date:20120816


On 16/08/2012 4:26 PM, jesmin jahan wrote:

Hi Mark,

Thanks for your previous reply.
I tried to run single point energy simulation with some proteins.
I got .log files with content like this:

Energies (kJ/mol)
Bond  AngleProper Dih.  Improper Dih.GB Polarization
 1.54109e+043.84351e+038.47152e+033.58425e+02   -1.69666e+04
   LJ-14 Coulomb-14LJ (SR)   Coulomb (SR)  Potential
 4.29664e+033.63997e+042.22900e+05   -5.18818e+042.22832e+05
 Kinetic En.   Total EnergyTemperature Pressure (bar)
 1.08443e+091.08465e+092.73602e+070.0e+00
...

Computing:   M-Number M-Flops  % Flops
-
  Generalized Born Coulomb 0.005711   0.274 0.2
  GB Coulomb + LJ  0.416308  25.39518.5
  Outer nonbonded loop 0.016367   0.164 0.1
  1,4 nonbonded interactions   0.008410   0.757 0.6
  Born radii (HCT/OBC) 0.439486  80.42658.5
  Born force chain rule0.439486   6.592 4.8
  NS-Pairs 0.943653  19.81714.4
  Reset In Box 0.003179   0.010 0.0
  CG-CoM   0.006358   0.019 0.0
  Bonds0.003219   0.190 0.1
  Angles   0.005838   0.981 0.7
  Propers  0.011273   2.582 1.9
  Virial   0.003899   0.070 0.1
  Stop-CM  0.003179   0.032 0.0
  Calc-Ekin0.006358   0.172 0.1
-
  Total 137.479   100.0
-


 D O M A I N   D E C O M P O S I T I O N   S T A T I S T I C S

  av. #atoms communicated per step for force:  2 x 6859.0


  R E A L   C Y C L E   A N D   T I M E   A C C O U N T I N G

  Computing: Nodes Number G-CyclesSeconds %
---
  Domain decomp.16  10.0430.0 1.4
  Comm. coord.  16  10.0030.0 0.1
  Neighbor search   16  10.1030.0 3.5
  Force 16  11.5300.551.5
  Wait + Comm. F16  10.2640.1 8.9
  Write traj.   16  10.0620.0 2.1
  Update16  10.0010.0 0.0
  Comm. energies16  20.9330.331.4
  Rest  16   0.0310.0 1.1
---
  Total 16   2.9700.9   100.0
---

NOTE: 31 % of the run time was spent communicating energies,
   you might want to use the -gcom option of mdrun


Parallel run - timing based on wallclock.

NODE (s)   Real (s)  (%)
Time:  0.056  0.056100.0
(Mnbf/s)   (GFlops)   (ns/day)  (hour/ns)
Performance:  7.497  2.442  1.535 15.637


From the log file, it seems, the time includes the time for LJ and
Columb Potential Energy. But as I said before, I am only interested to
GB-energy times. I am doing a comparative study of GB-energy
performance (values vs time) for different molecular dynamic packages.


Since the LJ calculation also needs the distances, GROMACS does them in 
the same loops and makes no apology for being efficient. :-) If you're 
really trying to measure the time for the GB energy in isolation, then 
you will need to construct a different model physics that lacks LJ 
interactions. Or perhaps you don't really want to measure the time for 
GB energy in isolation. Depends what you're planning on using the 
information for, but usually measuring a time representative of the 
calculation you plan to run later is a good way to avoid having to 
account for lots of subtleties of different packages.



That's why I was trying to deduct the time for any other extra energy
computation time from it.

Can anyone tell me how to get the exact time of GB-polarization energy
(including Born radii) and excluding the times for any other
additional energy (like LJ and Columb etc) from gromacs simutation?


The .tpr you use for the rerun doesn't have to be one that will produce

Re: [gmx-users] Questions regarding Polarization Energy Calculation

2012-08-16 Thread jesmin jahan

Hi Mark,

Thanks for your reply.
If I open the .tpr file using notepad, it seems to be a binary file.
Then, how to remove the  the bonded terms and zero the VDW parameters?

I really need to compare how fast different well known package can
compute GB-polarization energy and how good the energy values are?
That's why time is an important factor me my experiments and I  really
want to measure the time for GB energy in isolation !

Thanks,
Jesmin

 On Thu, Aug 16, 2012 at 2:44 AM, Mark Abraham mark.abra...@anu.edu.au wrote:

 On 16/08/2012 4:26 PM, jesmin jahan wrote:

 Hi Mark,

 Thanks for your previous reply.
 I tried to run single point energy simulation with some proteins.
 I got .log files with content like this:

 Energies (kJ/mol)
 Bond  AngleProper Dih.  Improper Dih.GB Polarization
  1.54109e+043.84351e+038.47152e+033.58425e+02   -1.69666e+04
LJ-14 Coulomb-14LJ (SR)   Coulomb (SR)  Potential
  4.29664e+033.63997e+042.22900e+05   -5.18818e+042.22832e+05
  Kinetic En.   Total EnergyTemperature Pressure (bar)
  1.08443e+091.08465e+092.73602e+070.0e+00
 ...

 Computing:   M-Number M-Flops  % Flops
 -
   Generalized Born Coulomb 0.005711   0.274 0.2
   GB Coulomb + LJ  0.416308  25.39518.5
   Outer nonbonded loop 0.016367   0.164 0.1
   1,4 nonbonded interactions   0.008410   0.757 0.6
   Born radii (HCT/OBC) 0.439486  80.42658.5
   Born force chain rule0.439486   6.592 4.8
   NS-Pairs 0.943653  19.81714.4
   Reset In Box 0.003179   0.010 0.0
   CG-CoM   0.006358   0.019 0.0
   Bonds0.003219   0.190 0.1
   Angles   0.005838   0.981 0.7
   Propers  0.011273   2.582 1.9
   Virial   0.003899   0.070 0.1
   Stop-CM  0.003179   0.032 0.0
   Calc-Ekin0.006358   0.172 0.1
 -
   Total 137.479   100.0
 -


  D O M A I N   D E C O M P O S I T I O N   S T A T I S T I C S

   av. #atoms communicated per step for force:  2 x 6859.0


   R E A L   C Y C L E   A N D   T I M E   A C C O U N T I N G

   Computing: Nodes Number G-CyclesSeconds %
 ---
   Domain decomp.16  10.0430.0 1.4
   Comm. coord.  16  10.0030.0 0.1
   Neighbor search   16  10.1030.0 3.5
   Force 16  11.5300.551.5
   Wait + Comm. F16  10.2640.1 8.9
   Write traj.   16  10.0620.0 2.1
   Update16  10.0010.0 0.0
   Comm. energies16  20.9330.331.4
   Rest  16   0.0310.0 1.1
 ---
   Total 16   2.9700.9   100.0
 ---

 NOTE: 31 % of the run time was spent communicating energies,
you might want to use the -gcom option of mdrun


 Parallel run - timing based on wallclock.

 NODE (s)   Real (s)  (%)
 Time:  0.056  0.056100.0
 (Mnbf/s)   (GFlops)   (ns/day)  (hour/ns)
 Performance:  7.497  2.442  1.535 15.637


 From the log file, it seems, the time includes the time for LJ and
 Columb Potential Energy. But as I said before, I am only interested to
 GB-energy times. I am doing a comparative study of GB-energy
 performance (values vs time) for different molecular dynamic packages.


 Since the LJ calculation also needs the distances, GROMACS does them in the 
 same loops and makes no apology for being efficient. :-) If you're really 
 trying to measure the time for the GB energy in isolation, then you will 
 need to construct a different model physics that lacks LJ interactions. Or 
 perhaps you don't really want to measure the time for GB energy in 
 isolation. Depends what

Re: [gmx-users] Questions regarding Polarization Energy Calculation


On 16/08/2012 5:08 PM, jesmin jahan wrote:

Hi Mark,

Thanks for your reply.
If I open the .tpr file using notepad, it seems to be a binary file.
Then, how to remove the  the bonded terms and zero the VDW parameters?


In the .top file from which you made the .tpr. (And contributing .itp 
files) Parts of chapter 5 may help with this process.


Mark



I really need to compare how fast different well known package can
compute GB-polarization energy and how good the energy values are?
That's why time is an important factor me my experiments and I  really
want to measure the time for GB energy in isolation !

Thanks,
Jesmin

On Thu, Aug 16, 2012 at 2:44 AM, Mark Abraham mark.abra...@anu.edu.au wrote:

On 16/08/2012 4:26 PM, jesmin jahan wrote:

Hi Mark,

Thanks for your previous reply.
I tried to run single point energy simulation with some proteins.
I got .log files with content like this:

Energies (kJ/mol)
 Bond  AngleProper Dih.  Improper Dih.GB Polarization
  1.54109e+043.84351e+038.47152e+033.58425e+02   -1.69666e+04
LJ-14 Coulomb-14LJ (SR)   Coulomb (SR)  Potential
  4.29664e+033.63997e+042.22900e+05   -5.18818e+042.22832e+05
  Kinetic En.   Total EnergyTemperature Pressure (bar)
  1.08443e+091.08465e+092.73602e+070.0e+00
...

Computing:   M-Number M-Flops  % Flops
-
   Generalized Born Coulomb 0.005711   0.274 0.2
   GB Coulomb + LJ  0.416308  25.39518.5
   Outer nonbonded loop 0.016367   0.164 0.1
   1,4 nonbonded interactions   0.008410   0.757 0.6
   Born radii (HCT/OBC) 0.439486  80.42658.5
   Born force chain rule0.439486   6.592 4.8
   NS-Pairs 0.943653  19.81714.4
   Reset In Box 0.003179   0.010 0.0
   CG-CoM   0.006358   0.019 0.0
   Bonds0.003219   0.190 0.1
   Angles   0.005838   0.981 0.7
   Propers  0.011273   2.582 1.9
   Virial   0.003899   0.070 0.1
   Stop-CM  0.003179   0.032 0.0
   Calc-Ekin0.006358   0.172 0.1
-
   Total 137.479   100.0
-


  D O M A I N   D E C O M P O S I T I O N   S T A T I S T I C S

   av. #atoms communicated per step for force:  2 x 6859.0


   R E A L   C Y C L E   A N D   T I M E   A C C O U N T I N G

   Computing: Nodes Number G-CyclesSeconds %
---
   Domain decomp.16  10.0430.0 1.4
   Comm. coord.  16  10.0030.0 0.1
   Neighbor search   16  10.1030.0 3.5
   Force 16  11.5300.551.5
   Wait + Comm. F16  10.2640.1 8.9
   Write traj.   16  10.0620.0 2.1
   Update16  10.0010.0 0.0
   Comm. energies16  20.9330.331.4
   Rest  16   0.0310.0 1.1
---
   Total 16   2.9700.9   100.0
---

NOTE: 31 % of the run time was spent communicating energies,
you might want to use the -gcom option of mdrun


 Parallel run - timing based on wallclock.

 NODE (s)   Real (s)  (%)
 Time:  0.056  0.056100.0
 (Mnbf/s)   (GFlops)   (ns/day)  (hour/ns)
Performance:  7.497  2.442  1.535 15.637


From the log file, it seems, the time includes the time for LJ and
Columb Potential Energy. But as I said before, I am only interested to
GB-energy times. I am doing a comparative study of GB-energy
performance (values vs time) for different molecular dynamic packages.


Since the LJ calculation also needs the distances, GROMACS does them in the 
same loops and makes no apology for being efficient. :-) If you're really 
trying to measure the time for the GB energy in isolation, then you will need 
to

Re: [gmx-users] CHARMM36 - Smaller Area per lipid for POPE - Why?

2012-08-16 Thread Felipe Pineda, PhD


Hi Sébastian,

I think the magic word in this issue would be surface tension and the 
proper ensemble for the simulation NPgammaT. This is very well discussed 
in the paper I advised to you a couple of days ago. The issue is by no 
means trivial, although I'm not an expert to judge it. You can find an 
imho very well-founded theoretical discussion in, e.g., Lindahl, E. and 
Edholm, O. Spatial and energetic-entropic decomposition of surface 
tension in lipid bilayers from molecular dynamics simulations. J. Chem. 
Phys.(2000)113, 3882.


Good luck!

Felipe

On 08/15/2012 08:23 PM, Sebastien Cote wrote:

Thanks for the advices Chris.

My peptide is known to be more favorably to PE than PC membrane that is why I 
am using POPE.

