcia (Spain)
 Tlf.(+34)868887434


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[gmx-users] mdrun_mpi error

[aiswarya pawar]

Hi users,

Am running the mdrun_mpi on cluster with the md.mdp parameters as-

; VARIOUS PREPROCESSING OPTIONS
title= Position Restrained Molecular Dynamics


; RUN CONTROL PARAMETERS
constraints = all-bonds
integrator = md
dt = 0.002 ; 2fs !
nsteps = 250 ; total 5000 ps.
nstcomm = 10
nstxout = 500 ; collect data every 1 ps
nstxtcout = 500
nstvout = 0
nstfout = 0
nstlist = 10
ns_type = grid
rlist = 1.0
coulombtype = PME
rcoulomb = 1.0
vdwtype = cut-off
rvdw = 1.4
pme_order = 4
ewald_rtol = 1e-5
optimize_fft = yes
DispCorr = no
; Berendsen temperature coupling is on
Tcoupl = v-rescale
tau_t = 0.1 0.1
tc-grps = protein non-protein
ref_t = 300 300
; Pressure coupling is on
Pcoupl = parrinello-rahman
Pcoupltype = isotropic
tau_p = 1.0
compressibility = 4.5e-5
ref_p = 1.0
; Generate velocites is on at 300 K.
gen_vel = yes
gen_temp = 300.0
gen_seed = -1


The grompp runs fine. but when i run the mdrun_mpi i get an error such as-

Child exited abnormally!
Killing remote processes...DONE


Aiswarya
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[gmx-users] gromacs installation error

[aiswarya pawar]

Hi Gromacs users,


Am trying to install gromacs-4.5.5 version on IBM cluster with Linux
platform and am getting an error such as configure: error: Cannot find
fftw3f library.

The steps i followed-

Installed fftw-3.3 version

./configure --enable-threads --enable-float
make
make install

setenv CPPFLAGS -I/home/fftw/include
setenv LDFLAGS -L/home/fftw/lib

In gromacs-4.5.5 directory

./configure --enable-mpi --program-suffix=_mpi --with-fft=fftw3

in this i got the error.

please help.


Thanks,
Aiswarya
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Re: [gmx-users] gromacs installation error

[aiswarya . pawar]

Hi,

Thanks for the reply, I check the path and everything still I get this error.


Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for it!

-Original Message-
From: Javier Cerezo j...@um.es
Sender: gmx-users-boun...@gromacs.org
Date: Tue, 06 Dec 2011 13:30:55 
To: Discussion list for GROMACS usersgmx-users@gromacs.org
Reply-To: Discussion list for GROMACS users gmx-users@gromacs.org
Subject: Re: [gmx-users] gromacs installation error

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[gmx-users] increase the time frame

[aiswarya pawar]

Hi users,

Iam running a minimization on protein complex in vacuum. i have set the
parameters as following-

; Lines starting with ';' ARE COMMENTS
; Everything following ';' is also comment

title= Energy Minimization; Title of run

; The following line tell the program the standard locations where to find
certain files
cpp= /lib/cpp; Preprocessor


; Define can be used to control processes
define  = -DFLEXIBLE

; Parameters describing what to do, when to stop and what to save
integrator= steepest; Algorithm (steep = steepest descent
minimization)
emtol= 1000.0   ; Stop minimization when the maximum force  1.0
kJ/mol
emstep  = 0.01
nsteps= 5; Maximum number of (minimization) steps to
perform
nstenergy= 1  ; Write energies to disk every nstenergy steps
energygrps= Protein; Which energy group(s) to write to disk

; Parameters describing how to find the neighbors of each atom and how to
calculate the interactions
nstxout = 1
nstlist= 10; Frequency to update the neighbor list and long
range forces
ns_type= grid  ; Method to determine neighbor list (simple,
grid)
rlist= 1.0; Cut-off for making neighbor list (short range
forces)
coulombtype= cutoff   ; Treatment of long range electrostatic
interactions
rcoulomb= 1.0; long range electrostatic cut-off
rvdw= 1.4; long range Van der Waals cut-off
constraints= none; Bond types to replace by constraints
pbc= no; Periodic Boundary Conditions (yes/no)

But from this i could write only 2 frames i need to increase the time
frames, what is to be changed in the parameters.

Thanks,
Aiswarya
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Re: [gmx-users] increase the time frame

[aiswarya pawar]

After running this minimization when i did gmxcheck i got this output

trn version: GMX_trn_file (single precision)
Reading frame   0 time9.000
# Atoms  4113
Reading frame   3 time   57.000
Timesteps at t=31 don't match (12, 26)
Reading frame   4 time   69.000
Timesteps at t=57 don't match (26, 12)
Reading frame  14 time  192.000
Timesteps at t=184 don't match (13, 8)
Last frame 14 time  192.000


Item#frames
Step15
Time15
Lambda  15
Coords  15
Velocities   0
Forces   0
Box 15


why is it saying that Timesteps at t=31 don't match (12, 26).


On Fri, Oct 21, 2011 at 12:25 PM, Mark Abraham mark.abra...@anu.edu.auwrote:

 On 21/10/2011 5:09 PM, aiswarya pawar wrote:

 Hi users,

 Iam running a minimization on protein complex in vacuum. i have set the
 parameters as following-

 ; Lines starting with ';' ARE COMMENTS
 ; Everything following ';' is also comment

 title= Energy Minimization; Title of run

 ; The following line tell the program the standard locations where to find
 certain files
 cpp= /lib/cpp; Preprocessor


 ; Define can be used to control processes
 define  = -DFLEXIBLE

 ; Parameters describing what to do, when to stop and what to save
 integrator= steepest; Algorithm (steep = steepest descent
 minimization)
 emtol= 1000.0   ; Stop minimization when the maximum force 
 1.0 kJ/mol
 emstep  = 0.01
 nsteps= 5; Maximum number of (minimization) steps to
 perform
 nstenergy= 1  ; Write energies to disk every nstenergy steps
 energygrps= Protein; Which energy group(s) to write to disk

 ; Parameters describing how to find the neighbors of each atom and how to
 calculate the interactions
 nstxout = 1
 nstlist= 10; Frequency to update the neighbor list and
 long range forces
 ns_type= grid  ; Method to determine neighbor list (simple,
 grid)
 rlist= 1.0; Cut-off for making neighbor list (short range
 forces)
 coulombtype= cutoff   ; Treatment of long range electrostatic
 interactions
 rcoulomb= 1.0; long range electrostatic cut-off
 rvdw= 1.4; long range Van der Waals cut-off
 constraints= none; Bond types to replace by constraints
 pbc= no; Periodic Boundary Conditions (yes/no)

 But from this i could write only 2 frames i need to increase the time
 frames, what is to be changed in the parameters.


 This will write every frame of the EM, but if it only has two steps...

 Mark
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[gmx-users] Minimization error

[aiswarya . pawar]

Hi Users,

I performed a simple minimization for a protein complex in vacuum. Didn't get 
any error while performing the minimization but when visualised the pdb file 
after the minimization the chains of the protein complex separated.

What could be the reason.

Thanks,
Aiswarya 
Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for it!-- 
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Re: [gmx-users] Minimization error

[aiswarya pawar]

Hi,

All the parameters are ok, still i get the complex separated.


On Wed, Oct 19, 2011 at 7:02 PM, Justin A. Lemkul jalem...@vt.edu wrote:



 aiswarya.pa...@gmail.com wrote:

 Hi Users,

 I performed a simple minimization for a protein complex in vacuum. Didn't
 get any error while performing the minimization but when visualised the pdb
 file after the minimization the chains of the protein complex separated.

 What could be the reason.


 Please see FAQ #3 under the heading:

 http://www.gromacs.org/**Documentation/FAQs#Analysis_**and_Visualizationhttp://www.gromacs.org/Documentation/FAQs#Analysis_and_Visualization

 -Justin


  Thanks,
 Aiswarya Sent from my BlackBerry® on Reliance Mobile, India's No. 1
 Network. Go for it!


 --
 ==**==

 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/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

 ==**==

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[gmx-users] non interactive command

[aiswarya pawar]

Hi users,

I have n number of program to run so my index file is huge, i want to know
if i use the command option g_energy -flags  choice.txt , it takes up the
numbers given right? but if i have n numbers in the choice txt. how would it
take in each run , ie it will take 1st two numbers and what about the rest?


Thanks
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Re: [gmx-users] non interactive command

[aiswarya pawar]

justin,

if i use echo command then i need to run again and again for each selection
right? how can i run as whole bunch.

