from:"Dr. Vitaly Chaban"

I think this is in topology, not in MDP. With PBC, you just specify
what happens to the particle after it crosses the edge of the box in
certain direction.

I have no preference regarding LINCS vs harmonic bonds.

You can also freeze only the rim atoms of the nanotube from both
ends and this will be almost the same as infinite tube. This solution
is faster on my taste.


Dr. Vitaly V. Chaban


On Thu, Sep 26, 2013 at 2:39 PM, Steven Neumann s.neuman...@gmail.com wrote:
 Dear Gmx Users,

 I have my carbon nanotube and I wish to make it infinite in lenght. Which
 mdp options whall be used? pbc = xy and z is the infinite dimension?
 another issue: Would you apply bonds between carbon atoms within the
 nanotube or constraints using LINCS? Which of them is less computationally
 expensive for the run?

 Thank you in advance,

 Steven
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Re: [gmx-users] trjcat after trjconv

I do not think that I ever tried myself, but is seems all the same.
Why do you ask?


Dr. Vitaly V. Chaban


On Thu, Sep 26, 2013 at 3:40 PM, Venkat Reddy venkat...@gmail.com wrote:
 Dear all,
 I have a basic doubt. Is there any difference between the two processes
 where
 1) I concatenate the trajectories and do trjconv to remove PBC, which is a
 default process
 2) Do trjconv on all the xtc files separately and then concatenate them.

 Thank you for your time

 --
 With Best Wishes
 Venkat Reddy Chirasani
 PhD student
 Laboratory of Computational Biophysics
 Department of Biotechnology
 IIT Madras
 Chennai
 INDIA-600036
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Re: [gmx-users] carbon nanotube - ifnite in length ?

I am just curious why the system would explode without
periodic_molecules = yes. If the PBC procedure is applied before
harmonic bond potential is calculated, than the opposite nanotube
atoms should be (already) seen as neighboring. This looks the same as
the solvent molecule, one atom of which crossed the box boundary.

No?



Dr. Vitaly V. Chaban


On Thu, Sep 26, 2013 at 3:59 PM, Justin Lemkul jalem...@vt.edu wrote:


 On 9/26/13 8:39 AM, Steven Neumann wrote:

 Dear Gmx Users,

 I have my carbon nanotube and I wish to make it infinite in lenght. Which
 mdp options whall be used? pbc = xy and z is the infinite dimension?
 another issue: Would you apply bonds between carbon atoms within the
 nanotube or constraints using LINCS? Which of them is less computationally
 expensive for the run?


 Use pbc = xyz in conjunction with periodic_molecules = yes otherwise the
 topology gets messed up trying to form unreasonable bonds.  The
 periodic_molecules keyword in the .mdp allows for bonds to be maintained
 over PBC.

 I remember a very old post somewhere in the archive that said one should not
 apply pressure coupling along the axis of the nanotube, due to some
 difficulties with maintaining the bonded geometry, but since I have never
 done CNT simulations, take the fact that I'm just repeating what I've heard
 for what it's worth :)

 Constraints always come with the cost of communication, so I would imagine
 harmonic bonds are less expensive.  I really don't see constraints as a
 limiting factor for performance, though.

 -Justin

 --
 ==

 Justin A. Lemkul, Ph.D.
 Postdoctoral Fellow

 Department of Pharmaceutical Sciences
 School of Pharmacy
 Health Sciences Facility II, Room 601
 University of Maryland, Baltimore
 20 Penn St.
 Baltimore, MD 21201

 jalem...@outerbanks.umaryland.edu | (410) 706-7441

 ==
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Re: [gmx-users] Preprocessor statements

Unlikely possible... But yeah, the feature might be handy.


Dr. Vitaly V. Chaban


On Thu, Sep 26, 2013 at 4:20 PM, grita cemilyi...@arcor.de wrote:
 Hi guys,

 Is it possible to specify in the topol.top file preprocessor statements, so
 that you can stop the simulation prematurely?

 I pull two molecules together and I'd like to stop the simulation if the
 center of mass distance of the molecules is less than xx nm.

 Best,
 grita

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Re: [gmx-users] carbon nanotube - ifnite in length ?

Steven -

I would use a simple harmonic bond.


Dr. Vitaly V. Chaban


On Thu, Sep 26, 2013 at 5:12 PM, Steven Neumann s.neuman...@gmail.com wrote:
 Thank you for this. And also I wish to attach a chain to my nanotube so they
 will be both able to move together. Is that a matter of distance restraints
 between nanotube atom and first atom of my chain or again - LINCS? Both
 chain and nanotube are made of the same type of 8 type of atoms. Please,
 advise.