Experimentally, the liquid phase transition is at 298K for POPE (if I am not 
mistaken). Is your 323K refer to some simulations?

At first I wanted to use the new CHARMM36 lipids parameters because they are 
supposed to solve the previous CHARMM27 issue with the area per lipid. However, 
I am consistently obtained smaller APL then experiment and I am not able to 
reproduce the published APL obtained for POPE, even if I am starting from their 
equilibrated 80-POPE membrane and use same simulation conditions. That was the 
reason for starting this thread on the mailing list.

Unfortunately, my peptide conformational space in solution is only 
well-represented by CHARMM27 (equivalently in CHARMM36), so I can not use 
Berger's lipid parameters with OPLS or GROMOS even if it would be preferable as 
they do not have APL inconsistency and are united-atom.

I will made some tests in the NPAT ensemble. Perhaps the NPAT effects can be 
made neglegible by using bigger membrane compared to my peptide's size (?).

Sebastien



From: chris.ne...@mail.utoronto.ca
To: gmx-users@gromacs.org
Date: Wed, 15 Aug 2012 17:29:29 +
Subject: [gmx-users] CHARMM36 - Smaller Area per lipid for POPE - Why?

The area per lipid (APL) will certainly affect the free energy of 
peptide/protein binding to a lipid bilayer.
I have not used charmm lipids extensively, but from what I understand they 
older charmm lipids required
NPAT to get the correct APL. The newer charmm lipids were supposed to solve 
that problem, but I have heard
it said that, though the problem has been alleviated to some extend, it still 
remains.

If I were you, I'd use POPC in place of POPE. POPE is notorious for giving 
too-small APL's in simulations and I think
it even requires temperatures of 323 K to enter the liquid phase.

That said, I don't have a specific answer to your question of whether there are 
other affects of NPAT vs. NPT.
It is plausible that NPAT-based fluctuations could affect the pathway or the 
kinetics.

PS: I was not referring to lipid rafts, but the separate diffusion of the upper 
and lower leaflets. Once the peptide is
fully inserted, if it spans both leaflets, this will tend to reduce this 
leaflet-specific diffusion and would represent an
entropic penalty for binding (not sure how large).

Chris.


Dear Peter,

I also used h-bonds and I also switch LJ interaction from 0.8 nm to 1.2 nm (as 
in Klauda's paper). I will retry with a more solvated membrane.

Would you have any thought on how the NPAT ensemble might affect 
peptide-membrane interactions like I am studying i.e. peptide is totally 
solvated, then adsorb, and finally may insert? The paper on peptide-membrane 
interaction like this usually use united-atom lipid in the NPT ensemble. Most 
of the work I have seen on Charmm membrane in the NPAT ensemble were for 
embedded membrane protein.

Sorry, but I only have experience with large pre-embedded membrane proteins,
and those are governed both by signal sequences and post-translational
modification.

Chris's last email on the subject might lead to the hypothesis that lipid
raft translation as the leaflets slide past one another could be a
contributing factor to adsorbption of your species.


Thanks,

Sebastien

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+---+
| Luis Felipe Pineda De Castro, PhD

[gmx-users] RE: RE: RE: Doubts over g_lie usage

2012-08-16 Thread J Peterson

Thank you so much for your time and explanation.

I am recalculating the energy co-ordinates and using it in g_lie
calculations.

I have read the manual and changed the .mdp file I am using. The following
is the mdp file, please check for the correctness. The text in bold font are
newly included after your suggestions. Can I use this mdp to calculate the
LIE correctly?

cpp =  /usr/bin/cpp
constraints =  all-bonds
integrator  =  md
dt  =  0.002; ps !
nsteps  =  500  ; total 1 ps.
nstcomm =  1
nstxout =  5000
nstvout =  5000
nstfout =  0
nstlog  =  5000
nstenergy   =  500
nstxtcout   =  500
nstlist =  10
ns_type =  grid
rlist   =  1.2  ; short-range neighborlist cutoff
(in nm)
rcoulomb=  0.9  ; short-range electrostatic cutoff
(in nm)
vdwtype =  cut-off
rvdw=  1.4  ; gromos96 force field/ short-range
van der Waals cutoff (in nm)
;coulombtype =  PME ; Particle Mesh Ewald for long-range
electrostatics
;fourierspacing  =  0.12; grid spacing for FFT
;fourier_nx  =  0
;fourier_ny  =  0
;fourier_nz  =  0
;pme_order   =  4
;ewald_rtol  =  1e-5
*coulombtype  =  Reaction-Field-zero
epsilon_rf   =  0*
optimize_fft=  yes
pbc =  xyz
; modified Berendsen temperature coupling is on in two groups
Tcoupl  =  V-rescale; modified Berendsen thermostat
tc-grps =  S04   SOL
tau_t   =  0.1   0.1
ref_t   =  300   300
; Energy monitoring
energygrps  =  S04  SOL

; Mode for center of mass motion removal
comm-mode   =  Linear
; Groups for center of mass motion removal
comm-grps   =  System

; Pressure coupling is now 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=  173529

~

Thanks

Peterson J



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Re: [gmx-users] Ordering of hydrogen bonds in -hbn and -hbm output in g_hbond

2012-08-16 Thread Erik Marklund

I think the confusion arises form 
15 aug 2012 kl. 22.53 skrev Justin Lemkul:

 
 
 On 8/15/12 4:49 PM, Andrew DeYoung wrote:
 Hi,
 
 I am a novice user of g_hbond (actually, I am using double precision --
 g_hbond_d -- but I think all of the parameters should be the same).
 
 I would like to use the output of the -hbn switch (which generates
 hbond.ndx) in tandem with the -hbm switch (which generates an existence
 matrix hbmap.xpm) to determine, using my own script, which hydrogen bonds
 exist at each timestep in my trajectory.  My question is, how does the order
 of entries in the [ hbonds ] section in hbond.ndx relate to the order of
 entries in hbmap.xpm?
 
 I am running Gromacs 4.5.5.  The man page for g_hbond_d clearly states:
 
 -hbm:  existence matrix for all hydrogen bonds over all frames... .
 Ordering is identical to that in -hbn index file.
 
 However, I did a test of a system with two hydrogen bonds (which exist at
 different times), and it seems (although I am not at all certain) that the
 opposite is actually true.
 
 My hbond.ndx file contains the following section at the end of the file:
 
 [ hbonds ]
 457458587
 457458737
 
 And my hbmap.xpm file indeed contains two entries (following the enumeration
 of x-axis values/times):
 
 ooo  oo  ooo
 oo   o  ooo
 oo o ooo  oo  o    o
 oo,
 
 o o   
 
 which tells me that one of the hydrogen bonds exists for a very large
 fraction of the trajectory, whereas the other exists for only two timesteps
 during the trajectory.
 
 I visualized the system in VMD.  I clearly see that the hydrogen bond 457
 458 737 (i.e., the _first_ entry in the [ hbonds ] section of the index
 file) is the one that exists for the vast majority of the trajectory.
 Conversely, the hydrogen bond 457 458 587 is clearly the one that exists for
 only two timesteps in the trajectory.
 
 Based on this, it seems that the top-to-bottom order of hbmap.xpm is
 actually _opposite_ that of the [ hbonds ] section in hbond.ndx.
 
 Has anyone else tested this?  If so, what conclusion did you reach about the
 ordering in the -hbn and -hbm output files.  Or do you see a mistake in my
 reasoning above?
 
 One assumption I have made in my above reasoning is that o means the
 hydrogen bond exists, whereas   means the hydrogen bond does NOT exist.
 I am not 100% sure that this is correct, but plotting the matrix as an EPS
 file using xpm2ps seems to say that I am correct.
 
 
 Your interpretation of the contents is correct.  The first entry in 
 hbonds.ndx is also the first entry in the .xpm file, which is the last line 
 (index zero, hence the first entry).  I have a script that calculates 
 hydrogen bond existence time (plot_hbmapl.pl) from these two files if you 
 want to confirm your outcome.
 
 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/scripts.html
 
 -Justin
 
 -- 
 
 
 Justin A. Lemkul, Ph.D.
 Research Scientist
 Department of Biochemistry
 Virginia Tech
 Blacksburg, VA
 jalemkul[at]vt.edu | (540) 231-9080
 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
 
 
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---
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Husargatan 3, Box 596,75124 Uppsala, Sweden
phone:+46 18 471 6688fax: +46 18 511 755
er...@xray.bmc.uu.se
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Re: [gmx-users] Ordering of hydrogen bonds in -hbn and -hbm output in g_hbond

2012-08-16 Thread Erik Marklund

Hi,

I think the confusion arises from how the xpm data is displayed. If you have 
the hb-index on the y-axis in a plot with the positive y-direction pointing 
upwards (as in most plots), then the first line in the xpm file is actually 
displayed at the bottom. For matrices, however, the indexing starts from the 
top, not the bottom.

Perhaps we should aim at making this more clear in the program output. It's 
confusing and a reoccurring topic on the user list.

Erik
 
15 aug 2012 kl. 22.53 skrev Justin Lemkul:

 
 
 On 8/15/12 4:49 PM, Andrew DeYoung wrote:
 Hi,
 
 I am a novice user of g_hbond (actually, I am using double precision --
 g_hbond_d -- but I think all of the parameters should be the same).
 
 I would like to use the output of the -hbn switch (which generates
 hbond.ndx) in tandem with the -hbm switch (which generates an existence
 matrix hbmap.xpm) to determine, using my own script, which hydrogen bonds
 exist at each timestep in my trajectory.  My question is, how does the order
 of entries in the [ hbonds ] section in hbond.ndx relate to the order of
 entries in hbmap.xpm?
 
 I am running Gromacs 4.5.5.  The man page for g_hbond_d clearly states:
 
 -hbm:  existence matrix for all hydrogen bonds over all frames... .
 Ordering is identical to that in -hbn index file.
 
 However, I did a test of a system with two hydrogen bonds (which exist at
 different times), and it seems (although I am not at all certain) that the
 opposite is actually true.
 
 My hbond.ndx file contains the following section at the end of the file:
 
 [ hbonds ]
 457458587
 457458737
 
 And my hbmap.xpm file indeed contains two entries (following the enumeration
 of x-axis values/times):
 
 ooo  oo  ooo
 oo   o  ooo
 oo o ooo  oo  o    o
 oo,
 
 o o   
 
 which tells me that one of the hydrogen bonds exists for a very large
 fraction of the trajectory, whereas the other exists for only two timesteps
 during the trajectory.
 
 I visualized the system in VMD.  I clearly see that the hydrogen bond 457
 458 737 (i.e., the _first_ entry in the [ hbonds ] section of the index
 file) is the one that exists for the vast majority of the trajectory.
 Conversely, the hydrogen bond 457 458 587 is clearly the one that exists for
 only two timesteps in the trajectory.
 
 Based on this, it seems that the top-to-bottom order of hbmap.xpm is
 actually _opposite_ that of the [ hbonds ] section in hbond.ndx.
 
 Has anyone else tested this?  If so, what conclusion did you reach about the
 ordering in the -hbn and -hbm output files.  Or do you see a mistake in my
 reasoning above?
 
 One assumption I have made in my above reasoning is that o means the
 hydrogen bond exists, whereas   means the hydrogen bond does NOT exist.
 I am not 100% sure that this is correct, but plotting the matrix as an EPS
 file using xpm2ps seems to say that I am correct.
 
 
 Your interpretation of the contents is correct.  The first entry in 
 hbonds.ndx is also the first entry in the .xpm file, which is the last line 
 (index zero, hence the first entry).  I have a script that calculates 
 hydrogen bond existence time (plot_hbmapl.pl) from these two files if you 
 want to confirm your outcome.
 
 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/scripts.html
 
 -Justin
 
 -- 
 
 
 Justin A. Lemkul, Ph.D.
 Research Scientist
 Department of Biochemistry
 Virginia Tech
 Blacksburg, VA
 jalemkul[at]vt.edu | (540) 231-9080
 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
 
 
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Re: [gmx-users] box vectors - regd

2012-08-16 Thread ramesh cheerla

Dear Mark,

Once again I am very thankful to you for your reply, I
have  extracted box vectors from .XTC file  by using  g_traj with  -ob
 option with this I was able to get only six vector components viz  XX
YY ZZ  YX  ZX  and ZY only how about remaining three vector components
XY XZ and  YZ .
I have used triclinic box for my simulations I know that XY XZ and YZ
will be zero, moreover  I have used  pcoupltype  = anisotropic 
with compressibility values as compressibility = 4.5e-5  4.5e-5
4.5e-5  0.0  0.0  0.0  in my .mdp file.
Here my question is why I am not getting XY XZ and  YZ components in
my output file though they might be zero. Is this because of above
specified .mdp options  or something else ?
Can you please let me know what might be the probable reason ?