Thanks

On Wed, Sep 28, 2011 at 10:31 PM, Justin A. Lemkul jalem...@vt.edu wrote:



 aiswarya pawar wrote:

 Hi users,

 I have n number of program to run so my index file is huge, i want to know
 if i use the command option g_energy -flags  choice.txt , it takes up the
 numbers given right? but if i have n numbers in the choice txt. how would it
 take in each run , ie it will take 1st two numbers and what about the rest?


 You should only provide the chosen number(s), otherwise the program will
 try to read all of them.  In the case where you have many different programs
 to run, it is vastly easier to run, for instance:

 echo x y | g_program -flags

 -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/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

 ==**==
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Re: [gmx-users] non interactive command

[aiswarya pawar]

i have N number of selection ie it should run as a batch. like its should
select group1: 0 and select group2: 32, this is 1st run then after this next
run should be  select group1: 1 and select group2: 32 and so on.

On Wed, Sep 28, 2011 at 10:56 PM, Justin A. Lemkul jalem...@vt.edu wrote:



 aiswarya pawar wrote:

 justin,

 if i use echo command then i need to run again and again for each
 selection right? how can i run as whole bunch.


 I don't understand your question.  You can write a trivial shell script for
 all of your analysis, e.g.:

 #!/bin/bash

 echo 4 4 | g_rms -f traj.xtc -s topol.tpr

 echo 1 | g_gyrate -f traj.xtc -s topol.tpr

 (etc)

 -Justin

  Thanks


 On Wed, Sep 28, 2011 at 10:31 PM, Justin A. Lemkul jalem...@vt.edumailto:
 jalem...@vt.edu wrote:



aiswarya pawar wrote:

Hi users,

I have n number of program to run so my index file is huge, i
want to know if i use the command option g_energy -flags 
choice.txt , it takes up the numbers given right? but if i have
n numbers in the choice txt. how would it take in each run , ie
it will take 1st two numbers and what about the rest?


You should only provide the chosen number(s), otherwise the program
will try to read all of them.  In the case where you have many
different programs to run, it is vastly easier to run, for instance:

echo x y | g_program -flags

-Justin

-- ==**__==

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


 http://www.bevanlab.biochem.__**vt.edu/Pages/Personal/justinhttp://vt.edu/Pages/Personal/justin

 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://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.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

 ==**==
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[gmx-users] g_analyze doubt

[aiswarya pawar]

Hi users,

I have data with the time frame and the distances, how will compute the
autocorrelation of this. i did g_analyze but still dont understand what
should be the y axis data when providing input for g_analyze. please help.

Thanks
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Re: [gmx-users] g_analyze doubt

[aiswarya pawar]

HI Mark,

i have a .xvg data for the distance of two atoms in each time frame.


0.00e+00  7.191033e-01
1.00e+00  7.304224e-01
2.00e+00  8.983867e-01
3.00e+00  8.779736e-01
4.00e+00  8.236583e-01
5.00e+00  8.298320e-01
6.00e+00  7.703011e-01
7.00e+00  8.569826e-01
8.00e+00  7.428180e-01
9.00e+00  7.487683e-01
1.00e+01  8.106729e-01
1.10e+01  8.702058e-01
1.20e+01  8.823072e-01
1.30e+01  8.902194e-01
1.40e+01  6.122664e-01
1.50e+01  5.804662e-01
1.60e+01  6.207849e-01
1.70e+01  4.852896e-01
1.80e+01  5.297776e-01
1.90e+01  5.432515e-01
2.00e+01  5.888653e-01
2.10e+01  4.620140e-01


Now i want to find the autocorrelation of the time frame. so i should
provide this file as such for input in g_analyze ie x as time and y as
distance? or are there any criteria for the g_analyze input.

Thanks,


On Mon, Sep 26, 2011 at 12:38 PM, Mark Abraham mark.abra...@anu.edu.auwrote:

 On 26/09/2011 4:51 PM, aiswarya pawar wrote:

 Hi users,

 I have data with the time frame and the distances, how will compute the
 autocorrelation of this. i did g_analyze but still dont understand what
 should be the y axis data when providing input for g_analyze. please help.


 I don't understand your question. Your first sentence implies you know what
 quantity you want to autocorrelate, and the second implies you don't.

 g_analyze needs a time series in an .xvg file of some data to compute an
 autocorrelation. Usually, an .xvg file written by a GROMACS tool is already
 prepared for such further analysis.

 Mark
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Re: [gmx-users] g_analyze doubt

[aiswarya pawar]

Mark,

i read the help but i still didnt understand how do i compute the time
series for this data, should i use this data as such for the input?

Thanks,

On Mon, Sep 26, 2011 at 12:44 PM, Mark Abraham mark.abra...@anu.edu.auwrote:

 On 26/09/2011 5:10 PM, aiswarya pawar wrote:

 HI Mark,

 i have a .xvg data for the distance of two atoms in each time frame.


 0.00e+00  7.191033e-01
 1.00e+00  7.304224e-01
 2.00e+00  8.983867e-01
 3.00e+00  8.779736e-01
 4.00e+00  8.236583e-01
 5.00e+00  8.298320e-01
 6.00e+00  7.703011e-01
 7.00e+00  8.569826e-01
 8.00e+00  7.428180e-01
 9.00e+00  7.487683e-01
 1.00e+01  8.106729e-01
 1.10e+01  8.702058e-01
 1.20e+01  8.823072e-01
 1.30e+01  8.902194e-01
 1.40e+01  6.122664e-01
 1.50e+01  5.804662e-01
 1.60e+01  6.207849e-01
 1.70e+01  4.852896e-01
 1.80e+01  5.297776e-01
 1.90e+01  5.432515e-01
 2.00e+01  5.888653e-01
 2.10e+01  4.620140e-01


 Now i want to find the autocorrelation of the time frame. so i should
 provide this file as such for input in g_analyze ie x as time and y as
 distance? or are there any criteria for the g_analyze input.


 Have you read g_analyze -h and tried it out?


 Mark
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[gmx-users] g_analyze

[aiswarya . pawar]

Hi users,

I have got a data from g_mindist ie water and protein atom distance in each 
time frame. Now I have to find the auto correlation function using g_analyze 
but my output file from g_mindist has the time frame,water molecule number. How 
do I compute the ACF. In ACF data set the x axis is for time and what data 
provided in y axis.


Thanks
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[gmx-users] g_mindist doubt

[aiswarya pawar]

Hi users,

The g_mindist gives the minimum distance between the atoms other than the
actual distance.

Thanks
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Re: [gmx-users] g_mindist doubt

[aiswarya pawar]

Hi Tsjerk,

i used the command in format-

g_mindist -f md.xtc -s md.tpr -n 13.ndx -od 13.xvg -on 13.xvg -o 13.out -b
500 -e 1500 -d 0.5

so here i obtain the output-

atmpair.out-

0.00e+0013 21161
1.00e+0013 21161
2.00e+0013 21161
3.00e+0013 21161
4.00e+0013 21161
5.00e+0013 21161
6.00e+0013 21161
7.00e+0013 21161
8.00e+0013 21161
9.00e+0013 21161
1.00e+0113 21161
1.10e+0113 21161
1.20e+0113 21161
1.30e+0113 21161
1.40e+0113 21161
1.50e+0113 18698
1.60e+0113 21161
1.70e+0113 18698
1.80e+0113 18698
1.90e+0113 18698
2.00e+0113 18698
2.10e+0113 21455
2.20e+0113  7142
2.30e+0113  7142


and distance output-

0.00e+00  1.360443e+00
1.00e+00  1.246777e+00
2.00e+00  1.386871e+00
3.00e+00  1.250959e+00
4.00e+00  1.314306e+00
5.00e+00  1.273990e+00
6.00e+00  1.175991e+00
7.00e+00  1.154678e+00
8.00e+00  1.249905e+00
9.00e+00  1.110049e+00
1.00e+01  1.023204e+00
1.10e+01  1.004968e+00
1.20e+01  1.214452e+00
1.30e+01  1.297469e+00
1.40e+01  1.307791e+00
1.50e+01  1.276168e+00
1.60e+01  1.552775e+00
1.70e+01  1.668275e+00
1.80e+01  1.786125e+00
1.90e+01  1.733398e+00
2.00e+01  1.656987e+00
2.10e+01  1.715875e+00
2.20e+01  1.848419e+00
2.30e+01  1.932844e+00


Now my doubt is the whether these distances shown are the exact distance ie
actual or the minimum distance measured between the two atoms.

Thanks

On Thu, Sep 22, 2011 at 12:13 PM, Tsjerk Wassenaar tsje...@gmail.comwrote:

 Hi Aiswarya,

 What did you do, what did you get, what did you expect and what is
 your hunch regarding the difference between your result and your
 expectation?