 Steven


 On Thu, Sep 26, 2013 at 3:19 PM, Dr. Vitaly Chaban vvcha...@gmail.com
 wrote:

 I am just curious why the system would explode without
 periodic_molecules = yes. If the PBC procedure is applied before
 harmonic bond potential is calculated, than the opposite nanotube
 atoms should be (already) seen as neighboring. This looks the same as
 the solvent molecule, one atom of which crossed the box boundary.

 No?



 Dr. Vitaly V. Chaban


 On Thu, Sep 26, 2013 at 3:59 PM, Justin Lemkul jalem...@vt.edu wrote:
 
 
  On 9/26/13 8:39 AM, Steven Neumann wrote:
 
  Dear Gmx Users,
 
  I have my carbon nanotube and I wish to make it infinite in lenght.
  Which
  mdp options whall be used? pbc = xy and z is the infinite dimension?
  another issue: Would you apply bonds between carbon atoms within the
  nanotube or constraints using LINCS? Which of them is less
  computationally
  expensive for the run?
 
 
  Use pbc = xyz in conjunction with periodic_molecules = yes otherwise
  the
  topology gets messed up trying to form unreasonable bonds.  The
  periodic_molecules keyword in the .mdp allows for bonds to be maintained
  over PBC.
 
  I remember a very old post somewhere in the archive that said one should
  not
  apply pressure coupling along the axis of the nanotube, due to some
  difficulties with maintaining the bonded geometry, but since I have
  never
  done CNT simulations, take the fact that I'm just repeating what I've
  heard
  for what it's worth :)
 
  Constraints always come with the cost of communication, so I would
  imagine
  harmonic bonds are less expensive.  I really don't see constraints as
  a
  limiting factor for performance, though.
 
  -Justin
 
  --
  ==
 
  Justin A. Lemkul, Ph.D.
  Postdoctoral Fellow
 
  Department of Pharmaceutical Sciences
  School of Pharmacy
  Health Sciences Facility II, Room 601
  University of Maryland, Baltimore
  20 Penn St.
  Baltimore, MD 21201
 
  jalem...@outerbanks.umaryland.edu | (410) 706-7441
 
  ==
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Re: [gmx-users] Calculation of binding enthalpy in vacuum

Dear John -

I think you can achieve the goal even faster if you just define two
groups, such as MOL1 and MOL2 in MDP and then see the interaction
energy between them using g_energy.

5% is a decent agreement. Usually, even basis set superposition error
is larger (if you include this correction).

Dr. Vitaly V. Chaban


On Mon, Sep 23, 2013 at 9:32 AM, Jong Wha Lee jongwh...@postech.ac.kr wrote:
 Dear Gromacs users,



 I’m trying to calculate the binding enthalpy of a host molecule with a
 guest molecule in vacuum. I cannot perform QM calculations because some
 systems I’m studying are too large.



 I know that free energy calculations are possible with Gromacs, but they
 require some cautions.



 Instead of calculating free energies, I have subtracted the total energy of
 the guest (△EG) and the host (△EH) from the total energy of the complex
 (△EC). In other words,



 △E = △EC - △EH - △EG, where all energies are total energy obtained from
 g_energy.



 In this case, would the calculated △E be the binding enthalpy in vacuum
 (gas phase)?



 I’ve tried QM calculations, and the △E obtained with Gromacs matches QM
 calculations in ~ 5% range. But I’m still unsure on how proper this method
 is. Could you advise me on this?



 Thank you in advance,



 John Lee

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Re: [gmx-users] Funky output trajectory (lines all over the place)

Dear Jonathan -

Is it not a PBC effect? Try to display atoms as spheres - it will look
better. Otherwise, use the options in trjconv to remove PBC in the
visualized structure(s).

Dr. Vitaly V. Chaban


On Mon, Sep 23, 2013 at 9:22 AM, Jonathan Saboury jsab...@gmail.com wrote:
 I tried minimizing a box of cyclohexanes and water. The first frame is
 fine, but after that seemingly random lines form in vmd with the
 cyclohexanes. The waters seem to minimizing just fine though.

 I am sure I am just doing something extremely silly and I just don't know
 it because of ignorance. I have no formal training on simulations, you are
 my only hope!

 Perhaps using the em.gro with the em.trr is not the correct way to
 visualize? I used the command: vmd em.gro em.trr

 Or something is wrong with my em.mdp?
 em.mdp: http://pastebin.com/raw.php?i=LPPN5xRF

 Commands used: http://pastebin.com/raw.php?i=Jk0fKLJj
 Here are all the files, in case you need them:
 http://www.sendspace.com/file/gx8j97

 Sorry for dumping all of this, but I am genuinely stuck. I've tried reading
 about the mdp file format but i only understand ~5%. If I could have done
 more I would have tried :/

 Thank you all, it is really appreciated.