Thank you in advance.


On Thu, Aug 16, 2012 at 11:17 AM, Mark Abraham mark.abra...@anu.edu.au wrote:
 On 16/08/2012 3:22 PM, ramesh cheerla wrote:

 Dear Mark,

   Thank you for your reply, as you suggested I will go
 through the sec 7.4 and 8 of the manual and moreover how would I get
 exact box vectors XX YY ZZ XY XZ  YX YZ  ZX ZY  for each frame of
 trajectory in gromacs


 They're in the trajectory file with each frame.


 As I am new to gromacs I have no Idea where these will be stored (
 other than gro file ). In NAMD  .XTC file contains box vectors for
 each step of the simulation like this is there any file in gromacs
 that stores these box vectors for each step,


 Same.


   if so how can i extract
 them.


 Probably however you did so with NAMD, or with g_traj or gmxdump.

 Mark



 Please suggest me a way.

 Thank you.

 On Thu, Aug 16, 2012 at 4:52 AM, Mark Abraham mark.abra...@anu.edu.au
 wrote:

 On 16/08/2012 5:46 AM, ramesh cheerla wrote:

 Dear Gromacs users,

I am using gromacs for simulations of a polymer,  for that  I
 am planing to see how  lattice parameters a , b  c are varying
 during simulation. Here lattice parameter a is the length of unit
 cell  along X- direction, b is the length of the unit cell along
 Y axis and c  is along Z -axis.
 For my polymer polymer chains are not exactly oriented  along Z-
 direction they are  a little bit tilted from the Z- axis.  a and b
 are  along x and Y  directions respectively so that I can get
 lattice parameters a and b just by dividing box lengths along
 those directions with the number of  unit cells in those directions.
 As the c- direction and Z- direction are not exactly same ( c is a
 little bit tilted from Z ) in this case I shouldn't divide the box
 length along Z - direction with the number of unit cells in that
 direction to get lattice parameter c. Here my questions are:
 1) How can I calculate exact  C lattice parameter from simulation
 data ? is there any way to get appropriate c?
 2) How one can get box vectors XX YY ZZ XY XZ YX YZ ZX and  ZY  for
 total trajectory, as g_energy is giving only Box - X , Box-Y  and Box-
 Z but i need exact box vectors for valid lattice parameters
 calculations.


 Sounds like g_energy is reminding you that you had a rectilinear
 simulation
 cell when you started, and still do. There are various ways to measure
 angles that will help you address your problem, if you check out manual
 sections 7.4 and 8.

 Mark
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[gmx-users] About Number of Components of eigen Vector

2012-08-16 Thread vidhya sankar

Dear justin Thank you for your gem of Reply  


I am doing ED. With respect to my all  900 C-alpha atoms

So I have used the output of g_covar namely eigvec.trr  as input to g_anaeig_d  
as follows


g_anaeig_d  -v eigenvec.trr -comp eig1.xvg -first 1 -last 3 -xvg none

I have obtained eig1.xvg  i am using First  three  eigen Vector My Doubt is Are 
these three  Eigen vector is divided in to three Components or Four components 

because  My  eig.xvg contains four segment for Each vector , Each segment  
ending with  symbol follows 

@ xaxis ticklabel start type spec
@ xaxis ticklabel start -0
@ yaxis tick major 0.1
@ yaxis tick minor 0.05
@ yaxis ticklabel start type spec
@ yaxis ticklabel start -0.1
@ zeroxaxis bar on
@ zeroxaxis bar linestyle 3
   1.    0.03973
    2.    0.03619

    .
   .
   
   1.   -0.03491
    2.   -0.03068

    .
    .
   .
  
1.   -0.01246
.
.

1.   -0.01428
.
.

Thanks In Advance
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[gmx-users] RMSF error when fitting to average structure

Dear all,

I have a 70 ns trajectory for which the last 60 ns appears to be
equilibrated.  I'm attempting to create a plot of RMSF but I want to align
it to the equilibrated structure, not the starting structure.  I first ran
g_rmsf using the starting structure as the reference structure over only the
last 60 ns and output the average structure (with B-factor column) using the
-ox flag.  I would now like to use this average, equilibrium structure as
the reference structure for fitting the entire trajectory.  

When I try and use this average structure as a reference structure with the
-s flag, I get the following error:

WARNING: if there are broken molecules in the trajectory file,
 they can not be made whole without a run input file 

I'm not sure if the broken molecule it's referring to is the average
structure, which I presume could be broken due to the unnatural bond
lengths and angles resulting from averaging or if there's a problem trying
to use a pdb file (which is the only -ox output file option) instead of a
.tpr file, which is the format of the original starting structure, which
worked.

Does anyone have a suggestion as to how to obtain this rmsf plot?

Thank you,
Tom



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[gmx-users] simmulated annealing excess temperature........................

2012-08-16 Thread tarak karmakar

Dear All,

In my simulation I want the temperature of the system to be reached at
300 K only after 3 ps. But after 3ps I see temperature became 402 K.
So am I doing any mistake in the '.mdp' file given below?

define= -DFLEXIBLE
constraints= h-bonds
integrator  = sd
dt= 0.001  ; 1fs
nsteps   = 3000   ; 3ps
nstcomm   = 1
nstxout  = 1000   ; frequency to write coordinates
to output trajectory
nstvout  = 0  ; frequency to write velocities
to output trajectory; the last velocities are always written
nstfout   = 0  ; frequency to write forces to
output trajectory
nstlog= 10 ; frequency to write energies to log file
nstenergy = 100 ; frequency to write energies to edr file
nstcalcenergy  = 100
vdwtype= cut-off
coulombtype= cut-off
pbc= no
table-extension   = 20.0
nstlist= 100
ns_type= grid
rlist= 1.0

rcoulomb   = 1.2
rvdw   = 1.2

comm-mode  = angular
comm-grps= system
optimize_fft= yes

;heating
annealing  = single
annealing_npoints  = 2
annealing_time   = 0 3
annealing_temp  = 0 300

ld_seed = 8072012

;temperature coupling is on
Tcoupl = berendsen
tau_t = 0.01
tc_grps = system
ref_t = 0

;Pressure coupling is off
Pcoupl = no

; Generate velocites is on
gen_vel = yes
gen_temp = 0
gen_seed = 8042012



Thanks,
-- 
Tarak
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Re: [gmx-users] RMSF error when fitting to average structure




On 8/16/12 10:13 AM, tdgrant1 wrote:

Dear all,

I have a 70 ns trajectory for which the last 60 ns appears to be
equilibrated.  I'm attempting to create a plot of RMSF but I want to align
it to the equilibrated structure, not the starting structure.  I first ran
g_rmsf using the starting structure as the reference structure over only the
last 60 ns and output the average structure (with B-factor column) using the
-ox flag.  I would now like to use this average, equilibrium structure as
the reference structure for fitting the entire trajectory.

When I try and use this average structure as a reference structure with the
-s flag, I get the following error:

WARNING: if there are broken molecules in the trajectory file,
  they can not be made whole without a run input file

I'm not sure if the broken molecule it's referring to is the average
structure, which I presume could be broken due to the unnatural bond
lengths and angles resulting from averaging or if there's a problem trying
to use a pdb file (which is the only -ox output file option) instead of a
.tpr file, which is the format of the original starting structure, which
worked.

Does anyone have a suggestion as to how to obtain this rmsf plot?



The warning about broken molecules relates to the trajectory (as stated in the 
message), so periodicity effects are not accounted for if you are not using a 
.tpr file.  Thus you could get erroneous results unless you have already 
corrected for PBC effects using trjconv before running g_rmsf.


-Justin

--


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


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Re: [gmx-users] simmulated annealing excess temperature........................




On 8/16/12 12:57 PM, tarak karmakar wrote:

Dear All,

In my simulation I want the temperature of the system to be reached at
300 K only after 3 ps. But after 3ps I see temperature became 402 K.
So am I doing any mistake in the '.mdp' file given below?



You have a few.

1. You should not run MD with flexible water.
2. Finite cutoffs lead to rounding errors and accumulation of heat.  This is 
most likely the source of your problem.  I seem to recall Mark (or maybe someone 
else) already told you about this point.


-Justin


define= -DFLEXIBLE
constraints= h-bonds
integrator  = sd
dt= 0.001  ; 1fs
nsteps   = 3000   ; 3ps
nstcomm   = 1
nstxout  = 1000   ; frequency to write coordinates
to output trajectory
nstvout  = 0  ; frequency to write velocities
to output trajectory; the last velocities are always written
nstfout   = 0  ; frequency to write forces to
output trajectory
nstlog= 10 ; frequency to write energies to log file
nstenergy = 100 ; frequency to write energies to edr file
nstcalcenergy  = 100
vdwtype= cut-off
coulombtype= cut-off
pbc= no
table-extension   = 20.0
nstlist= 100
ns_type= grid
rlist= 1.0

rcoulomb   = 1.2
rvdw   = 1.2

comm-mode  = angular
comm-grps= system
optimize_fft= yes

;heating
annealing  = single
annealing_npoints  = 2
annealing_time   = 0 3
annealing_temp  = 0 300

ld_seed = 8072012

;temperature coupling is on
Tcoupl = berendsen
tau_t = 0.01
tc_grps = system
ref_t = 0

;Pressure coupling is off
Pcoupl = no

; Generate velocites is on
gen_vel = yes
gen_temp = 0
gen_seed = 8042012



Thanks,



--


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


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Re: [gmx-users] simmulated annealing excess temperature........................

2012-08-16 Thread tarak karmakar

Thanks a lot for the quick reply...probably I  have
overlooked this point earlier
..now I'm getting it properly

On Thu, Aug 16, 2012 at 10:33 PM, Justin Lemkul jalem...@vt.edu wrote:


 On 8/16/12 12:57 PM, tarak karmakar wrote:

 Dear All,

 In my simulation I want the temperature of the system to be reached at
 300 K only after 3 ps. But after 3ps I see temperature became 402 K.
 So am I doing any mistake in the '.mdp' file given below?


 You have a few.

 1. You should not run MD with flexible water.
 2. Finite cutoffs lead to rounding errors and accumulation of heat.  This is
 most likely the source of your problem.  I seem to recall Mark (or maybe
 someone else) already told you about this point.

 -Justin


 define= -DFLEXIBLE
 constraints= h-bonds
 integrator  = sd
 dt= 0.001  ; 1fs
 nsteps   = 3000   ; 3ps
 nstcomm   = 1
 nstxout  = 1000   ; frequency to write coordinates
 to output trajectory
 nstvout  = 0  ; frequency to write velocities
 to output trajectory; the last velocities are always written
 nstfout   = 0  ; frequency to write forces to
 output trajectory
 nstlog= 10 ; frequency to write energies to
 log file
 nstenergy = 100 ; frequency to write energies to edr file
 nstcalcenergy  = 100
 vdwtype= cut-off
 coulombtype= cut-off
 pbc= no
 table-extension   = 20.0
 nstlist= 100
 ns_type= grid
 rlist= 1.0

 rcoulomb   = 1.2
 rvdw   = 1.2

 comm-mode  = angular
 comm-grps= system
 optimize_fft= yes

 ;heating
 annealing  = single
 annealing_npoints  = 2
 annealing_time   = 0 3
 annealing_temp  = 0 300

 ld_seed = 8072012

 ;temperature coupling is on
 Tcoupl = berendsen
 tau_t = 0.01
 tc_grps = system
 ref_t = 0

 ;Pressure coupling is off
 Pcoupl = no

 ; Generate velocites is on
 gen_vel = yes
 gen_temp = 0
 gen_seed = 8042012



 Thanks,


 --
 

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

 
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-- 
Tarak Karmakar
Molecular Simulation Lab.
Chemistry and Physics of Materials Unit
Jawaharlal Nehru Centre for Advanced Scientific Research
Jakkur P. O.
Bangalore - 560 064
Karnataka, INDIA
Ph. (lab) : +91-80-22082809
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[gmx-users] Ca ion simulation incorporated in protein structure

2012-08-16 Thread ram bio

Dear Gromacs Users,

I am trying to simulate a modeled protein -ligand complex in lipid
bilayer using Gromacs 4.5.4 with Charmm27 FF. For my project purpose
which is to see the effect of substitution of ions (Ca instead of Na
ions) in the protein structure on protein ligand interactions ,  I
have modeled the protein with Ca ions in the protein instead of Na
ions. For the same, I was wondering if Gromacs 4.5.4 with Charmm27 FF
can simulate Ca ions if incorporated in the protein instead of Na ions
as i described here.