 Tsjerk

 On Thu, Sep 22, 2011 at 8:21 AM, aiswarya pawar
 aiswarya.pa...@gmail.com wrote:
  Hi users,
 
  The g_mindist gives the minimum distance between the atoms other than the
  actual distance.
 
  Thanks
 
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 --
 Tsjerk A. Wassenaar, Ph.D.

 post-doctoral researcher
 Molecular Dynamics Group
 * Groningen Institute for Biomolecular Research and Biotechnology
 * Zernike Institute for Advanced Materials
 University of Groningen
 The Netherlands
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[gmx-users] surface atoms

[aiswarya pawar]

Hi users,

what are options for obtaining the surface atoms exposed to solvent, i need
the list of these atoms.

Thanks
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[gmx-users] Running the batch command

[aiswarya . pawar]

Hi users,

Am using g_mindist to calculate the distances. Now I have to calculate for each 
atom ie around 1000atoms. If I try running this command in a shell script, how 
would designate the index file, ie my index file has protein atoms and water 
atoms, and have to find distance between one protein atom to all the water 
atoms.

How would be the flow of the script.


Thanks
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[gmx-users] residue numbering different

[aiswarya pawar]

Hi Users,

When i list the residues in a index file it shows a numbering of residues
and when open the same protein in VMD and check the residue numbering its
different. i want to visualise the protein in VMD and select a residue
number from VMD and use in gromacs ie want to make an index file in gromacs
so how would go about.

Thanks
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Re: [gmx-users] g_dist error

[aiswarya pawar]

Mark,

the command line goes like this-

g_dist -f md.xtc -s md.tpr -dist 0.5 -e 500

the index file has group1- a_1322 ( this is just a single atom from a
protein. its in sidechain)
  group2- a_OW ( this is water atoms)

now as per the utility it should give me and output as-

t:1 1322 a 54119 OW 0.389

but am getting something different

On Tue, Sep 13, 2011 at 11:24 AM, Mark Abraham mark.abra...@anu.edu.auwrote:

  On 13/09/2011 3:40 PM, aiswarya pawar wrote:


 Hi Mark,

 The -dist option says- print all the atoms in group 2 that are closer than
 a certain distance to the center of mass of group 1.
 That means it should give me the distance from OW to protein atom.


 If you choose correct groups that are correctly defined with respect to
 your trajectory and use a large enough distance cutoff.



 And when am already specifying only one atom from protein ie say 1322. why
 do i get this kind of output-


 We can't tell. We don't know what your command line is, what's in your
 simulation system, the contents of your index groups, or which groups you've
 selected for which role. Clearly something is not working properly, and our
 time constraints mean that we're going to assume you've done something
 wrong, in the absence of evidence to the contrary.

 Mark



 t: 275  20230 SOL 62618 OW  0.341434 (nm)
 t: 275  22019 SOL 67985 OW  0.171584 (nm)
 t: 276  10768 SOL 34232 OW  0.303328 (nm)
 t: 276  20230 SOL 62618 OW  0.325176 (nm)
 t: 276  22019 SOL 67985 OW  0.187259 (nm)
 t: 277  10768 SOL 34232 OW  0.306008 (nm)
 t: 277  20230 SOL 62618 OW  0.326195 (nm)
 t: 277  22019 SOL 67985 OW  0.181089 (nm)
 t: 278  10768 SOL 34232 OW  0.274507 (nm)
 t: 278  22019 SOL 67985 OW  0.292652 (nm)
 t: 279  10618 SOL 33782 OW  0.319922 (nm)
 t: 280  10618 SOL 33782 OW  0.330082 (nm)
 t: 280  22019 SOL 67985 OW  0.330203 (nm)
 t: 281  8273 SOL 26747 OW  0.278731 (nm)
 t: 281  10618 SOL 33782 OW  0.325434 (nm)
 t: 281  11535 SOL 36533 OW  0.200327 (nm)
 t: 281  17036 SOL 53036 OW  0.343946 (nm)
 t: 282  8273 SOL 26747 OW  0.256558 (nm)
 t: 282  11535 SOL 36533 OW  0.327147 (nm)
 t: 283  8273 SOL 26747 OW  0.165061 (nm)
 t: 283  10618 SOL 33782 OW  0.306578 (nm)
 t: 283  17191 SOL 53501 OW  0.333075 (nm)
 t: 284  8273 SOL 26747 OW  0.19427 (nm)
 t: 284  10618 SOL 33782 OW  0.321927 (nm)
 t: 284  17191 SOL 53501 OW  0.30832 (nm)




 On Tue, Sep 13, 2011 at 10:40 AM, Mark Abraham mark.abra...@anu.edu.auwrote:

  On 13/09/2011 2:27 PM, aiswarya.pa...@gmail.com wrote:

 Iam -dist option because I need the distance between two groups


  That is not what g_dist -dist does. Please read g_dist -h.


   excluding -dist gives me X,Y,Z output which I don't want.


  And other output which you do, but you have to use -o to get it. Read
 g_dist -h.


   And am not specifying an -o.


  You need to specify -o to achieve your purpose. However, as I said quite
 a while ago, there is no value in measuring the distance between a protein
 phase and a water phase if they are in contact...

 Mark


  Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for 
 it!

 -Original Message-
 From: Justin A. Lemkul jalem...@vt.edu jalem...@vt.edu
 Date: Mon, 12 Sep 2011 22:35:28
 To: aiswarya.pa...@gmail.com aiswarya.pa...@gmail.com; Discussion list 
 for GROMACS usersgmx-users@gromacs.org gmx-users@gromacs.org
 Reply-To: jalem...@vt.edu
 Subject: Re: [gmx-users] g_dist error


 aiswarya.pa...@gmail.com wrote:

  Even if I specify an atom say 1277 atom number to find distance against the 
 OW atoms. I get the same result of SOL-OW distance. Is it a bug cause even 
 after specifying one atom from a protein why doesn't it give me the result 
 for the SOL.



  As was suggested several messages ago, please do NOT combine -o and -dist.  
 If
 you want to measure a distance, use -o.  If you want g_dist to print a list 
 of
 atoms that satisfy some given criteria, use -dist, but not together.

 -Justin


  Thanks
 Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for 
 it!

 -Original Message-
 From: Justin A. Lemkul jalem...@vt.edu jalem...@vt.edu
 Sender: gmx-users-boun...@gromacs.org
 Date: Mon, 12 Sep 2011 07:52:54
 To: Discussion list for GROMACS usersgmx-users@gromacs.org 
 gmx-users@gromacs.org
 Reply-To: jalem...@vt.edu,
  Discussion list for GROMACS users gmx-users@gromacs.org 
 gmx-users@gromacs.org
 Subject: Re: [gmx-users] g_dist error



 aiswarya pawar wrote:

  hi Justin,

 As far i referred the OW,HW1 etc are water atoms so how can it be
 distance between the SOL protein atoms, instead it is SOL water atoms.


  The printed distance indicates that there is a certain water molecule that 
 is
 just over 2 hydrogen bonding lengths away from your protein's backbone.  
 Sounds
 normal to me.

 -Justin


  Thanks

 On Mon, Sep 12, 2011 at 4:49 PM, Justin A. Lemkul jalem...@vt.edu 
 mailto:jalem...@vt.edu jalem...@vt.edu wrote:



 aiswarya pawar wrote

Re: [gmx-users] g_dist error

[aiswarya pawar]

g_dist -f md.xtc -s md.tpr -dist 0.5 -e 500 if the index name not given it
takes the default index file, so there isnt any wrong in selecting the
atoms.

On Tue, Sep 13, 2011 at 1:24 PM, Mark Abraham mark.abra...@anu.edu.auwrote:

  On 13/09/2011 4:14 PM, aiswarya pawar wrote:

 Mark,

 the command line goes like this-

 g_dist -f md.xtc -s md.tpr -dist 0.5 -e 500


 This command line is not using an index file. The index groups defined for
 the grompp that produced the .tpr are being used (which may be the default
 ones, depending what you did). Please copy and show the interactive input
 you made to g_dist after it showed the groups it knew about.



 the index file has group1- a_1322 ( this is just a single atom from a
 protein. its in sidechain)
   group2- a_OW ( this is water atoms)


 Your output is listing the time of the frame, and the residue number,
 residue name, atom number, and atom name of the matching atom. Apparently a
 water molecule can sometimes be closer than 0.2nm, and sometimes not.