 -Jonathan Saboury
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Re: [gmx-users] script to convert the TIP3P water model into TIP4P

I am confused. Why do you want 4-sites water?


Dr. Vitaly V. Chaban


On Mon, Sep 23, 2013 at 10:36 AM, ABEL Stephane 175950
stephane.a...@cea.fr wrote:
 Hello all,

 It is not a gromacs problem per se, but I hope that some gromacs users can 
 help me. I would to do simulations of phospholipid bilayers with the 
 TIP4P/2005 water model. I have downloaded in the Klauda's website several 
 bilayer starting conformations. However, since CHARMM uses the TIP3 water 
 model, I am confused to convert the water coordinates into a water four 
 sites. Does somebody has a little script to share with me that can help me?

 Thank you for kindly help

 Stephane
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[gmx-users] trjconv and Floating point exception

Using trjconv -f traj.xtc -o confout.gro -dump 1500, I routinely
get the following error:

Select a group: 0
Selected 0: 'System'
Reading frame   0 time0.000
Precision of traj.xtc is 0.004 (nm)
Using output precision of 0.001 (nm)

Back Off! I just backed up confout.gro to ./#confout.gro.1#
Reading frame   17000 time 510.000   Floating point exception (core dumped)

What is it because of? Insufficient memory? Or something with the
trajectory file (it works nice if -dump 20). The traj.xtc file
is 11GB, the memory is 64GB.

Thanks!
Dr. Vitaly V. Chaban
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Re: [gmx-users] Re: Re: Calculation of binding enthalpy in vacuum

On Mon, Sep 23, 2013 at 2:40 PM, Jong Wha Lee jongwh...@postech.ac.kr wrote:
 Dear Vitaly,



 Thank you for your suggestion.



 I have also tried calculating interaction energies by specifying energygrps
 in .mdp file, but calculated energies deviate greatly from QM calculated
 energies and experimental results. I suspect that the structure of each
 component in complex differs from the structures when they were alone,
 because this will lead to a deviation in equilibrium binding enthalpy from
 the interaction energies that is calculated with energygrps line in .mdp
 file.


This might be because of electrostatics treatment method. Use simple
cut-off scheme and specify a really large cut-off radius, which
exceeds the sum of the sizes of your binding particles.

I made tons of such comparisons, QM vs. MM. It works pretty well.




 My guest of interest have two charges at a short distance, which is very
 unfavorable and the charges will try to be furthest apart. However, my host
 molecule can stability the charges via oppositely charged groups, and so now
 the guest molecule forms a bent structure. In this case, shouldn't the
 change in energy due to the different conformation of the guest be taken
 into account, to discuss equilibrium binding enthalpy? I feel maybe this
 wouldn't be well represented with interaction energies.


The binding energy is an energy gain, dE, in the following reaction
A + B - AB, dE

A, B, and AB are optimized geometries: in vacuum, in solvent or
anywhere. So, if a molecule changes its conformation during binding,
this energy gain/loss should be a part of the binding energy, I see no
methodological problem here.


Dr. Vitaly V. Chaban
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Re: [gmx-users] trjconv and Floating point exception

Dr. Vitaly V. Chaban


On Mon, Sep 23, 2013 at 2:10 PM, Justin Lemkul jalem...@vt.edu wrote:


 On 9/23/13 6:41 AM, Dr. Vitaly Chaban wrote:

 Using trjconv -f traj.xtc -o confout.gro -dump 1500, I routinely
 get the following error:

 Select a group: 0
 Selected 0: 'System'
 Reading frame   0 time0.000
 Precision of traj.xtc is 0.004 (nm)
 Using output precision of 0.001 (nm)

 Back Off! I just backed up confout.gro to ./#confout.gro.1#
 Reading frame   17000 time 510.000   Floating point exception (core
 dumped)


 Looks like a corruption in the trajectory.  What does gmxcheck say about
 traj.xtc?


gmxcheck -f traj.xtc

Reading frame 17000 time 510.000   Killed


 Can you bypass the frame using -b and dump out the desired frame?


No. The process comes to 5.1 ms and is killed.