Thanks and Regards,
Pramod
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Re: [gmx-users] Ca ion simulation incorporated in protein structure




On 8/16/12 2:45 PM, ram bio wrote:

Dear Gromacs Users,

I am trying to simulate a modeled protein -ligand complex in lipid
bilayer using Gromacs 4.5.4 with Charmm27 FF. For my project purpose
which is to see the effect of substitution of ions (Ca instead of Na
ions) in the protein structure on protein ligand interactions ,  I
have modeled the protein with Ca ions in the protein instead of Na
ions. For the same, I was wondering if Gromacs 4.5.4 with Charmm27 FF
can simulate Ca ions if incorporated in the protein instead of Na ions
as i described here.



Check the ions.itp file in the charmm27.ff folder in $GMXLIB.

-Justin

--


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


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[gmx-users] Re: RMSF error when fitting to average structure

Hi Justin,

I did indeed correct for periodic boundary conditions prior to running rmsf,
so I'm not sure what the problem would be there.  

Is there any way of producing an average structure from rmsf (or any other
program for that matter) that is not output as a .pdb file but as a .tpr
file?  

Thanks,
Tom



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Re: [gmx-users] Re: RMSF error when fitting to average structure




On 8/16/12 3:19 PM, tdgrant1 wrote:

Hi Justin,

I did indeed correct for periodic boundary conditions prior to running rmsf,
so I'm not sure what the problem would be there.



The message you got was a warning, not an error.  The warning is generic and is 
printed by any Gromacs program that does not receive a .tpr file passed to the 
-s flag.  It is not necessarily indicative of any problem but is written to be 
helpful to the user.



Is there any way of producing an average structure from rmsf (or any other
program for that matter) that is not output as a .pdb file but as a .tpr
file?



You can easily produce a .tpr file from any coordinate file using an existing 
topology and .mdp file.  Coordinate files are not generally written in .tpr format.


-Justin
--


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


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[gmx-users] Re: RMSF error when fitting to average structure

Oh okay, thanks.  I didn't realize warnings were just that, only warnings and
didn't stop the program.  The program did not finish however, and the
problem was a Segmentation Fault.  The output literally was:

Select a group: 0
Selected 0: 'System'
Reading frame   0 time0.000   
WARNING: if there are broken molecules in the trajectory file,
 they can not be made whole without a run input file

Segmentation fault

Could this be related to the input file, or do you think this is something
else entirely?

Thanks,
Tom



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Re: [gmx-users] Re: RMSF error when fitting to average structure




On 8/16/12 3:54 PM, tdgrant1 wrote:

Oh okay, thanks.  I didn't realize warnings were just that, only warnings and
didn't stop the program.  The program did not finish however, and the
problem was a Segmentation Fault.  The output literally was:

Select a group: 0
Selected 0: 'System'
Reading frame   0 time0.000
WARNING: if there are broken molecules in the trajectory file,
  they can not be made whole without a run input file

Segmentation fault

Could this be related to the input file, or do you think this is something
else entirely?



Depending on how many atoms are in the entire system (is it a fully solvated 
protein, anything else?) then you probably ran out of memory.  These analyses 
are normally performed only on the solute of interest or a subset of those atoms 
(like a protein backbone).


-Justin

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[gmx-users] Re: RMSF error when fitting to average structure

This System as described by group 0 in the previous message is actually
only the solute, a protein-tRNA complex of ~15000 atoms.  I tried running
only the backbone and even only c-alphas (808 atoms total) and I still
received a segmentation fault.



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Re: [gmx-users] Re: RMSF error when fitting to average structure




On 8/16/12 4:11 PM, tdgrant1 wrote:

This System as described by group 0 in the previous message is actually
only the solute, a protein-tRNA complex of ~15000 atoms.  I tried running
only the backbone and even only c-alphas (808 atoms total) and I still
received a segmentation fault.



Do the number of atoms in the structure file passed to -s and the number of 
atoms in the trajectory passed to -f match?


-Justin

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[gmx-users] Re: RMSF error when fitting to average structure

No they do not.  The trajectory contains all the atoms, including the solvent
(~300,000 atoms), whereas the structure passed to -s is the averaged
structure from the last 60ns of simulation and only includes the non-solvent
atoms (~15,000).  Should I rerun rmsf on the last 60ns but select System
instead of non-solvent, and then use that averaged structure to pass to the
-s flag?



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Re: [gmx-users] Re: RMSF error when fitting to average structure




On 8/16/12 4:19 PM, tdgrant1 wrote:

No they do not.  The trajectory contains all the atoms, including the solvent
(~300,000 atoms), whereas the structure passed to -s is the averaged
structure from the last 60ns of simulation and only includes the non-solvent
atoms (~15,000).  Should I rerun rmsf on the last 60ns but select System
instead of non-solvent, and then use that averaged structure to pass to the
-s flag?



I don't see how getting the average structure of a 300k atom system is 
meaningful - that will certainly chew up lots of memory ;)


What I would suggest is one of the following:

1. Create a .tpr file with your averaged structure from an existing topology and 
run g_rmsf.


2. Use trjconv to create a subset trajectory (.xtc) that matches the number of 
atoms in the reference structure.


3. Avoid ever choosing System for analysis - choose the backbone or whatever 
custom index group you wish to use.  I don't see an inherent problem with using 
the System in the reference structure (your RNA) but you never know when 
there's some curious mismatch in the interpretation down the line.  Could be a 
bug, but I'm not prepared to believe that yet from the evidence at hand.


-Justin

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[gmx-users] atom numbering

2012-08-16 Thread dariush

Dear All,

I have bilayer system plus two proteins in my system. I numbered residues
manually, but after minimization number of residues for both protein 1 and 2
starts from 1. It means in VMD when I am going to pick res. 3 (resid 3), it
will highlight two res. 3, one in protein 1 and one in protein 2.
Do you know how should I figure it out?

Thanks,
Dariush




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Re: [gmx-users] atom numbering




On 8/16/12 5:22 PM, dariush wrote:

Dear All,

I have bilayer system plus two proteins in my system. I numbered residues
manually, but after minimization number of residues for both protein 1 and 2
starts from 1. It means in VMD when I am going to pick res. 3 (resid 3), it
will highlight two res. 3, one in protein 1 and one in protein 2.
Do you know how should I figure it out?



genconf -renumber

-Justin

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[gmx-users] Protein-POPC bilayer


 Hi,

I have a question about the Protein-POPC system:
To insert a protein in lipid bilayer, I am suggested to simulate POPC in water 
separately before insertion, it might decrease the time of final simulation. 
It's OK!

In the article suggested me by dear Peter C. Lai, I read that POPC was 
simulated in anisotropic pressure coupling at first and then after insertion of 
protein, semi-isotropic pressure coupling is applied. 
Now, would you please telling me why you used this procedure?
And,
Would my system be correct  if I use semi-isotropic pressure coupling instead 
of anisotropic pressure coupling for the first step?

Thanks in advance for your replies.


Sincerely,
Shima
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Re: [gmx-users] Protein-POPC bilayer

2012-08-16 Thread Jianguo Li

After inserting the protein, the equilibrium box length in the x and y 
dimension should be different, so you need anisotropic pressure coupling during 
the 1st step. After equilibrium, the ratio of box length in x,y is fixed, so 
you can use semi-isotropic method.

--Jianguo




From: Shima Arasteh shima_arasteh2...@yahoo.com
To: Discussion list for GROMACS users gmx-users@gromacs.org 
Sent: Friday, 17 August 2012, 7:26
Subject: [gmx-users] Protein-POPC bilayer


 Hi,

I have a question about the Protein-POPC system:
To insert a protein in lipid bilayer, I am suggested to simulate POPC in water 
separately before insertion, it might decrease the time of final simulation. 
It's OK!

In the article suggested me by dear Peter C. Lai, I read that POPC was 
simulated in anisotropic pressure coupling at first and then after insertion of 
protein, semi-isotropic pressure coupling is applied. 
Now, would you please telling me why you used this procedure?
And,
Would my system be correct  if I use semi-isotropic pressure coupling instead 
of anisotropic pressure coupling for the first step?

Thanks in advance for your replies.


Sincerely,
Shima
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Re: [gmx-users] Protein-POPC bilayer




On 8/16/12 9:14 PM, Jianguo Li wrote:

After inserting the protein, the equilibrium box length in the x and y 
dimension should be different, so you need anisotropic pressure coupling during 
the 1st step. After equilibrium, the ratio of box length in x,y is fixed, so 
you can use semi-isotropic method.



Most pre-equilibrated bilayers have (roughly) equivalent x and y box dimensions. 
 Why do you think they should inherently be different?


In my experience, anisotropic coupling leads to major deformations in the x-y 
plane, taking a bilayer that is initially a square (roughly) in the x-y plane 
and turning it into a rectangle.  I'd be very curious to hear Peter's answer to 
this question.  I used to use anisotropic coupling, but now I use semiisotropic 
exclusively.


-Justin

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Re: [gmx-users] Protein-POPC bilayer

2012-08-16 Thread Jianguo Li

What I think is that anisotropic coupling may be 
faster in equilibrium. Suppose the protein is quite different in x and y 
dimensions, after  insertion, I think it is faster to get equilibrium 
the box length separately. I agree with you that semi-isotropic coupling in the 
first step can also do the job, but I expect it may take longer 
time to reach equilibrium. 


--Jianguo


From: Justin Lemkul jalem...@vt.edu
To: Jianguo Li ljg...@yahoo.com.sg; Discussion list for GROMACS users 
gmx-users@gromacs.org 
Sent: Friday, 17 August 2012, 9:19
Subject: Re: [gmx-users] Protein-POPC bilayer



On 8/16/12 9:14 PM, Jianguo Li wrote:
 After inserting the protein, the equilibrium box length in the x and y 
 dimension should be different, so you need anisotropic pressure coupling 
 during the 1st step. After equilibrium, the ratio of box length in x,y is 
 fixed, so you can use semi-isotropic method.
 

Most pre-equilibrated bilayers have (roughly) equivalent x and y box 
dimensions.  Why do you think they should inherently be different?

In my experience, anisotropic coupling leads to major deformations in the x-y 
plane, taking a bilayer that is initially a square (roughly) in the x-y plane 
and turning it into a rectangle.  I'd be very curious to hear Peter's answer to 
this question.  I used to use anisotropic coupling, but now I use semiisotropic 
exclusively.

-Justin

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Re: [gmx-users] Protein-POPC bilayer




On 8/16/12 9:43 PM, Jianguo Li wrote:

What I think is that anisotropic coupling may be faster in equilibrium. Suppose
the protein is quite different in x and y dimensions, after  insertion, I think
it is faster to get equilibrium the box length separately. I agree with you that
semi-isotropic coupling in the first step can also do the job, but I expect it
may take longer time to reach equilibrium.



What I generally see is basically the opposite.  Using anisotropic pressure 
coupling leads to a steady change in box dimensions, but this is not the case 
with semiisotropic coupling.  It depends, I suppose, on how one produces the 
membrane protein system - adequate deletion of lipids can accommodate for a 
protein of any shape without affecting box vectors.


-Justin

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Re: [gmx-users] Protein-POPC bilayer


On 17/08/2012 11:46 AM, Justin Lemkul wrote:



On 8/16/12 9:43 PM, Jianguo Li wrote:
What I think is that anisotropic coupling may be faster in 
equilibrium. Suppose
the protein is quite different in x and y dimensions, after 
insertion, I think
it is faster to get equilibrium the box length separately. I agree 
with you that
semi-isotropic coupling in the first step can also do the job, but I 
expect it

may take longer time to reach equilibrium.



What I generally see is basically the opposite.  Using anisotropic 
pressure coupling leads to a steady change in box dimensions, but this 
is not the case with semiisotropic coupling.  It depends, I suppose, 
on how one produces the membrane protein system - adequate deletion of 
lipids can accommodate for a protein of any shape without affecting 
box vectors.


Or depends on the force field or lipid?

Mark
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Re: [gmx-users] Protein-POPC bilayer

You always use semi-isotropic for bilayer work. The Z is decoupled from x-y 
due to symmetry.