 Mark



 now as per the utility it should give me and output as-

 t:1 1322 a 54119 OW 0.389

 but am getting something different

 On Tue, Sep 13, 2011 at 11:24 AM, Mark Abraham mark.abra...@anu.edu.auwrote:

  On 13/09/2011 3:40 PM, aiswarya pawar wrote:


 Hi Mark,

 The -dist option says- print all the atoms in group 2 that are closer than
 a certain distance to the center of mass of group 1.
 That means it should give me the distance from OW to protein atom.


  If you choose correct groups that are correctly defined with respect to
 your trajectory and use a large enough distance cutoff.



 And when am already specifying only one atom from protein ie say 1322. why
 do i get this kind of output-


  We can't tell. We don't know what your command line is, what's in your
 simulation system, the contents of your index groups, or which groups you've
 selected for which role. Clearly something is not working properly, and our
 time constraints mean that we're going to assume you've done something
 wrong, in the absence of evidence to the contrary.

 Mark



 t: 275  20230 SOL 62618 OW  0.341434 (nm)
 t: 275  22019 SOL 67985 OW  0.171584 (nm)
 t: 276  10768 SOL 34232 OW  0.303328 (nm)
 t: 276  20230 SOL 62618 OW  0.325176 (nm)
 t: 276  22019 SOL 67985 OW  0.187259 (nm)
 t: 277  10768 SOL 34232 OW  0.306008 (nm)
 t: 277  20230 SOL 62618 OW  0.326195 (nm)
 t: 277  22019 SOL 67985 OW  0.181089 (nm)
 t: 278  10768 SOL 34232 OW  0.274507 (nm)
 t: 278  22019 SOL 67985 OW  0.292652 (nm)
 t: 279  10618 SOL 33782 OW  0.319922 (nm)
 t: 280  10618 SOL 33782 OW  0.330082 (nm)
 t: 280  22019 SOL 67985 OW  0.330203 (nm)
 t: 281  8273 SOL 26747 OW  0.278731 (nm)
 t: 281  10618 SOL 33782 OW  0.325434 (nm)
 t: 281  11535 SOL 36533 OW  0.200327 (nm)
 t: 281  17036 SOL 53036 OW  0.343946 (nm)
 t: 282  8273 SOL 26747 OW  0.256558 (nm)
 t: 282  11535 SOL 36533 OW  0.327147 (nm)
 t: 283  8273 SOL 26747 OW  0.165061 (nm)
 t: 283  10618 SOL 33782 OW  0.306578 (nm)
 t: 283  17191 SOL 53501 OW  0.333075 (nm)
 t: 284  8273 SOL 26747 OW  0.19427 (nm)
 t: 284  10618 SOL 33782 OW  0.321927 (nm)
 t: 284  17191 SOL 53501 OW  0.30832 (nm)




 On Tue, Sep 13, 2011 at 10:40 AM, Mark Abraham 
 mark.abra...@anu.edu.auwrote:

  On 13/09/2011 2:27 PM, aiswarya.pa...@gmail.com wrote:

 Iam -dist option because I need the distance between two groups


  That is not what g_dist -dist does. Please read g_dist -h.


   excluding -dist gives me X,Y,Z output which I don't want.


  And other output which you do, but you have to use -o to get it. Read
 g_dist -h.


   And am not specifying an -o.


  You need to specify -o to achieve your purpose. However, as I said quite
 a while ago, there is no value in measuring the distance between a protein
 phase and a water phase if they are in contact...

 Mark


  Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for 
 it!

 -Original Message-
 From: Justin A. Lemkul jalem...@vt.edu jalem...@vt.edu
 Date: Mon, 12 Sep 2011 22:35:28
 To: aiswarya.pa...@gmail.com aiswarya.pa...@gmail.com; Discussion list 
 for GROMACS usersgmx-users@gromacs.org gmx-users@gromacs.org
 Reply-To: jalem...@vt.edu
 Subject: Re: [gmx-users] g_dist error


 aiswarya.pa...@gmail.com wrote:

  Even if I specify an atom say 1277 atom number to find distance against 
 the OW atoms. I get the same result of SOL-OW distance. Is it a bug cause 
 even after specifying one atom from a protein why doesn't it give me the 
 result for the SOL.



  As was suggested several messages ago, please do NOT combine -o and -dist. 
  If
 you want to measure a distance, use -o.  If you want g_dist to print a list 
 of
 atoms that satisfy some given criteria, use -dist, but not together.

 -Justin


  Thanks
 Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for 
 it!

 -Original Message-
 From: Justin A. Lemkul jalem...@vt.edu jalem...@vt.edu
 Sender: gmx-users-boun

[gmx-users] Re: no output in g_dist

[aiswarya pawar]

Hi everyone,

when am doing this g_dist between the protein and water am getting the
distance between water-water. why it is so?? and is there a way i can find
distance in each time frame.

Thanks

On Thu, Sep 8, 2011 at 5:55 PM, aiswarya pawar aiswarya.pa...@gmail.comwrote:

 Hi users,

 To get the distance between water and protein i did -

  g_dist -f md.xtc -s md.tpr -o distance.xvg -dist 1 -b 1 -e 11

 from this i should obtain an output file as distance.xvg which i dont get.

 and my output is printed on the terminal as-

 t: 1  136 SOL 2336 OW  0.772373 (nm)
 t: 1  136 SOL 2337 HW1  0.706358 (nm)
 t: 1  136 SOL 2338 HW2  0.807787 (nm)
 t: 1  139 SOL 2345 OW  0.821094 (nm)
 t: 1  139 SOL 2346 HW1  0.810919 (nm)
 t: 1  139 SOL 2347 HW2  0.771526 (nm)
 t: 1  7237 SOL 23640 HW1  0.997056 (nm)
 t: 1  11793 SOL 37307 OW  0.868929 (nm)
 t: 1  11793 SOL 37308 HW1  0.927205 (nm)
 t: 1  11793 SOL 37309 HW2  0.776699 (nm)
 t: 2  125 SOL 2303 OW  0.940527 (nm)

 In this

 t: 1  136 SOL 2336 OW  0.772373 (nm)

 does the 't' states the time frame, 136 SOL states the SOL molecule number
 and 2336 OW the residue contact from protein and the 0.772373 nm the
 distance between them.

 Thanks


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[gmx-users] g_dist error

[aiswarya pawar]

Hi Users,

Am using g_dist to find the distance between water and protein. but my
output has the values of SOL-water distance.

t: 1  136 SOL 2336 OW  0.772373 (nm)

Thanks
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[gmx-users] g_dist output error

[aiswarya pawar]

Hi gromacs Users,

Am using g_dist to find the distance between water and protein. for
that i made a index file such as-

a CA(protein atoms)

a OW(water atoms)

i then run this cmd- g_dist -f md.xtc -s md.tpr -n index.ndx -e 500 -dist 0.35

instead of getting the result for protein-SOL distance . my output
shows SOL-OW distance as seen below-

t: 1  136 SOL 2336 OW  0.772373 (nm)
 can anyone tell me whats wrong with this.
Thanks
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Re: [gmx-users] g_dist error

[aiswarya pawar]

Hi Justin,

Am using g_dist to find the distance between water and protein. for
that i made a index file such as-

a CA(protein atoms)

a OW(water atoms)

i then run this cmd- g_dist -f md.xtc -s md.tpr -n index.ndx -e 500 -dist 0.35


instead of getting the result for protein-SOL distance . my output
shows SOL-OW distance as seen below-

t: 1  136 SOL 2336 OW  0.772373 (nm)

even after specifying am getting an wrong output.

Thanks



On Mon, Sep 12, 2011 at 4:49 PM, Justin A. Lemkul jalem...@vt.edu wrote:



 aiswarya pawar wrote:

 Hi Users,

 Am using g_dist to find the distance between water and protein. but my
 output has the values of SOL-water distance.

 t: 1  136 SOL 2336 OW  0.772373 (nm)


 This is not a water-water distance, it is the output of the -dist option
 telling you that water molecule 136 has its OW atom at 0.7723273 nm from
 whatever your reference group is.

 -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/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

 ==**==
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Re: [gmx-users] g_dist error

[aiswarya pawar]

hi Justin,

As far i referred the OW,HW1 etc are water atoms so how can it be distance
between the SOL protein atoms, instead it is SOL water atoms.

Thanks

On Mon, Sep 12, 2011 at 4:49 PM, Justin A. Lemkul jalem...@vt.edu wrote:



 aiswarya pawar wrote:

 Hi Users,

 Am using g_dist to find the distance between water and protein. but my
 output has the values of SOL-water distance.

 t: 1  136 SOL 2336 OW  0.772373 (nm)


 This is not a water-water distance, it is the output of the -dist option
 telling you that water molecule 136 has its OW atom at 0.7723273 nm from
 whatever your reference group is.