 -Justin

 --
 ==

 Justin A. Lemkul, Ph.D.
 Postdoctoral Fellow

 Department of Pharmaceutical Sciences
 School of Pharmacy
 Health Sciences Facility II, Room 601
 University of Maryland, Baltimore
 20 Penn St.
 Baltimore, MD 21201

 jalem...@outerbanks.umaryland.edu | (410) 706-7441

 ==
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Re: [gmx-users] Constraining a part of the system

2013-09-17 Thread Dr. Vitaly Chaban

the smart way is to constrain everything at once in MDP...
Dr. Vitaly V. Chaban


On Tue, Sep 17, 2013 at 10:50 PM, HANNIBAL LECTER
hanniballecte...@gmail.com wrote:
 Is there a smart way of writing the constraint sections in the topology
 file other than entering the values manually ?


 On Tue, Sep 17, 2013 at 10:10 AM, rahul seth
 rahul.seth.grom...@gmail.comwrote:

 Thanks


 On Tue, Sep 17, 2013 at 10:03 AM, Justin Lemkul jalem...@vt.edu wrote:

 
 
  On 9/17/13 10:00 AM, HANNIBAL LECTER wrote:
 
  Is there a way to constraint bonds of a part of the system while keeping
  the other part flexible? For example for a simulation with two
 proteins, I
  would like to constraint the bonds of one and would like to keep the
 other
  flexible.
 
  I would prefer to use LINCS to constraint the system
 
 
  Set the constraints explicitly in the topology of one protein using a
  [constraints] directive.  Then set constraints = none in the .mdp file.
   The constraints read from the topology will override the .mdp setting
  while leaving all other bonds unconstrained.
 
  -Justin
 
  --
  ==**
 
  Justin A. Lemkul, Ph.D.
  Postdoctoral Fellow
 
  Department of Pharmaceutical Sciences
  School of Pharmacy
  Health Sciences Facility II, Room 601
  University of Maryland, Baltimore
  20 Penn St.
  Baltimore, MD 21201
 
  jalemkul@outerbanks.umaryland.**edu jalem...@outerbanks.umaryland.edu
 | (410)
  706-7441
 
  ==**
 
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Re: [gmx-users] identical results or exactly the same results?

2013-09-15 Thread Dr. Vitaly Chaban

The [numerical] results will depend on architecture you are running on. No
matter where the binary input file was prepared.



Dr. Vitaly V. Chaban


On Sun, Sep 15, 2013 at 10:22 AM, Albert mailmd2...@gmail.com wrote:

 Hello:

  I've got a md.tpr file generated by grompp, I am just wondering will the
 results be identical or would be exactly the same if I run it in different
 machine?

 thank you very much.

 best
 Albert
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Re: [gmx-users] Number Density

2013-09-15 Thread Dr. Vitaly Chaban

I would guess that the density is zero at the center, since you do not have
solvent molecules inside the membrane.

Yes, the output density is number of interaction sites per nm^3, calculated
in each slice, whose size you had specified.


Dr. Vitaly V. Chaban


On Sun, Sep 15, 2013 at 5:23 PM, Sun Moon sunmoon1...@yahoo.com wrote:

 Dear users,
 To calculate Number Density of solvent via size box for a bilayer
 membrane, I used g_density
 program as the following:
 g_density -f md.xtc -s md.tpr -o density-Num-SOL.xvg -d z
 -dens number -n index-group.ndx
 I got
 @title
 Partial densities
 @xaxis  label Box (nm)
 @yaxis  label Number density (nm\S-3\N)
0  96.8219
 0.131123  96.1793
 0.26224695.33
 0.393369  93.1889
 0.524492  89.4451
 0.655615  82.8209
 0.786738  73.8842
 0.917861  63.6742
  1.04898  52.7296
  1.18011  42.8748
  1.31123  33.0874
  1.44235  23.2632
  1.57348  13.9631
   1.7046  7.12264
  1.83572  2.95836
  1.96684  1.03366
  2.09797 0.293438
  2.229090.0784924
  2.360210.0134454
  2.49134   0.00272543
  2.62246   0.00254373
  2.75358   0.00872137
   2.88470.0168977
  3.015830.0168977
  3.14695   0.00853968
  3.278070.0143539
   3.40920.0230753
  3.540320.0121736
  3.67144   0.00345221
  3.80257   0.00908476
  3.933690.0403363
  4.06481 0.203317
  4.195930.806
  4.32706  2.62005
  4.45818  6.88243
   4.5893  13.8779
  4.72043  22.6425
  4.85155  32.1406
  4.98267  41.1066
  5.11379  50.7564
  5.24492  60.6579
  5.37604  71.2691
  5.50716  80.5771
  5.63829  87.9612
  5.76941  93.1096
  5.90053  95.5782
  6.03165  96.5369
  6.16278  96.4884
   6.2939  96.6515
  6.42502  96.3772
 What is the concept number density with gromacs? Is it especial
 volume (nm-3)? If so, why does in the central of box this amount is
 zero?
 What is N in “(nm\S-3\N)” dimension for number density?
 Thanks in advance,
 SUN
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Re: Fwd: [gmx-users] SD integrator

2013-09-15 Thread Dr. Vitaly Chaban

Are you sure that the source of instability is the CNT, not the protein? If
yes, what makes you to think so?