I don't think I mention anything differently in the paper.

Pcoupltype   = semiisotropic


On 2012-08-16 04:26:38PM -0700, Shima Arasteh wrote:
 
  Hi,
 
 I have a question about the Protein-POPC system:
 To insert a protein in lipid bilayer, I am suggested to simulate POPC in 
 water separately before insertion, it might decrease the time of final 
 simulation. It's OK!
 
 In the article suggested me by dear Peter C. Lai, I read that POPC was 
 simulated in anisotropic pressure coupling at first and then after insertion 
 of protein, semi-isotropic pressure coupling is applied. 
 Now, would you please telling me why you used this procedure?
 And,
 Would my system be correct  if I use semi-isotropic pressure coupling instead 
 of anisotropic pressure coupling for the first step?
 
 Thanks in advance for your replies.
 
 
 Sincerely,
 Shima
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==
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Re: [gmx-users] Protein-POPC bilayer




On 8/16/12 10:21 PM, Mark Abraham wrote:

On 17/08/2012 11:46 AM, Justin Lemkul wrote:



On 8/16/12 9:43 PM, Jianguo Li wrote:

What I think is that anisotropic coupling may be faster in equilibrium. Suppose
the protein is quite different in x and y dimensions, after insertion, I think
it is faster to get equilibrium the box length separately. I agree with you that
semi-isotropic coupling in the first step can also do the job, but I expect it
may take longer time to reach equilibrium.



What I generally see is basically the opposite.  Using anisotropic pressure
coupling leads to a steady change in box dimensions, but this is not the case
with semiisotropic coupling.  It depends, I suppose, on how one produces the
membrane protein system - adequate deletion of lipids can accommodate for a
protein of any shape without affecting box vectors.


Or depends on the force field or lipid?



Certainly a possibility.  I think that the statement in the manual makes it 
pretty clear though that the algorithm itself is likely responsible for at least 
some of the observed deformations - Beware that anisotropic scaling can lead to 
extreme deformation of the simulation box.


-Justin

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Research Scientist
Department of Biochemistry
Virginia Tech
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Re: [gmx-users] Protein-POPC bilayer

Here is my MDP file I use for POPC work for NPT-after-NVT equilibration, 
in caes you lost it from the time before:
You can choose to use V-rescale and Berendsen if you want but the Nose-Hoover/
Parinello-Rahman with the paraeters below was stable for me with 238 POPC
and 21524 water.


integrator  = md; leap-frog integrator
nsteps  = 250 ; 2 * 5 = 100 ps
dt  = 0.002 ; 2 fs
; Output control
nstxout = 1000   ; save coordinates every 0.2 ps
nstvout = 1000   ; save velocities every 0.2 ps
nstenergy   = 100   ; save energies every 0.2 ps
nstlog  = 100   ; update log file every 0.2 ps

continuation= yes; NOT first dynamics run
constraint_algorithm = lincs; holonomic constraints
constraints = h-bonds ; all bonds (even heavy atom-H bonds) constrained
lincs_iter  = 1 ; accuracy of LINCS
lincs_order = 4 ; also related to accuracy
; Neighborsearching
ns_type = grid  ; search neighboring grid cells
nstlist = 5 ; 10 fs
rlist   = 1.2   ; short-range neighborlist cutoff (in nm)
rlistlong   = 1.4
rcoulomb= 1.2   ; short-range electrostatic cutoff (in nm)
rvdw= 1.2   ; short-range van der Waals cutoff (in nm)
vdwtype = switch
rvdw_switch = 0.8
; Electrostatics
coulombtype = PME   ; Particle Mesh Ewald for long-range 
electrostatics
pme_order   = 4 ; cubic interpolation
fourierspacing  = 0.16  ; grid spacing for FFT
; Temperature coupling is on
tcoupl  = Nose-Hoover ; modified Berendsen thermostat
tc-grps = POPC SOL  ; two coupling groups - more accurate
tau_t   = 0.5   0.5 ; time constant, in ps
ref_t   = 300   300 ; reference temperature, one for each group, in 
K
pcoupl  = Parrinello-Rahman; no pressure coupling in NVT
pcoupltype  = semiisotropic
tau_p   = 4
ref_p   = 1.01325 1.01325
compressibility = 4.5e-5 4.5e-5

; Periodic boundary conditions
pbc = xyz   ; 3-D PBC
; Dispersion correction
DispCorr= no; account for cut-off vdW scheme
; Velocity generation
gen_vel = no   ; assign velocities from Maxwell distribution
;gen_temp= 300   ; temperature for Maxwell distribution
;gen_seed= -1; generate a random seed
nstcomm = 1
comm_mode   = Linear
comm_grps   = POPC SOL

On 2012-08-16 09:32:17PM -0500, Peter C. Lai wrote:
 You always use semi-isotropic for bilayer work. The Z is decoupled from x-y 
 due to symmetry.
 
 I don't think I mention anything differently in the paper.
 
 Pcoupltype   = semiisotropic
 
 
 On 2012-08-16 04:26:38PM -0700, Shima Arasteh wrote:
  
   Hi,
  
  I have a question about the Protein-POPC system:
  To insert a protein in lipid bilayer, I am suggested to simulate POPC in 
  water separately before insertion, it might decrease the time of final 
  simulation. It's OK!
  
  In the article suggested me by dear Peter C. Lai, I read that POPC was 
  simulated in anisotropic pressure coupling at first and then after 
  insertion of protein, semi-isotropic pressure coupling is applied. 
  Now, would you please telling me why you used this procedure?
  And,
  Would my system be correct  if I use semi-isotropic pressure coupling 
  instead of anisotropic pressure coupling for the first step?
  
  Thanks in advance for your replies.
  
  
  Sincerely,
  Shima
  -- 
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  http://lists.gromacs.org/mailman/listinfo/gmx-users
  * Only plain text messages are allowed!
  * Please search the archive at 
  http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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 -- 
 ==
 Peter C. Lai  | University of Alabama-Birmingham
 Programmer/Analyst| KAUL 752A
 Genetics, Div. of Research| 705 South 20th Street
 p...@uab.edu  | Birmingham AL 35294-4461
 (205) 690-0808|
 ==
 
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RE: [gmx-users] Protein-POPC bilayer

2012-08-16 Thread Dallas Warren

Not directly related to bilayers, but our work with liquid phases has found 
some interesting things with anisotropic versus isotropic.  Basically, even 
though anisotropic allows things to structure without constraints to how they 
want to be, there is some artifacts that drive it too far, beyond what is 
reasonable and you get severe box distortion and failure.  Will be saying a 
little on that in an upcoming paper 

Catch ya,

Dr. Dallas Warren
Drug Discovery Biology
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.war...@monash.edu
+61 3 9903 9304
-
When the only tool you own is a hammer, every problem begins to resemble a 
nail. 

 -Original Message-
 From: gmx-users-boun...@gromacs.org [mailto:gmx-users-
 boun...@gromacs.org] On Behalf Of Justin Lemkul
 Sent: Friday, 17 August 2012 12:33 PM
 To: Discussion list for GROMACS users
 Subject: Re: [gmx-users] Protein-POPC bilayer
 
 
 
 On 8/16/12 10:21 PM, Mark Abraham wrote:
  On 17/08/2012 11:46 AM, Justin Lemkul wrote:
 
 
  On 8/16/12 9:43 PM, Jianguo Li wrote:
  What I think is that anisotropic coupling may be faster in
 equilibrium. Suppose
  the protein is quite different in x and y dimensions, after
 insertion, I think
  it is faster to get equilibrium the box length separately. I agree
 with you that
  semi-isotropic coupling in the first step can also do the job, but
 I expect it
  may take longer time to reach equilibrium.
 
 
  What I generally see is basically the opposite.  Using anisotropic
 pressure
  coupling leads to a steady change in box dimensions, but this is not
 the case
  with semiisotropic coupling.  It depends, I suppose, on how one
 produces the
  membrane protein system - adequate deletion of lipids can
 accommodate for a
  protein of any shape without affecting box vectors.
 
  Or depends on the force field or lipid?
 
 
 Certainly a possibility.  I think that the statement in the manual
 makes it
 pretty clear though that the algorithm itself is likely responsible for
 at least
 some of the observed deformations - Beware that anisotropic scaling
 can lead to
 extreme deformation of the simulation box.
 
 -Justin
 
 --
 
 
 Justin A. Lemkul, Ph.D.
 Research Scientist
 Department of Biochemistry
 Virginia Tech
 Blacksburg, VA
 jalemkul[at]vt.edu | (540) 231-9080
 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
 
 
 --
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Re: [gmx-users] Questions regarding Polarization Energy Calculation

2012-08-16 Thread jesmin jahan

Hi Mark,

According to your advice   remove the  the bonded terms and zero the
VDW parameters,
I removed everything under [ bond] , [angles], [pairs] and [ dihedrals
], and run the simulation mdrun rerun.

I  got output something like the following:


   Energies (kJ/mol)
GB PolarizationLJ (SR)   Coulomb (SR)  PotentialKinetic En.
   -2.23121e+037.54287e+07   -3.47729e+047.53917e+070.0e+00
   Total EnergyTemperature Pressure (bar)
7.53917e+070.0e+000.0e+00

where the previous output was something like this:

Energies (kJ/mol)
   Bond  AngleProper Dih.  Improper Dih.GB Polarization
2.12480e+034.80088e+021.06648e+039.04861e+01   -2.23122e+03
  LJ-14 Coulomb-14LJ (SR)   Coulomb (SR)  Potential
7.05695e+025.47366e+03   -4.16856e+02   -8.74797e+03   -1.45483e+03
Kinetic En.   Total EnergyTemperature Pressure (bar)
0.0e+00   -1.45483e+030.0e+000.0e+00



   Energies (kJ/mol)
GB PolarizationLJ (SR)   Coulomb (SR)  PotentialKinetic En.
   -2.23121e+034.17621e+13   -3.47729e+044.17621e+130.0e+00
   Total EnergyTemperature Pressure (bar)
4.17621e+130.0e+000.0e+00


So, you can see, although it has managed to remove some extra terms,
the LJ and Columb potential are still there. I searched for VWD
parameters. Although I saw various options for VWD,  its not clear
from the options, how to turn it off. Could you kindly tell me more
clearly about it?


I was also looking into the forcefield.itp file. I set the gen-pairs
to no , fudgeLJ 1 and fudgeQQ to 1 which were yes, .5 and .83
respectively originally.

[ defaults ]
; nbfunccomb-rule   gen-pairs   fudgeLJ fudgeQQ
1   2  no 1 1

Please let me know how to get rid of calculation of other energies
(LJ, Culumb and Total Potential) and how to set the parameters for
this properly.

Thanks for your help.

Sincerely,
Jesmin
On Thu, Aug 16, 2012 at 3:27 AM, Mark Abraham mark.abra...@anu.edu.au wrote:
 On 16/08/2012 5:08 PM, jesmin jahan wrote:

 Hi Mark,

 Thanks for your reply.
 If I open the .tpr file using notepad, it seems to be a binary file.
 Then, how to remove the  the bonded terms and zero the VDW parameters?


 In the .top file from which you made the .tpr. (And contributing .itp files)
 Parts of chapter 5 may help with this process.

 Mark



 I really need to compare how fast different well known package can
 compute GB-polarization energy and how good the energy values are?
 That's why time is an important factor me my experiments and I  really
 want to measure the time for GB energy in isolation !

 Thanks,
 Jesmin

 On Thu, Aug 16, 2012 at 2:44 AM, Mark Abraham mark.abra...@anu.edu.au
 wrote:

 On 16/08/2012 4:26 PM, jesmin jahan wrote:

 Hi Mark,

 Thanks for your previous reply.
 I tried to run single point energy simulation with some proteins.
 I got .log files with content like this:

 Energies (kJ/mol)
  Bond  AngleProper Dih.  Improper Dih.GB
 Polarization
   1.54109e+043.84351e+038.47152e+033.58425e+02
 -1.69666e+04
 LJ-14 Coulomb-14LJ (SR)   Coulomb (SR)
 Potential
   4.29664e+033.63997e+042.22900e+05   -5.18818e+04
 2.22832e+05
   Kinetic En.   Total EnergyTemperature Pressure (bar)
   1.08443e+091.08465e+092.73602e+070.0e+00
 ...