 -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/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

 ==**==
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Re: [gmx-users] g_dist output error

[aiswarya pawar]

hi Justin,

As far i referred the OW,HW1 etc are water atoms so how can it be distance
between the SOL protein atoms, instead it is SOL water atoms.

Thanks

On Mon, Sep 12, 2011 at 4:53 PM, Justin A. Lemkul jalem...@vt.edu wrote:



 aiswarya pawar wrote:

 Hi gromacs Users,

 Am using g_dist to find the distance between water and protein. for that i
 made a index file such as-

 a CA(protein atoms)

 a OW(water atoms)

 i then run this cmd- g_dist -f md.xtc -s md.tpr -n index.ndx -e 500 -dist
 0.35


 instead of getting the result for protein-SOL distance . my output shows
 SOL-OW distance as seen below-

 t: 1  136 SOL 2336 OW  0.772373 (nm)
  can anyone tell me whats wrong with this.


 Please see my previous message.  This is not a SOL-water distance.

 -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/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

 ==**==
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Re: [gmx-users] g_dist error

[aiswarya . pawar]

Even if I specify an atom say 1277 atom number to find distance against the OW 
atoms. I get the same result of SOL-OW distance. Is it a bug cause even after 
specifying one atom from a protein why doesn't it give me the result for the 
SOL.


Thanks
Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for it!

-Original Message-
From: Justin A. Lemkul jalem...@vt.edu
Sender: gmx-users-boun...@gromacs.org
Date: Mon, 12 Sep 2011 07:52:54 
To: Discussion list for GROMACS usersgmx-users@gromacs.org
Reply-To: jalem...@vt.edu,
Discussion list for GROMACS users gmx-users@gromacs.org
Subject: Re: [gmx-users] g_dist error



aiswarya pawar wrote:
 hi Justin,
 
 As far i referred the OW,HW1 etc are water atoms so how can it be 
 distance between the SOL protein atoms, instead it is SOL water atoms.
 

The printed distance indicates that there is a certain water molecule that is 
just over 2 hydrogen bonding lengths away from your protein's backbone.  Sounds 
normal to me.

-Justin

 Thanks
 
 On Mon, Sep 12, 2011 at 4:49 PM, Justin A. Lemkul jalem...@vt.edu 
 mailto:jalem...@vt.edu wrote:
 
 
 
 aiswarya pawar wrote:
 
 Hi Users,
 
 Am using g_dist to find the distance between water and protein.
 but my output has the values of SOL-water distance.
 
 t: 1  136 SOL 2336 OW  0.772373 (nm)
 
 
 This is not a water-water distance, it is the output of the -dist
 option telling you that water molecule 136 has its OW atom at
 0.7723273 nm from whatever your reference group is.
 
 -Justin
 
 -- 
 ==__==
 
 Justin A. Lemkul
 Ph.D. Candidate
 ICTAS Doctoral Scholar
 MILES-IGERT Trainee
 Department of Biochemistry
 Virginia Tech
 Blacksburg, VA
 jalemkul[at]vt.edu http://vt.edu | (540) 231-9080
 http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin
 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
 
 ==__==
 -- 
 gmx-users mailing listgmx-users@gromacs.org
 mailto:gmx-users@gromacs.org
 http://lists.gromacs.org/__mailman/listinfo/gmx-users
 http://lists.gromacs.org/mailman/listinfo/gmx-users
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 Can't post? Read http://www.gromacs.org/__Support/Mailing_Lists
 http://www.gromacs.org/Support/Mailing_Lists
 
 

-- 


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_dist error

[aiswarya . pawar]

Iam -dist option because I need the distance between two groups, excluding 
-dist gives me X,Y,Z output which I don't want. And am not specifying an -o.

Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for it!

-Original Message-
From: Justin A. Lemkul jalem...@vt.edu
Date: Mon, 12 Sep 2011 22:35:28 
To: aiswarya.pa...@gmail.com; Discussion list for GROMACS 
usersgmx-users@gromacs.org
Reply-To: jalem...@vt.edu
Subject: Re: [gmx-users] g_dist error



aiswarya.pa...@gmail.com wrote:
 Even if I specify an atom say 1277 atom number to find distance against the 
 OW atoms. I get the same result of SOL-OW distance. Is it a bug cause even 
 after specifying one atom from a protein why doesn't it give me the result 
 for the SOL.
 
 

As was suggested several messages ago, please do NOT combine -o and -dist.  If 
you want to measure a distance, use -o.  If you want g_dist to print a list of 
atoms that satisfy some given criteria, use -dist, but not together.

-Justin

 Thanks
 Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for it!
 
 -Original Message-
 From: Justin A. Lemkul jalem...@vt.edu
 Sender: gmx-users-boun...@gromacs.org
 Date: Mon, 12 Sep 2011 07:52:54 
 To: Discussion list for GROMACS usersgmx-users@gromacs.org
 Reply-To: jalem...@vt.edu,
   Discussion list for GROMACS users gmx-users@gromacs.org
 Subject: Re: [gmx-users] g_dist error
 
 
 
 aiswarya pawar wrote:
 hi Justin,

 As far i referred the OW,HW1 etc are water atoms so how can it be 
 distance between the SOL protein atoms, instead it is SOL water atoms.

 
 The printed distance indicates that there is a certain water molecule that is 
 just over 2 hydrogen bonding lengths away from your protein's backbone.  
 Sounds 
 normal to me.
 
 -Justin
 
 Thanks

 On Mon, Sep 12, 2011 at 4:49 PM, Justin A. Lemkul jalem...@vt.edu 
 mailto:jalem...@vt.edu wrote:



 aiswarya pawar wrote:

 Hi Users,

 Am using g_dist to find the distance between water and protein.
 but my output has the values of SOL-water distance.

 t: 1  136 SOL 2336 OW  0.772373 (nm)


 This is not a water-water distance, it is the output of the -dist
 option telling you that water molecule 136 has its OW atom at
 0.7723273 nm from whatever your reference group is.

 -Justin

 -- 
 ==__==

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

 ==__==
 -- 
 gmx-users mailing listgmx-users@gromacs.org
 mailto:gmx-users@gromacs.org
 http://lists.gromacs.org/__mailman/listinfo/gmx-users
 http://lists.gromacs.org/mailman/listinfo/gmx-users
 Please search the archive at
 http://www.gromacs.org/__Support/Mailing_Lists/Search
 http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
 Please don't post (un)subscribe requests to the list. Use the www
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 mailto:gmx-users-requ...@gromacs.org.
 Can't post? Read http://www.gromacs.org/__Support/Mailing_Lists
 http://www.gromacs.org/Support/Mailing_Lists


 

-- 


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_dist error

[aiswarya pawar]

Hi Mark,

The -dist option says- print all the atoms in group 2 that are closer than a
certain distance to the center of mass of group 1.
That means it should give me the distance from OW to protein atom.

And when am already specifying only one atom from protein ie say 1322. why
do i get this kind of output-

t: 275  20230 SOL 62618 OW  0.341434 (nm)
t: 275  22019 SOL 67985 OW  0.171584 (nm)
t: 276  10768 SOL 34232 OW  0.303328 (nm)
t: 276  20230 SOL 62618 OW  0.325176 (nm)
t: 276  22019 SOL 67985 OW  0.187259 (nm)
t: 277  10768 SOL 34232 OW  0.306008 (nm)
t: 277  20230 SOL 62618 OW  0.326195 (nm)
t: 277  22019 SOL 67985 OW  0.181089 (nm)
t: 278  10768 SOL 34232 OW  0.274507 (nm)
t: 278  22019 SOL 67985 OW  0.292652 (nm)
t: 279  10618 SOL 33782 OW  0.319922 (nm)
t: 280  10618 SOL 33782 OW  0.330082 (nm)
t: 280  22019 SOL 67985 OW  0.330203 (nm)
t: 281  8273 SOL 26747 OW  0.278731 (nm)
t: 281  10618 SOL 33782 OW  0.325434 (nm)
t: 281  11535 SOL 36533 OW  0.200327 (nm)
t: 281  17036 SOL 53036 OW  0.343946 (nm)
t: 282  8273 SOL 26747 OW  0.256558 (nm)
t: 282  11535 SOL 36533 OW  0.327147 (nm)
t: 283  8273 SOL 26747 OW  0.165061 (nm)
t: 283  10618 SOL 33782 OW  0.306578 (nm)
t: 283  17191 SOL 53501 OW  0.333075 (nm)
t: 284  8273 SOL 26747 OW  0.19427 (nm)
t: 284  10618 SOL 33782 OW  0.321927 (nm)
t: 284  17191 SOL 53501 OW  0.30832 (nm)




On Tue, Sep 13, 2011 at 10:40 AM, Mark Abraham mark.abra...@anu.edu.auwrote:

  On 13/09/2011 2:27 PM, aiswarya.pa...@gmail.com wrote:

 Iam -dist option because I need the distance between two groups


 That is not what g_dist -dist does. Please read g_dist -h.


   excluding -dist gives me X,Y,Z output which I don't want.