 Computing:   M-Number M-Flops  %
 Flops

 -
Generalized Born Coulomb 0.005711   0.274
 0.2
GB Coulomb + LJ  0.416308  25.395
 18.5
Outer nonbonded loop 0.016367   0.164
 0.1
1,4 nonbonded interactions   0.008410   0.757
 0.6
Born radii (HCT/OBC) 0.439486  80.426
 58.5
Born force chain rule0.439486   6.592
 4.8
NS-Pairs 0.943653  19.817
 14.4
Reset In Box 0.003179   0.010
 0.0
CG-CoM   0.006358   0.019
 0.0
Bonds0.003219   0.190
 0.1
Angles   0.005838   0.981
 0.7
Propers  0.011273   2.582
 1.9
Virial   0.003899   0.070
 0.1
Stop-CM  0.003179   0.032
 0.0
Calc-Ekin0.006358   0.172
 0.1

 -
Total 137.479
 100.0

Re: [gmx-users] Protein-POPC bilayer

In  2.1.6. Membrane bilayer construction part of the article you mentioned:

Asingle POPC molecule is parameterized using a
CHARMM36 force field conversion for GROMACS7. The result-
ing system,which consists of around 238 lipids is then equilibrated
for at least 50 ns at 310 K and 1 atm under NPT ensemble with
anisotropic pressure coupling or until the are a per lipid converges
close to the consensus value of around 63–65Å per headgroup.

This is where I asked the question about.

Thanks.

 

 
Sincerely,
Shima


- Original Message -
From: Peter C. Lai p...@uab.edu
To: Shima Arasteh shima_arasteh2...@yahoo.com; Discussion list for GROMACS 
users gmx-users@gromacs.org
Cc: 
Sent: Friday, August 17, 2012 7:17 AM
Subject: Re: [gmx-users] Protein-POPC bilayer

Here is my MDP file I use for POPC work for NPT-after-NVT equilibration, 
in caes you lost it from the time before:
You can choose to use V-rescale and Berendsen if you want but the Nose-Hoover/
Parinello-Rahman with the paraeters below was stable for me with 238 POPC
and 21524 water.


integrator      = md            ; leap-frog integrator
nsteps          = 250         ; 2 * 5 = 100 ps
dt              = 0.002         ; 2 fs
; Output control
nstxout         = 1000           ; save coordinates every 0.2 ps
nstvout         = 1000           ; save velocities every 0.2 ps
nstenergy       = 100           ; save energies every 0.2 ps
nstlog          = 100           ; update log file every 0.2 ps

continuation    = yes            ; NOT first dynamics run
constraint_algorithm = lincs    ; holonomic constraints
constraints     = h-bonds     ; all bonds (even heavy atom-H bonds) constrained
lincs_iter      = 1             ; accuracy of LINCS
lincs_order     = 4             ; also related to accuracy
; Neighborsearching
ns_type         = grid          ; search neighboring grid cells
nstlist         = 5             ; 10 fs
rlist           = 1.2           ; short-range neighborlist cutoff (in nm)
rlistlong       = 1.4
rcoulomb        = 1.2           ; short-range electrostatic cutoff (in nm)
rvdw            = 1.2           ; short-range van der Waals cutoff (in nm)
vdwtype         = switch
rvdw_switch     = 0.8
; Electrostatics
coulombtype     = PME           ; Particle Mesh Ewald for long-range 
electrostatics
pme_order       = 4             ; cubic interpolation
fourierspacing  = 0.16          ; grid spacing for FFT
; Temperature coupling is on
tcoupl          = Nose-Hoover     ; modified Berendsen thermostat
tc-grps         = POPC SOL      ; two coupling groups - more accurate
tau_t           = 0.5   0.5     ; time constant, in ps
ref_t           = 300   300     ; reference temperature, one for each group, in 
K
pcoupl          = Parrinello-Rahman            ; no pressure coupling in NVT
pcoupltype      = semiisotropic
tau_p           = 4
ref_p           = 1.01325 1.01325
compressibility = 4.5e-5 4.5e-5

; Periodic boundary conditions
pbc             = xyz           ; 3-D PBC
; Dispersion correction
DispCorr        = no    ; account for cut-off vdW scheme
; Velocity generation
gen_vel         = no           ; assign velocities from Maxwell distribution
;gen_temp        = 300           ; temperature for Maxwell distribution
;gen_seed        = -1            ; generate a random seed
nstcomm         = 1
comm_mode       = Linear
comm_grps       = POPC SOL

On 2012-08-16 09:32:17PM -0500, Peter C. Lai wrote:
 You always use semi-isotropic for bilayer work. The Z is decoupled from x-y 
 due to symmetry.
 
 I don't think I mention anything differently in the paper.
 
 Pcoupltype               = semiisotropic
 
 
 On 2012-08-16 04:26:38PM -0700, Shima Arasteh wrote:
  
   Hi,
  
  I have a question about the Protein-POPC system:
  To insert a protein in lipid bilayer, I am suggested to simulate POPC in 
  water separately before insertion, it might decrease the time of final 
  simulation. It's OK!
  
  In the article suggested me by dear Peter C. Lai, I read that POPC was 
  simulated in anisotropic pressure coupling at first and then after 
  insertion of protein, semi-isotropic pressure coupling is applied. 
  Now, would you please telling me why you used this procedure?
  And,
  Would my system be correct  if I use semi-isotropic pressure coupling 
  instead of anisotropic pressure coupling for the first step?
  
  Thanks in advance for your replies.
  
  
  Sincerely,
  Shima
  -- 
  gmx-users mailing list    gmx-users@gromacs.org
  http://lists.gromacs.org/mailman/listinfo/gmx-users
  * Only plain text messages are allowed!
  * 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
 
 -- 
 ==
 Peter C. Lai            | University of Alabama-Birmingham

Re: [gmx-users] Protein-POPC bilayer

Can't remember why I said that, since it's not what I used. Stupid 
autocorrect? Sorry!

On 2012-08-16 08:35:23PM -0700, Shima Arasteh wrote:
 In  2.1.6. Membrane bilayer construction part of the article you mentioned:
 
 Asingle POPC molecule is parameterized using a
 CHARMM36 force field conversion for GROMACS7. The result-
 ing system,which consists of around 238 lipids is then equilibrated
 for at least 50 ns at 310 K and 1 atm under NPT ensemble with
 anisotropic pressure coupling or until the are a per lipid converges
 close to the consensus value of around 63–65Å per headgroup.
 
 This is where I asked the question about.
 
 Thanks.
 
  
 
  
 Sincerely,
 Shima
 
 
 - Original Message -
 From: Peter C. Lai p...@uab.edu
 To: Shima Arasteh shima_arasteh2...@yahoo.com; Discussion list for GROMACS 
 users gmx-users@gromacs.org
 Cc: 
 Sent: Friday, August 17, 2012 7:17 AM
 Subject: Re: [gmx-users] Protein-POPC bilayer
 
 Here is my MDP file I use for POPC work for NPT-after-NVT equilibration, 
 in caes you lost it from the time before:
 You can choose to use V-rescale and Berendsen if you want but the Nose-Hoover/
 Parinello-Rahman with the paraeters below was stable for me with 238 POPC
 and 21524 water.
 
 
 integrator      = md            ; leap-frog integrator
 nsteps          = 250         ; 2 * 5 = 100 ps
 dt              = 0.002         ; 2 fs
 ; Output control
 nstxout         = 1000           ; save coordinates every 0.2 ps
 nstvout         = 1000           ; save velocities every 0.2 ps
 nstenergy       = 100           ; save energies every 0.2 ps
 nstlog          = 100           ; update log file every 0.2 ps
 
 continuation    = yes            ; NOT first dynamics run
 constraint_algorithm = lincs    ; holonomic constraints
 constraints     = h-bonds     ; all bonds (even heavy atom-H bonds) 
 constrained
 lincs_iter      = 1             ; accuracy of LINCS
 lincs_order     = 4             ; also related to accuracy
 ; Neighborsearching
 ns_type         = grid          ; search neighboring grid cells
 nstlist         = 5             ; 10 fs
 rlist           = 1.2           ; short-range neighborlist cutoff (in nm)
 rlistlong       = 1.4
 rcoulomb        = 1.2           ; short-range electrostatic cutoff (in nm)
 rvdw            = 1.2           ; short-range van der Waals cutoff (in nm)
 vdwtype         = switch
 rvdw_switch     = 0.8
 ; Electrostatics
 coulombtype     = PME           ; Particle Mesh Ewald for long-range 
 electrostatics
 pme_order       = 4             ; cubic interpolation
 fourierspacing  = 0.16          ; grid spacing for FFT
 ; Temperature coupling is on
 tcoupl          = Nose-Hoover     ; modified Berendsen thermostat
 tc-grps         = POPC SOL      ; two coupling groups - more accurate
 tau_t           = 0.5   0.5     ; time constant, in ps
 ref_t           = 300   300     ; reference temperature, one for each group, 
 in K
 pcoupl          = Parrinello-Rahman            ; no pressure coupling in NVT
 pcoupltype      = semiisotropic
 tau_p           = 4
 ref_p           = 1.01325 1.01325
 compressibility = 4.5e-5 4.5e-5
 
 ; Periodic boundary conditions
 pbc             = xyz           ; 3-D PBC
 ; Dispersion correction
 DispCorr        = no    ; account for cut-off vdW scheme
 ; Velocity generation
 gen_vel         = no           ; assign velocities from Maxwell distribution
 ;gen_temp        = 300           ; temperature for Maxwell distribution
 ;gen_seed        = -1            ; generate a random seed
 nstcomm         = 1
 comm_mode       = Linear
 comm_grps       = POPC SOL
 
 On 2012-08-16 09:32:17PM -0500, Peter C. Lai wrote:
  You always use semi-isotropic for bilayer work. The Z is decoupled from x-y 
  due to symmetry.
  
  I don't think I mention anything differently in the paper.
  
  Pcoupltype               = semiisotropic
  
  
  On 2012-08-16 04:26:38PM -0700, Shima Arasteh wrote:
   
    Hi,
   
   I have a question about the Protein-POPC system:
   To insert a protein in lipid bilayer, I am suggested to simulate POPC in 
   water separately before insertion, it might decrease the time of final 
   simulation. It's OK!
   
   In the article suggested me by dear Peter C. Lai, I read that POPC was 
   simulated in anisotropic pressure coupling at first and then after 
   insertion of protein, semi-isotropic pressure coupling is applied. 
   Now, would you please telling me why you used this procedure?
   And,
   Would my system be correct  if I use semi-isotropic pressure coupling 
   instead of anisotropic pressure coupling for the first step?
   
   Thanks in advance for your replies.
   
   
   Sincerely,
   Shima
   -- 
   gmx-users mailing list    gmx-users@gromacs.org
   http://lists.gromacs.org/mailman/listinfo/gmx-users
   * Only plain text messages are allowed!
   * 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

Re: [gmx-users] Questions regarding Polarization Energy Calculation

On 17/08/2012 1:14 PM, jesmin jahan wrote:

Hi Mark,

According to your advice remove the the bonded terms and zero the
VDW parameters,
I removed everything under [ bond] , [angles], [pairs] and [ dihedrals
],

This only removes the bonded terms (in the sense of those atoms that
interact because of the presence of bonds). The VDW parameters for
non-bonded interactions are in ffnonbonded.itp for your force field. You
should probably follow the advice here
http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field#Modifying_a_force_field
to get a local copy you can change conveniently.

and run the simulation mdrun rerun.

I got output something like the following:

Energies (kJ/mol)
GB PolarizationLJ (SR) Coulomb (SR) PotentialKinetic En.
-2.23121e+037.54287e+07 -3.47729e+047.53917e+070.0e+00
Total EnergyTemperature Pressure (bar)
7.53917e+070.0e+000.0e+00

where the previous output was something like this:

Energies (kJ/mol)
Bond AngleProper Dih. Improper Dih.GB Polarization
2.12480e+034.80088e+021.06648e+039.04861e+01 -2.23122e+03
LJ-14 Coulomb-14LJ (SR) Coulomb (SR) Potential
7.05695e+025.47366e+03 -4.16856e+02 -8.74797e+03 -1.45483e+03
Kinetic En. Total EnergyTemperature Pressure (bar)
0.0e+00 -1.45483e+030.0e+000.0e+00

Energies (kJ/mol)
GB PolarizationLJ (SR) Coulomb (SR) PotentialKinetic En.
-2.23121e+034.17621e+13 -3.47729e+044.17621e+130.0e+00
Total EnergyTemperature Pressure (bar)
4.17621e+130.0e+000.0e+00

So, you can see, although it has managed to remove some extra terms,
the LJ and Columb potential are still there. I searched for VWD
parameters. Although I saw various options for VWD, its not clear
from the options, how to turn it off. Could you kindly tell me more
clearly about it?

I was also looking into the forcefield.itp file. I set the gen-pairs
to no , fudgeLJ 1 and fudgeQQ to 1 which were yes, .5 and .83
respectively originally.

[ defaults ]
; nbfunccomb-rule gen-pairs fudgeLJ fudgeQQ
1 2 no 1 1

Please let me know how to get rid of calculation of other energies
(LJ, Culumb and Total Potential) and how to set the parameters for
this properly.

You can't get rid of the total. It's the total. You're trying to keep
the (GB) Coulomb.

Mark

Thanks for your help.

Sincerely,
Jesmin
On Thu, Aug 16, 2012 at 3:27 AM, Mark Abraham mark.abra...@anu.edu.au wrote:

On 16/08/2012 5:08 PM, jesmin jahan wrote:

Hi Mark,

Thanks for your reply.
If I open the .tpr file using notepad, it seems to be a binary file.
Then, how to remove the the bonded terms and zero the VDW parameters?

In the .top file from which you made the .tpr. (And contributing .itp files)
Parts of chapter 5 may help with this process.

Mark

I really need to compare how fast different well known package can
compute GB-polarization energy and how good the energy values are?
That's why time is an important factor me my experiments and I really
want to measure the time for GB energy in isolation !

Thanks,
Jesmin

On Thu, Aug 16, 2012 at 2:44 AM, Mark Abraham mark.abra...@anu.edu.au
wrote:

On 16/08/2012 4:26 PM, jesmin jahan wrote:

Hi Mark,

Thanks for your previous reply.
I tried to run single point energy simulation with some proteins.
I got .log files with content like this:

Energies (kJ/mol)
Bond AngleProper Dih. Improper Dih.GB
Polarization
1.54109e+043.84351e+038.47152e+033.58425e+02
-1.69666e+04
LJ-14 Coulomb-14LJ (SR) Coulomb (SR)
Potential
4.29664e+033.63997e+042.22900e+05 -5.18818e+04
2.22832e+05
Kinetic En. Total EnergyTemperature Pressure (bar)
1.08443e+091.08465e+092.73602e+070.0e+00
...

Computing: M-Number M-Flops %
Flops

-
Generalized Born Coulomb 0.005711 0.274
0.2
GB Coulomb + LJ 0.416308 25.395
18.5
Outer nonbonded loop 0.016367 0.164
0.1
1,4 nonbonded interactions 0.008410 0.757
0.6
Born radii (HCT/OBC) 0.439486 80.426
58.5
Born force chain rule0.439486 6.592
4.8
NS-Pairs 0.943653 19.817
14.4
Reset In Box 0.003179 0.010
0.0
CG-CoM 0.006358 0.019
0.0
Bonds0.003219 0.190
0.1
Angles

[gmx-users] LINCS

2012-08-16 Thread shahid nayeem

Dear all
 One basic clarification. How does LINCS algorithm influences the results
 of final production run. In what respect a minimization, pr and final
 simulation done with constraints = none and with constraint= all_bonds are
 different.
 Shahid Nayeem
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Re: [gmx-users] Protein-POPC bilayer



Oh, It's OK. Thanks Peter. :-)
I used the the same .mdp file sent me by you 1 month ago, for the 
pre-equilibration of POPC in water. 

But as others said here, anisotropic pressure coupling might result in major 
changes in lipid bilayer. I don't know, but it seems it is better to use 
anisotropic pressure coupling for the pre-equilibration of bilayer!? Right?! 
Anisotropic would be a better option? 

Now, I'd like to know which one is suggested to be used for the 
pre-equilibration before insertion of protein? Anisotropic is suggested?

Please make me clear here. Thanks for all explanations.


Sincerely,
Shima


- Original Message -
From: Peter C. Lai p...@uab.edu
To: Shima Arasteh shima_arasteh2...@yahoo.com
Cc: Discussion list for GROMACS users gmx-users@gromacs.org
Sent: Friday, August 17, 2012 8:19 AM
Subject: Re: [gmx-users] Protein-POPC bilayer

Can't remember why I said that, since it's not what I used. Stupid 
autocorrect? Sorry!

On 2012-08-16 08:35:23PM -0700, Shima Arasteh wrote:
 In  2.1.6. Membrane bilayer construction part of the article you mentioned:
 
 Asingle POPC molecule is parameterized using a
 CHARMM36 force field conversion for GROMACS7. The result-
 ing system,which consists of around 238 lipids is then equilibrated
 for at least 50 ns at 310 K and 1 atm under NPT ensemble with
 anisotropic pressure coupling or until the are a per lipid converges
 close to the consensus value of around 63–65Å per headgroup.
 
 This is where I asked the question about.
 
 Thanks.
 
  
 
  
 Sincerely,
 Shima
 
 
 - Original Message -
 From: Peter C. Lai p...@uab.edu
 To: Shima Arasteh shima_arasteh2...@yahoo.com; Discussion list for GROMACS 
 users gmx-users@gromacs.org
 Cc: 
 Sent: Friday, August 17, 2012 7:17 AM
 Subject: Re: [gmx-users] Protein-POPC bilayer
 
 Here is my MDP file I use for POPC work for NPT-after-NVT equilibration, 
 in caes you lost it from the time before:
 You can choose to use V-rescale and Berendsen if you want but the Nose-Hoover/
 Parinello-Rahman with the paraeters below was stable for me with 238 POPC
 and 21524 water.
 
 
 integrator      = md            ; leap-frog integrator
 nsteps          = 250         ; 2 * 5 = 100 ps
 dt              = 0.002         ; 2 fs
 ; Output control
 nstxout         = 1000           ; save coordinates every 0.2 ps
 nstvout         = 1000           ; save velocities every 0.2 ps
 nstenergy       = 100           ; save energies every 0.2 ps
 nstlog          = 100           ; update log file every 0.2 ps
 
 continuation    = yes            ; NOT first dynamics run
 constraint_algorithm = lincs    ; holonomic constraints
 constraints     = h-bonds     ; all bonds (even heavy atom-H bonds) 
 constrained
 lincs_iter      = 1             ; accuracy of LINCS
 lincs_order     = 4             ; also related to accuracy
 ; Neighborsearching
 ns_type         = grid          ; search neighboring grid cells
 nstlist         = 5             ; 10 fs
 rlist           = 1.2           ; short-range neighborlist cutoff (in nm)
 rlistlong       = 1.4
 rcoulomb        = 1.2           ; short-range electrostatic cutoff (in nm)
 rvdw            = 1.2           ; short-range van der Waals cutoff (in nm)
 vdwtype         = switch
 rvdw_switch     = 0.8
 ; Electrostatics
 coulombtype     = PME           ; Particle Mesh Ewald for long-range 
 electrostatics
 pme_order       = 4             ; cubic interpolation
 fourierspacing  = 0.16          ; grid spacing for FFT
 ; Temperature coupling is on
 tcoupl          = Nose-Hoover     ; modified Berendsen thermostat
 tc-grps         = POPC SOL      ; two coupling groups - more accurate
 tau_t           = 0.5   0.5     ; time constant, in ps
 ref_t           = 300   300     ; reference temperature, one for each group, 
 in K
 pcoupl          = Parrinello-Rahman            ; no pressure coupling in NVT
 pcoupltype      = semiisotropic
 tau_p           = 4
 ref_p           = 1.01325 1.01325
 compressibility = 4.5e-5 4.5e-5
 
 ; Periodic boundary conditions
 pbc             = xyz           ; 3-D PBC
 ; Dispersion correction
 DispCorr        = no    ; account for cut-off vdW scheme
 ; Velocity generation
 gen_vel         = no           ; assign velocities from Maxwell distribution
 ;gen_temp        = 300           ; temperature for Maxwell distribution
 ;gen_seed        = -1            ; generate a random seed
 nstcomm         = 1
 comm_mode       = Linear
 comm_grps       = POPC SOL
 
 On 2012-08-16 09:32:17PM -0500, Peter C. Lai wrote:
  You always use semi-isotropic for bilayer work. The Z is decoupled from x-y 
  due to symmetry.
  
  I don't think I mention anything differently in the paper.
  
  Pcoupltype               = semiisotropic
  
  
  On 2012-08-16 04:26:38PM -0700, Shima Arasteh wrote:
   
    Hi,
   
   I have a question about the Protein-POPC system:
   To insert a protein in lipid bilayer, I am suggested to simulate POPC in 
   water separately before insertion, it might

Re: [gmx-users] LINCS


On 17/08/2012 2:02 PM, shahid nayeem wrote:

Dear all

One basic clarification. How does LINCS algorithm influences the results
of final production run. In what respect a minimization, pr and final
simulation done with constraints = none and with constraint= all_bonds are
different.


Sounds like you should do some background reading on how and why 
constraints work. Manual and refs therein are good starting points. Or 
your favourite molecular simulation textbook. In a nutshell, you use 
them in production simulation because they're a reasonable model and 
allow a larger time step. You might avoid them when you're not yet at 
equilbrium, because their implementation can be brittle when your 
structure doesn't agree with the model physics.


Mark
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Only plain text messages are allowed!
* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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Re: [gmx-users] Protein-POPC bilayer

On 2012-08-16 09:04:35PM -0700, Shima Arasteh wrote:
 
 
 Oh, It's OK. Thanks Peter. :-)
 I used the the same .mdp file sent me by you 1 month ago, for the 
 pre-equilibration of POPC in water. 
 

Well if that worked out, then what is the problem?

What do you mean by pre-equlibration The only step that happens before
equilibraiton is energy minimzation... If NPT is crashing after EM then
try a few ns of NVT (with a V-rescale thermostat) first, but because VMD
gives you highly ordered bilayer (straight chains), I believe I was able
to go from EM directly to NPT without any problems.

 But as others said here, anisotropic pressure coupling might result in major 
 changes in lipid bilayer. I don't know, but it seems it is better to use 
 anisotropic pressure coupling for the pre-equilibration of bilayer!? Right?! 
 Anisotropic would be a better option? 
 
 Now, I'd like to know which one is suggested to be used for the 
 pre-equilibration before insertion of protein? Anisotropic is suggested?
 
 Please make me clear here. Thanks for all explanations.

You are welcome to try using anisotropic pressure coupling. With a system of
the size I put forth, it could be large enough[1] to buffer against box 
shearing forces.

[1] Anezo et. al J. Phys. Chem. B 2003, 107, 9424-9433

If you already equilibrated the membrane before insertion then go ahead and 
do the insertion. As was stated before, if the box vectors and area per lipid
are in equilibrium by the end of the equilibration, you should be fine.

 

 
 Sincerely,
 Shima
 
 
 - Original Message -
 From: Peter C. Lai p...@uab.edu
 To: Shima Arasteh shima_arasteh2...@yahoo.com
 Cc: Discussion list for GROMACS users gmx-users@gromacs.org
 Sent: Friday, August 17, 2012 8:19 AM
 Subject: Re: [gmx-users] Protein-POPC bilayer
 
 Can't remember why I said that, since it's not what I used. Stupid 
 autocorrect? Sorry!
 
 On 2012-08-16 08:35:23PM -0700, Shima Arasteh wrote:
  In  2.1.6. Membrane bilayer construction part of the article you 
  mentioned:
  
  Asingle POPC molecule is parameterized using a
  CHARMM36 force field conversion for GROMACS7. The result-
  ing system,which consists of around 238 lipids is then equilibrated
  for at least 50 ns at 310 K and 1 atm under NPT ensemble with
  anisotropic pressure coupling or until the are a per lipid converges
  close to the consensus value of around 63–65Å per headgroup.
  
  This is where I asked the question about.
  
  Thanks.
  