 And other output which you do, but you have to use -o to get it. Read
 g_dist -h.


   And am not specifying an -o.


 You need to specify -o to achieve your purpose. However, as I said quite a
 while ago, there is no value in measuring the distance between a protein
 phase and a water phase if they are in contact...

 Mark


  Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for 
 it!

 -Original Message-
 From: Justin A. Lemkul jalem...@vt.edu jalem...@vt.edu
 Date: Mon, 12 Sep 2011 22:35:28
 To: aiswarya.pa...@gmail.com aiswarya.pa...@gmail.com; Discussion list 
 for GROMACS usersgmx-users@gromacs.org gmx-users@gromacs.org
 Reply-To: jalem...@vt.edu
 Subject: Re: [gmx-users] g_dist error


 aiswarya.pa...@gmail.com wrote:

  Even if I specify an atom say 1277 atom number to find distance against the 
 OW atoms. I get the same result of SOL-OW distance. Is it a bug cause even 
 after specifying one atom from a protein why doesn't it give me the result 
 for the SOL.



  As was suggested several messages ago, please do NOT combine -o and -dist.  
 If
 you want to measure a distance, use -o.  If you want g_dist to print a list of
 atoms that satisfy some given criteria, use -dist, but not together.

 -Justin


  Thanks
 Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for it!

 -Original Message-
 From: Justin A. Lemkul jalem...@vt.edu jalem...@vt.edu
 Sender: gmx-users-boun...@gromacs.org
 Date: Mon, 12 Sep 2011 07:52:54
 To: Discussion list for GROMACS usersgmx-users@gromacs.org 
 gmx-users@gromacs.org
 Reply-To: jalem...@vt.edu,
   Discussion list for GROMACS users gmx-users@gromacs.org 
 gmx-users@gromacs.org
 Subject: Re: [gmx-users] g_dist error



 aiswarya pawar wrote:

  hi Justin,

 As far i referred the OW,HW1 etc are water atoms so how can it be
 distance between the SOL protein atoms, instead it is SOL water atoms.


  The printed distance indicates that there is a certain water molecule that is
 just over 2 hydrogen bonding lengths away from your protein's backbone.  
 Sounds
 normal to me.

 -Justin


  Thanks

 On Mon, Sep 12, 2011 at 4:49 PM, Justin A. Lemkul jalem...@vt.edu 
 mailto:jalem...@vt.edu jalem...@vt.edu wrote:



 aiswarya pawar wrote:

 Hi Users,

 Am using g_dist to find the distance between water and protein.
 but my output has the values of SOL-water distance.

 t: 1  136 SOL 2336 OW  0.772373 (nm)


 This is not a water-water distance, it is the output of the -dist
 option telling you that water molecule 136 has its OW atom at
 0.7723273 nm from whatever your reference group is.

 -Justin

 --
 ==__==

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

 ==__==
 --
 gmx-users mailing listgmx-users@gromacs.org
 mailto:gmx-users@gromacs.org

[gmx-users] gridcount

[aiswarya pawar]

Hi all,

am facing an error while installing gridcount-

make[1]: *** [g_ri3Dc.o] Error 1
make[1]: Leaving directory `/home/proj11/aiswarya/Grid-count/src'
make: *** [all] Error 2

This error is while giving the make command.

Thanks
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[gmx-users] conversion of gromacs topology format

[aiswarya pawar]

Hi gromacs users,

Is there a way to convert gromacs topology format to Amber.

Thanks,
Aiswarya
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[gmx-users] no output in g_dist

[aiswarya pawar]

Hi users,

To get the distance between water and protein i did -

 g_dist -f md.xtc -s md.tpr -o distance.xvg -dist 1 -b 1 -e 11

from this i should obtain an output file as distance.xvg which i dont get.

and my output is printed on the terminal as-

t: 1  136 SOL 2336 OW  0.772373 (nm)
t: 1  136 SOL 2337 HW1  0.706358 (nm)
t: 1  136 SOL 2338 HW2  0.807787 (nm)
t: 1  139 SOL 2345 OW  0.821094 (nm)
t: 1  139 SOL 2346 HW1  0.810919 (nm)
t: 1  139 SOL 2347 HW2  0.771526 (nm)
t: 1  7237 SOL 23640 HW1  0.997056 (nm)
t: 1  11793 SOL 37307 OW  0.868929 (nm)
t: 1  11793 SOL 37308 HW1  0.927205 (nm)
t: 1  11793 SOL 37309 HW2  0.776699 (nm)
t: 2  125 SOL 2303 OW  0.940527 (nm)

In this

t: 1  136 SOL 2336 OW  0.772373 (nm)

does the 't' states the time frame, 136 SOL states the SOL molecule number
and 2336 OW the residue contact from protein and the 0.772373 nm the
distance between them.

Thanks
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[gmx-users] Re: no output in g_dist

[aiswarya pawar]

Thanks Lina and Justin.

Is this data good for finding the distance of protein and water as function
of time.


On Thu, Sep 8, 2011 at 5:55 PM, aiswarya pawar aiswarya.pa...@gmail.comwrote:

 Hi users,

 To get the distance between water and protein i did -

  g_dist -f md.xtc -s md.tpr -o distance.xvg -dist 1 -b 1 -e 11

 from this i should obtain an output file as distance.xvg which i dont get.

 and my output is printed on the terminal as-

 t: 1  136 SOL 2336 OW  0.772373 (nm)
 t: 1  136 SOL 2337 HW1  0.706358 (nm)
 t: 1  136 SOL 2338 HW2  0.807787 (nm)
 t: 1  139 SOL 2345 OW  0.821094 (nm)
 t: 1  139 SOL 2346 HW1  0.810919 (nm)
 t: 1  139 SOL 2347 HW2  0.771526 (nm)
 t: 1  7237 SOL 23640 HW1  0.997056 (nm)
 t: 1  11793 SOL 37307 OW  0.868929 (nm)
 t: 1  11793 SOL 37308 HW1  0.927205 (nm)
 t: 1  11793 SOL 37309 HW2  0.776699 (nm)
 t: 2  125 SOL 2303 OW  0.940527 (nm)

 In this

 t: 1  136 SOL 2336 OW  0.772373 (nm)

 does the 't' states the time frame, 136 SOL states the SOL molecule number
 and 2336 OW the residue contact from protein and the 0.772373 nm the
 distance between them.

 Thanks


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[gmx-users] No addition of ions

[aiswarya pawar]

Hi Gromacs users,

Am running a MD simulation over a protein complex and before adding the
ions. we run a grompp option then we get result as model net charge as some
integer ie if +2.00. so we got to add 2 CL ions. But when i ran my protein
for grompp it didnt give me any net charge so am not able to add any ions.
is this correct??

Thanks,
Aiswarya
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Re: [gmx-users] Hydrogen existence time

[aiswarya pawar]

Emanuel,


Am trying out the procedure u have mentioned but on the other hand i found
out a article which mentions does the same.

https://extras.csc.fi/chem/courses/gmx2004/exercises/index.html

The article states-

use the g_hbond program to analyse hydrogen bonds. First select protein
twice, to get the intramolecular hydrogen bonds, then select protein and
water to get the protein-water h-bonds. Compare the numbers, and their
fluctuations. Is there a trend in the graphs, or a correlation between them?
You can also compute the residence time of the water molecules on the
different functional groups of the protein., e.g. the Ala sidechain. For
this we will have to make an index file first:

% make_ndx -f after_em_sol  EOF
a OW
q
EOF
% g_hbond -contact -n index -ac -r 0.6 -b 200
In the g_hbond command select Sidechain and OW. The -c option computes the
autocorrelation function of the contact time between Cβ and OW. View the
file hbac.xvg using xmgrace. Use xmgrace to integrate the ACF, this will
give you the correlation time. Is it higher or lower than you expected? Why?

Now do the same analysis for interactions between Carbonyl groups and Amide
groups and water oxygens. For these analyses you should put the distance to
0.35, the largest hydrogen bonding distance. Compare the residence times
with that on the hydrophobic sidechain.


as it mentioned the -contact wouldnt include any H bonds between the groups.
but i didnt understand what does OW states cause already there is an option
for water.
does this procedure be good for an residence time.