   
  
   
  Sincerely,
  Shima
  
  
  - Original Message -
  From: Peter C. Lai p...@uab.edu
  To: Shima Arasteh shima_arasteh2...@yahoo.com; Discussion list for 
  GROMACS users gmx-users@gromacs.org
  Cc: 
  Sent: Friday, August 17, 2012 7:17 AM
  Subject: Re: [gmx-users] Protein-POPC bilayer
  
  Here is my MDP file I use for POPC work for NPT-after-NVT equilibration, 
  in caes you lost it from the time before:
  You can choose to use V-rescale and Berendsen if you want but the 
  Nose-Hoover/
  Parinello-Rahman with the paraeters below was stable for me with 238 POPC
  and 21524 water.
  
  
  integrator      = md            ; leap-frog integrator
  nsteps          = 250         ; 2 * 5 = 100 ps
  dt              = 0.002         ; 2 fs
  ; Output control
  nstxout         = 1000           ; save coordinates every 0.2 ps
  nstvout         = 1000           ; save velocities every 0.2 ps
  nstenergy       = 100           ; save energies every 0.2 ps
  nstlog          = 100           ; update log file every 0.2 ps
  
  continuation    = yes            ; NOT first dynamics run
  constraint_algorithm = lincs    ; holonomic constraints
  constraints     = h-bonds     ; all bonds (even heavy atom-H bonds) 
  constrained
  lincs_iter      = 1             ; accuracy of LINCS
  lincs_order     = 4             ; also related to accuracy
  ; Neighborsearching
  ns_type         = grid          ; search neighboring grid cells
  nstlist         = 5             ; 10 fs
  rlist           = 1.2           ; short-range neighborlist cutoff (in nm)
  rlistlong       = 1.4
  rcoulomb        = 1.2           ; short-range electrostatic cutoff (in nm)
  rvdw            = 1.2           ; short-range van der Waals cutoff (in nm)
  vdwtype         = switch
  rvdw_switch     = 0.8
  ; Electrostatics
  coulombtype     = PME           ; Particle Mesh Ewald for long-range 
  electrostatics
  pme_order       = 4             ; cubic interpolation
  fourierspacing  = 0.16          ; grid spacing for FFT
  ; Temperature coupling is on
  tcoupl          = Nose-Hoover     ; modified Berendsen thermostat
  tc-grps         = POPC SOL      ; two coupling groups - more accurate
  tau_t           = 0.5   0.5     ; time constant, in ps
  ref_t           = 300   300     ; reference temperature, one for each 
  group, in K
  pcoupl          = Parrinello-Rahman            ; no pressure coupling in NVT
  pcoupltype      = semiisotropic
  tau_p           = 4
  ref_p           = 1.01325 1.01325

Re: [gmx-users] Protein-POPC bilayer



 :-)
  Thanks Peter.


Sincerely,
Shima


- Original Message -
From: Peter C. Lai p...@uab.edu
To: Shima Arasteh shima_arasteh2...@yahoo.com
Cc: Discussion list for GROMACS users gmx-users@gromacs.org
Sent: Friday, August 17, 2012 8:48 AM
Subject: Re: [gmx-users] Protein-POPC bilayer

On 2012-08-16 09:04:35PM -0700, Shima Arasteh wrote:
 
 
 Oh, It's OK. Thanks Peter. :-)
 I used the the same .mdp file sent me by you 1 month ago, for the 
 pre-equilibration of POPC in water. 
 

Well if that worked out, then what is the problem?

What do you mean by pre-equlibration The only step that happens before
equilibraiton is energy minimzation... If NPT is crashing after EM then
try a few ns of NVT (with a V-rescale thermostat) first, but because VMD
gives you highly ordered bilayer (straight chains), I believe I was able
to go from EM directly to NPT without any problems.

 But as others said here, anisotropic pressure coupling might result in major 
 changes in lipid bilayer. I don't know, but it seems it is better to use 
 anisotropic pressure coupling for the pre-equilibration of bilayer!? Right?! 
 Anisotropic would be a better option? 
 
 Now, I'd like to know which one is suggested to be used for the 
 pre-equilibration before insertion of protein? Anisotropic is suggested?
 
 Please make me clear here. Thanks for all explanations.

You are welcome to try using anisotropic pressure coupling. With a system of
the size I put forth, it could be large enough[1] to buffer against box 
shearing forces.

[1] Anezo et. al J. Phys. Chem. B 2003, 107, 9424-9433

If you already equilibrated the membrane before insertion then go ahead and 
do the insertion. As was stated before, if the box vectors and area per lipid
are in equilibrium by the end of the equilibration, you should be fine.

 

 
 Sincerely,
 Shima
 
 
 - Original Message -
 From: Peter C. Lai p...@uab.edu
 To: Shima Arasteh shima_arasteh2...@yahoo.com
 Cc: Discussion list for GROMACS users gmx-users@gromacs.org
 Sent: Friday, August 17, 2012 8:19 AM
 Subject: Re: [gmx-users] Protein-POPC bilayer
 
 Can't remember why I said that, since it's not what I used. Stupid 
 autocorrect? Sorry!
 
 On 2012-08-16 08:35:23PM -0700, Shima Arasteh wrote:
  In  2.1.6. Membrane bilayer construction part of the article you 
  mentioned:
  
  Asingle POPC molecule is parameterized using a
  CHARMM36 force field conversion for GROMACS7. The result-
  ing system,which consists of around 238 lipids is then equilibrated
  for at least 50 ns at 310 K and 1 atm under NPT ensemble with
  anisotropic pressure coupling or until the are a per lipid converges
  close to the consensus value of around 63–65Å per headgroup.
  
  This is where I asked the question about.
  
  Thanks.
  
   
  
   
  Sincerely,
  Shima
  
  
  - Original Message -
  From: Peter C. Lai p...@uab.edu
  To: Shima Arasteh shima_arasteh2...@yahoo.com; Discussion list for 
  GROMACS users gmx-users@gromacs.org
  Cc: 
  Sent: Friday, August 17, 2012 7:17 AM
  Subject: Re: [gmx-users] Protein-POPC bilayer
  
  Here is my MDP file I use for POPC work for NPT-after-NVT equilibration, 
  in caes you lost it from the time before:
  You can choose to use V-rescale and Berendsen if you want but the 
  Nose-Hoover/
  Parinello-Rahman with the paraeters below was stable for me with 238 POPC
  and 21524 water.
  
  
  integrator      = md            ; leap-frog integrator
  nsteps          = 250         ; 2 * 5 = 100 ps
  dt              = 0.002         ; 2 fs
  ; Output control
  nstxout         = 1000           ; save coordinates every 0.2 ps
  nstvout         = 1000           ; save velocities every 0.2 ps
  nstenergy       = 100           ; save energies every 0.2 ps
  nstlog          = 100           ; update log file every 0.2 ps
  
  continuation    = yes            ; NOT first dynamics run
  constraint_algorithm = lincs    ; holonomic constraints
  constraints     = h-bonds     ; all bonds (even heavy atom-H bonds) 
  constrained
  lincs_iter      = 1             ; accuracy of LINCS
  lincs_order     = 4             ; also related to accuracy
  ; Neighborsearching
  ns_type         = grid          ; search neighboring grid cells
  nstlist         = 5             ; 10 fs
  rlist           = 1.2           ; short-range neighborlist cutoff (in nm)
  rlistlong       = 1.4
  rcoulomb        = 1.2           ; short-range electrostatic cutoff (in nm)
  rvdw            = 1.2           ; short-range van der Waals cutoff (in nm)
  vdwtype         = switch
  rvdw_switch     = 0.8
  ; Electrostatics
  coulombtype     = PME           ; Particle Mesh Ewald for long-range 
  electrostatics
  pme_order       = 4             ; cubic interpolation
  fourierspacing  = 0.16          ; grid spacing for FFT
  ; Temperature coupling is on
  tcoupl          = Nose-Hoover     ; modified Berendsen thermostat
  tc-grps         = POPC SOL      ; two coupling groups - more accurate
  tau_t           = 0.5   0.5

Re: [gmx-users] LINCS

2012-08-16 Thread shahid nayeem

Right, I have a pdb where some of the residues are missing and when I
try to simulate it I get LINCS warning in between the atom of the two
ends of missing residues. So if I use a smaller time step (0.01) for
final production run and energy minimization with setting constraint =
none, making it computationally more expensive. Will these results
will be O.K.
Shahid Nayeem

On Fri, Aug 17, 2012 at 9:37 AM, Mark Abraham mark.abra...@anu.edu.au wrote:
 On 17/08/2012 2:02 PM, shahid nayeem wrote:

 Dear all

 One basic clarification. How does LINCS algorithm influences the results
 of final production run. In what respect a minimization, pr and final
 simulation done with constraints = none and with constraint= all_bonds
 are
 different.


 Sounds like you should do some background reading on how and why constraints
 work. Manual and refs therein are good starting points. Or your favourite
 molecular simulation textbook. In a nutshell, you use them in production
 simulation because they're a reasonable model and allow a larger time step.
 You might avoid them when you're not yet at equilbrium, because their
 implementation can be brittle when your structure doesn't agree with the
 model physics.

 Mark
 --
 gmx-users mailing listgmx-users@gromacs.org
 http://lists.gromacs.org/mailman/listinfo/gmx-users
 * Only plain text messages are allowed!
 * Please search the archive at
 http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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Re: [gmx-users] LINCS


On 17/08/2012 2:28 PM, shahid nayeem wrote:

Right, I have a pdb where some of the residues are missing and when I
try to simulate it I get LINCS warning in between the atom of the two
ends of missing residues. So if I use a smaller time step (0.01) for
final production run and energy minimization with setting constraint =
none, making it computationally more expensive. Will these results
will be O.K.


Does it sound OK to model missing residues with solvent (or vacuum) and 
have a chemical bond between the dangling ends? It's also definitely not 
OK to ignore the warning pdb2gmx gave you about this bond being too 
long. Plowing ahead blindly costs more time than than being careful and 
painstaking.


You need to either cap your chains or build in the missing residues with 
non-GROMACS software, but what's best depends what you're trying to observe.


Mark


Shahid Nayeem

On Fri, Aug 17, 2012 at 9:37 AM, Mark Abraham mark.abra...@anu.edu.au wrote:

On 17/08/2012 2:02 PM, shahid nayeem wrote:

Dear all

One basic clarification. How does LINCS algorithm influences the results
of final production run. In what respect a minimization, pr and final
simulation done with constraints = none and with constraint= all_bonds
are
different.


Sounds like you should do some background reading on how and why constraints
work. Manual and refs therein are good starting points. Or your favourite
molecular simulation textbook. In a nutshell, you use them in production
simulation because they're a reasonable model and allow a larger time step.
You might avoid them when you're not yet at equilbrium, because their
implementation can be brittle when your structure doesn't agree with the
model physics.

Mark
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Only plain text messages are allowed!
* Please search the archive at
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Re: [gmx-users] LINCS

2012-08-16 Thread shahid nayeem

I want to simulate without building the missing residue. Does gromacs
have an option of capping. I am using Gromacs 4.5.4. If not then
suggest some software which I may use.
Shahid nayeem

On Fri, Aug 17, 2012 at 10:03 AM, Mark Abraham mark.abra...@anu.edu.au wrote:
 On 17/08/2012 2:28 PM, shahid nayeem wrote:

 Right, I have a pdb where some of the residues are missing and when I
 try to simulate it I get LINCS warning in between the atom of the two
 ends of missing residues. So if I use a smaller time step (0.01) for
 final production run and energy minimization with setting constraint =
 none, making it computationally more expensive. Will these results
 will be O.K.


 Does it sound OK to model missing residues with solvent (or vacuum) and have
 a chemical bond between the dangling ends? It's also definitely not OK to
 ignore the warning pdb2gmx gave you about this bond being too long. Plowing
 ahead blindly costs more time than than being careful and painstaking.

 You need to either cap your chains or build in the missing residues with
 non-GROMACS software, but what's best depends what you're trying to observe.

 Mark


 Shahid Nayeem

 On Fri, Aug 17, 2012 at 9:37 AM, Mark Abraham mark.abra...@anu.edu.au
 wrote:

 On 17/08/2012 2:02 PM, shahid nayeem wrote:

 Dear all

 One basic clarification. How does LINCS algorithm influences the
 results
 of final production run. In what respect a minimization, pr and final
 simulation done with constraints = none and with constraint= all_bonds
 are
 different.


 Sounds like you should do some background reading on how and why
 constraints
 work. Manual and refs therein are good starting points. Or your favourite
 molecular simulation textbook. In a nutshell, you use them in production
 simulation because they're a reasonable model and allow a larger time
 step.
 You might avoid them when you're not yet at equilbrium, because their
 implementation can be brittle when your structure doesn't agree with the
 model physics.

 Mark
 --
 gmx-users mailing listgmx-users@gromacs.org
 http://lists.gromacs.org/mailman/listinfo/gmx-users
 * Only plain text messages are allowed!
 * 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.
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 --
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 http://lists.gromacs.org/mailman/listinfo/gmx-users
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Re: [gmx-users] LINCS