-Aiswarya


On Thu, Aug 25, 2011 at 5:18 AM, Mark Abraham mark.abra...@anu.edu.auwrote:

  On 25/08/2011 12:00 AM, aiswarya.pa...@gmail.com wrote:

 Mark,

 The residence time equation goes like this-

 P(r)= function (N(t) - N(t+r))dt

 Where function(x-y) takes the value of 1 when x=y(x not equal to 0 and y not 
 equal to 0) ie the site occupied and when x not equal to y or both x and y 
 =0. N(t) index of water molecule found in the hydration site at time t.


 So that's the autocorrelation of the existence function. Now you need a
 geometric criterion for existence. Note that g_hbond with well-constructed
 groups will calculate the autocorrelation of the existence function for an
 H-bond. See g_hbond -h.

 g_dist, some scripting and g_analyse might be necessary for other criteria.

 Mark


  Aiswarya
 --Original Message--
 From: Mark Abraham
 To: Aiswarya Pawar
 Subject: Re: [gmx-users] Hydrogen existence time
 Sent: 24 Aug 2011 6:09 PM

 On 24/08/2011 10:31 PM, aiswarya.pa...@gmail.com wrote:

  Any idea how can I calculate the residence time of water.

  First, seek define what you mean to calculate. If you can't write an
 equation down for it, you can't calculate it.

 Mark

 Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for it!





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Re: Re: Antw: Re: [gmx-users] Hydrogen existence time

[aiswarya pawar]

Dear Emanuel,

Thank you so much for the pseudo-code, it made me understand the flow.
from your code it shows that, your using distance and angle as an criteria
to select a water molecule in just one one time frame. right?? i didnt get
how to calculate the time of the frame. what programming should be applied
and what for.

Thanks,
Aiswarya

On Thu, Aug 25, 2011 at 1:53 PM, Emanuel Peter 
emanuel.pe...@chemie.uni-regensburg.de wrote:

 Hello Aiswarya,

 Your program should look like this, in pseudo-code:

 pseudo-code:

 do n_frames_of_your_trajectory

 g_mindist -f traj.trr -s .tpr -n (your_protein (first-group) , your_solvent
 (second-group)).ndx -o atm-pair.out -d your-distance-value -b  (one frame of
 your trajectory) -e (the same frame)

 processing the atm-pair.out list and write them into an index file : 1.ndx,
 with each water in one group

 take just these atoms  and residues, which are at your specific distance at
 your 'location'

 do

 measure the angle in relation to your protein for this frame for each
 specified water

 g_angle  -f traj.trr -s .tpr -n 1.ndx  -b (one frame of your trajectory) -e
 (the same frame)

 enddo

 read the angles from the output

 take just the one water with specific angle out of your list.

 (By using g_mindist -d , and g_angle  you specify one specific point in
 relation to your protein)
 (By using -b and -e you specify one specific time)

 save the residue number of this water and your frame

 calculate the time of this frame

 enddo

 now you have an array of residue numbers at this particular location for
 each time

 analyse this array, then you know the maximum frame-time of one
 water-molecule at this specific location.
 You will not get any information about one particular time - just an
 average.
 This must be your residence time.

 Your application needs some little programming.


  ** 24.08.11 18.14 Uhr 
 Emanuel,

 The residence time which am referring is the water molecule residing on the
 particular location at a specific time.

 Am not able to write a correct equation due to some character missing when
 typing from phone.

 Aiswarya

 Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for
 it!
 --
 *From: * aiswarya.pa...@gmail.com
 *Date: *Wed, 24 Aug 2011 16:13:05 +
 *To: *Gromacs mailgmx-users@gromacs.org
 *ReplyTo: * aiswarya.pa...@gmail.com
 *Subject: *Re: Antw: Re: [gmx-users] Hydrogen existence time

 Emanuel,

 The residence time which am referring is the water molecule residing on the
 particular location at a specific time.

 Am not able to write a correct equation due to small character missing when
 typing from phone.

 Aiswarya

 Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for
 it!
 --
 *From: * Emanuel Peter emanuel.pe...@chemie.uni-regensburg.de
 *Date: *Wed, 24 Aug 2011 16:16:37 +0200
 *To: *aiswarya.pa...@gmail.com; gmx-users@gromacs.org
 *Subject: *Antw: Re: [gmx-users] Hydrogen existence time

 As I told you, you can calculate the self-diffusion coefficient by using
 g_msd.
 Following:

 Large diffusion-coeff. -- means : The residence time is low.
 Small diffusion-coeff. -- means : The residence time is large 

 Mean-square-displacement means: Displacement of molecules per time.
 No displacement of molecule at all : if(msd == 0)  means: Infinite
 residence time.
 So I say from my idiotic point of view: msd ~ residence time ( I still do
 not know what you mean with this because
 this is usually related to chemical reactors in engineering and NOT in
 protein simulation )
 In your index-file you can index those molecules, which you need.
 Your equation does not make sense.

  aiswarya.pa...@gmail.com 24.08.11 16.01 Uhr 
 Mark,

 The residence time equation goes like this-

 P(r)= function (N(t) - N(t+r))dt

 Where function(x-y) takes the value of 1 when x=y(x not equal to 0 and y
 not equal to 0) ie the site occupied and when x not equal to y or both x and
 y =0. N(t) index of water molecule found in the hydration site at time t.

 Aiswarya
 --Original Message--
 From: Mark Abraham
 To: Aiswarya Pawar
 Subject: Re: [gmx-users] Hydrogen existence time
 Sent: 24 Aug 2011 6:09 PM

 On 24/08/2011 10:31 PM, aiswarya.pa...@gmail.com wrote:
  Any idea how can I calculate the residence time of water.

 First, seek define what you mean to calculate. If you can't write an
 equation down for it, you can't calculate it.

 Mark

 Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for
 it!**

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[gmx-users] Conversion of gromacs trajectory file

[aiswarya . pawar]

Hello Everyone,

Any idea how one can convert gromacs trajectory file to amber file. So as to 
use the amber tools.

Thank you,
Aiswarya
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Re: [gmx-users] Conversion of gromacs trajectory file

[aiswarya . pawar]

Hi Justin,

Thank for the quick response. I would try out your script for the conversion.

Best,
Aiswarya
--Original Message--
From: Justin A. Lemkul
To: Aiswarya Pawar
To: Discussion list for GROMACS users
ReplyTo: jalem...@vt.edu
Subject: Re: [gmx-users] Conversion of gromacs trajectory file
Sent: 24 Aug 2011 5:35 PM



aiswarya.pa...@gmail.com wrote:
 Hello Everyone,
 
 Any idea how one can convert gromacs trajectory file to amber file. So as to 
 use the amber tools.
 

The key is finding a compatible intermediate that can be converted.  I've found 
that PDB format is pretty universal.  I have a script that does the opposite 
(mdcrd to .xtc) linked from my site:

http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/scripts.html

It's a bit awkward, but does the job.  Perhaps you can reverse-engineer it for 
your purpose.

-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] Hydrogen existence time

[aiswarya . pawar]

Dear all,

Does Hydrogen bond existence in a time frame states the residence time of the 
water molecule?

Thank you,
Aiswarya
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Re: [gmx-users] Hydrogen existence time

[aiswarya . pawar]

Dear Justin,

So what does the hydrogen bond existence state?

Thanks
--Original Message--
From: Justin A. Lemkul
To: Aiswarya Pawar
To: Gromacs mail
ReplyTo: jalem...@vt.edu
Subject: Re: [gmx-users] Hydrogen existence time
Sent: 24 Aug 2011 5:54 PM



aiswarya.pa...@gmail.com wrote:
 Dear all,
 
 Does Hydrogen bond existence in a time frame states the residence time of the 
 water molecule?
 

Not necessarily, no.

-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



Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for it!-- 
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Re: [gmx-users] Hydrogen existence time

[aiswarya . pawar]

Any idea how can I calculate the residence time of water.

Aiswarya
--Original Message--
From: Justin A. Lemkul
To: Aiswarya Pawar
To: Gromacs mail
ReplyTo: jalem...@vt.edu
Subject: Re: [gmx-users] Hydrogen existence time
Sent: 24 Aug 2011 5:58 PM



aiswarya.pa...@gmail.com wrote:
 Dear Justin,
 
 So what does the hydrogen bond existence state?
 

The length of time for which a given hydrogen bond exists (i.e. satisfies the 
geometrical criteria in the context of some particular partner group).

-Justin

 Thanks
 --Original Message--
 From: Justin A. Lemkul
 To: Aiswarya Pawar
 To: Gromacs mail
 ReplyTo: jalem...@vt.edu
 Subject: Re: [gmx-users] Hydrogen existence time
 Sent: 24 Aug 2011 5:54 PM
 
 
 
 aiswarya.pa...@gmail.com wrote:
 Dear all,

 Does Hydrogen bond existence in a time frame states the residence time of 
 the water molecule?

 
 Not necessarily, no.
 
 -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



Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for it!-- 
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Re: Antw: Re: [gmx-users] Hydrogen existence time

[aiswarya . pawar]

Dear Emanuel,

Iam following what you have mentioned earlier. But as you said hydrogen bond 
correlation time gives the average hydrogen bond existence time. So I confused 
understanding whether an H Bond existence time would give me the residence time.

Aiswarya
Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for it!

-Original Message-
From: Emanuel Peter emanuel.pe...@chemie.uni-regensburg.de
Sender: gmx-users-boun...@gromacs.org
Date: Wed, 24 Aug 2011 15:42:11 
To: gmx-users@gromacs.org; jalem...@vt.edu
Reply-To: Discussion list for GROMACS users gmx-users@gromacs.org
Subject: Antw: Re: [gmx-users] Hydrogen existence time

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Re: [gmx-users] Hydrogen existence time

[aiswarya . pawar]

Mark,

The residence time equation goes like this-

P(r)= function (N(t) - N(t+r))dt

Where function(x-y) takes the value of 1 when x=y(x not equal to 0 and y not 
equal to 0) ie the site occupied and when x not equal to y or both x and y =0. 
N(t) index of water molecule found in the hydration site at time t.

Aiswarya
--Original Message--
From: Mark Abraham
To: Aiswarya Pawar
Subject: Re: [gmx-users] Hydrogen existence time
Sent: 24 Aug 2011 6:09 PM

On 24/08/2011 10:31 PM, aiswarya.pa...@gmail.com wrote:
 Any idea how can I calculate the residence time of water.

First, seek define what you mean to calculate. If you can't write an 
equation down for it, you can't calculate it.

Mark

Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for it!-- 
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Re: Antw: Re: [gmx-users] Hydrogen existence time

[aiswarya . pawar]

Emanuel,

The residence time which am referring is the water molecule residing on the 
particular location at a specific time.

Am not able to write a correct equation due to small character missing when 
typing from phone.

Aiswarya
Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for it!

-Original Message-
From: Emanuel Peter emanuel.pe...@chemie.uni-regensburg.de
Date: Wed, 24 Aug 2011 16:16:37 
To: aiswarya.pa...@gmail.com; gmx-users@gromacs.org
Subject: Antw: Re: [gmx-users] Hydrogen existence time

As I told you, you can calculate the self-diffusion coefficient by using g_msd.
Following:

Large diffusion-coeff. -- means : The residence time is low.
Small diffusion-coeff. -- means : The residence time is large 

Mean-square-displacement means: Displacement of molecules per time.
No displacement of molecule at all : if(msd == 0)  means: Infinite residence
time.
So I say from my idiotic point of view: msd ~ residence time ( I still do not
know what you mean with this because
this is usually related to chemical reactors in engineering and NOT in protein
simulation ) 
In your index-file you can index those molecules, which you need.
Your equation does not make sense. 

  24.08.11 16.01 Uhr 
Mark,

The residence time equation goes like this-

P(r)= function (N(t) - N(t+r))dt

Where function(x-y) takes the value of 1 when x=y(x not equal to 0 and y not
equal to 0) ie the site occupied and when x not equal to y or both x and y =0.
N(t) index of water molecule found in the hydration site at time t.

Aiswarya
--Original Message--
From: Mark Abraham
To: Aiswarya Pawar
Subject: Re: [gmx-users] Hydrogen existence time
Sent: 24 Aug 2011 6:09 PM

On 24/08/2011 10:31 PM, aiswarya.pa...@gmail.com wrote:
 Any idea how can I calculate the residence time of water.

First, seek define what you mean to calculate. If you can't write an 
equation down for it, you can't calculate it.

Mark

Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for it!

-- 
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Re: Antw: Re: [gmx-users] Hydrogen existence time

[aiswarya . pawar]

Emanuel,

The residence time which am referring is the water molecule residing on the 
particular location at a specific time.

Am not able to write a correct equation due to some character missing when 
typing from phone.

Aiswarya
Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for it!

-Original Message-
From: aiswarya.pa...@gmail.com
Date: Wed, 24 Aug 2011 16:13:05 
To: Gromacs mailgmx-users@gromacs.org
Reply-To: aiswarya.pa...@gmail.com
Subject: Re: Antw: Re: [gmx-users] Hydrogen existence time

Emanuel,

The residence time which am referring is the water molecule residing on the 
particular location at a specific time.

Am not able to write a correct equation due to small character missing when 
typing from phone.

Aiswarya
Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for it!

-Original Message-
From: Emanuel Peter emanuel.pe...@chemie.uni-regensburg.de
Date: Wed, 24 Aug 2011 16:16:37 
To: aiswarya.pa...@gmail.com; gmx-users@gromacs.org
Subject: Antw: Re: [gmx-users] Hydrogen existence time

As I told you, you can calculate the self-diffusion coefficient by using g_msd.
Following:

Large diffusion-coeff. -- means : The residence time is low.
Small diffusion-coeff. -- means : The residence time is large 

Mean-square-displacement means: Displacement of molecules per time.
No displacement of molecule at all : if(msd == 0)  means: Infinite residence
time.
So I say from my idiotic point of view: msd ~ residence time ( I still do not
know what you mean with this because
this is usually related to chemical reactors in engineering and NOT in protein
simulation ) 
In your index-file you can index those molecules, which you need.
Your equation does not make sense. 

  24.08.11 16.01 Uhr 
Mark,

The residence time equation goes like this-

P(r)= function (N(t) - N(t+r))dt

Where function(x-y) takes the value of 1 when x=y(x not equal to 0 and y not
equal to 0) ie the site occupied and when x not equal to y or both x and y =0.
N(t) index of water molecule found in the hydration site at time t.

Aiswarya
--Original Message--
From: Mark Abraham
To: Aiswarya Pawar
Subject: Re: [gmx-users] Hydrogen existence time
Sent: 24 Aug 2011 6:09 PM

On 24/08/2011 10:31 PM, aiswarya.pa...@gmail.com wrote:
 Any idea how can I calculate the residence time of water.

First, seek define what you mean to calculate. If you can't write an 
equation down for it, you can't calculate it.

Mark

Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for it!

-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
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Re: Antw: Re: [gmx-users] calculate residence time for a protein complex

[aiswarya . pawar]

Mark,

Sorry for the trouble. 

Aiswarya
Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for it!

-Original Message-
From: Emanuel Peter emanuel.pe...@chemie.uni-regensburg.de
Sender: gmx-users-boun...@gromacs.org
Date: Mon, 22 Aug 2011 12:36:02 
To: gmx-users@gromacs.org
Reply-To: Discussion list for GROMACS users gmx-users@gromacs.org
Subject: Antw: Re: [gmx-users] calculate residence time for a protein complex

-- 
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Re: Antw: Re: [gmx-users] calculate residence time for a protein complex

[aiswarya . pawar]

Dear Emanuel,
Thank you so much for the response.

I did the H bond count using the g_hbond. After this these H bond are 
correlated against time right?? I just want to make sure I got it right. And 
more over I should give a distance constrain so as to give me the existence of 
water at a time. 

I just want to be more clear on the correlation function of H bonding.

Thank you,
Aiswarya

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-Original Message-
From: Emanuel Peter emanuel.pe...@chemie.uni-regensburg.de
Sender: gmx-users-boun...@gromacs.org
Date: Mon, 22 Aug 2011 12:36:02 
To: gmx-users@gromacs.org
Reply-To: Discussion list for GROMACS users gmx-users@gromacs.org
Subject: Antw: Re: [gmx-users] calculate residence time for a protein complex

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[gmx-users] calculate residence time for a protein complex

[aiswarya pawar]

Hi,

I have simulated a protein complex and now i would like to know the residing
water molecules between the protein complex. g_hbond and trjorder helps in
giving the number of hydrogen bonds and distance. but is this the residence
time calculation. please help me with this. there few posts given in the
archives regarding the residence time which is not very clear to me. but
will the residence time calculation same for single protein and complex

Thank you,
Aiswarya
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[gmx-users] calculate residence time for a protein complex

[aiswarya pawar]

Hi,

I have simulated a protein complex and now i would like to know the residing
water molecules between the protein complex. g_hbond and trjorder helps in
giving the number of hydrogen bonds and distance. but is this the residence
time calculation. please help me with this. there few posts given in the
archives regarding the residence time which is not very clear to me. but
will the residence time calculation same for single protein and complex

Thank you,
Aiswarya
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
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