If you freeze all the atoms of the CNT, does it work well?


Dr. Vitaly V. Chaban


On Sun, Sep 15, 2013 at 11:07 PM, HANNIBAL LECTER 
hanniballecte...@gmail.com wrote:

 Thanks. From your publications it seems that you have been simulating with
 infinite CNTs. I am trying to use finite CNTs and I am generating my
 topology files according to

 http://chembytes.wikidot.com/grocnt.

 I am modeling the peripheral Carbon atoms with two bonds by specifying it
 in the atomname2type.n2t file. I am still not sure as to what is the source
 of this discrepancy. After a few tests I think this can be caused by
 improper parameterization of the bonds but I am not sure how to go about
 correcting any discrepancies.


 On Fri, Sep 13, 2013 at 5:53 PM, Dr. Vitaly Chaban vvcha...@gmail.comwrote:

 Do you couple CNT as a separate T-group? It should be done so.

 I think your systems blows up because of incorrectly defined bonded
 parameters for the tube, not due to thermostatting. For instance, you
 might
 not define all the valence angles and dihedrals.

 See my papers for the parameters for CNT, if you need such...


 Dr. Vitaly V. Chaban


 On Fri, Sep 13, 2013 at 8:55 PM, HANNIBAL LECTER 
 hanniballecte...@gmail.com
  wrote:

  However, even if position restraints are not used, the error can be
  reproduced. I am constraining the bonds in my CNTs though.
 
  I was wondering if you could point me to some parameters for CNT.
 
 
  On Fri, Sep 13, 2013 at 1:50 PM, HANNIBAL LECTER 
  hanniballecte...@gmail.com wrote:
 
  I am position restraining the CNT group. That affects the degrees of
  freedom.
  On Sep 13, 2013 1:43 PM, Dr. Vitaly Chaban vvcha...@gmail.com
 wrote:
 
  There must be some problem with degrees of freedom in your system...
 
 
  Dr. Vitaly V. Chaban
 
 
  -- Forwarded message --
  From: HANNIBAL LECTER hanniballecte...@gmail.com
  Date: Fri, Sep 13, 2013 at 7:15 PM
  Subject: [gmx-users] SD integrator
  To: Discussion list for GROMACS users gmx-users@gromacs.org
 
 
  Hi all,
 
  I have been posting for a while with my problems in simulating
 peptides
  inside CNTs. After a lot of trials it seems like simulating the CNT
 with
  bonds and angles seems like a wise thing to do.
 
  I am using the SD integrator + PR barostat. It seems like improper
  thermostatting can blow up the system. For example, when I am trying
 to
  simulate with tau-t for CNT as 1.0 the system blows up for 300K. The
  output
  temperatures (from g_energy) for CNT is about 150K for a ref-t of
 300K.
 
   However, if a stronger coupling is used tau-t = 0.005, the system
 works
  fine. Are there any artifacts for coupling the CNT group with such a
 low
  tau-t?
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Re: [gmx-users] Distance calculation

2013-09-14 Thread Dr. Vitaly Chaban

g_mindist also has something useful in this direction, I guess.



Dr. Vitaly V. Chaban


On Sat, Sep 14, 2013 at 12:10 AM, Rama ramkishn...@gmail.com wrote:


 Hi ,

 I there any tool to calculate distance between particular atom from one
 group(protein) to particular atom from another group(DMPC lipid in
 Bilayer).
 For Example: protein backbone Amide(HN) to acyl chain carbon atom(C2D) in
 DMPC lipid.

 Thanks
 Rama



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Fwd: [gmx-users] SD integrator

2013-09-13 Thread Dr. Vitaly Chaban

There must be some problem with degrees of freedom in your system...

Dr. Vitaly V. Chaban

-- Forwarded message --
From: HANNIBAL LECTER hanniballecte...@gmail.com
Date: Fri, Sep 13, 2013 at 7:15 PM
Subject: [gmx-users] SD integrator
To: Discussion list for GROMACS users gmx-users@gromacs.org

Hi all,

I have been posting for a while with my problems in simulating peptides
inside CNTs. After a lot of trials it seems like simulating the CNT with
bonds and angles seems like a wise thing to do.

I am using the SD integrator + PR barostat. It seems like improper
thermostatting can blow up the system. For example, when I am trying to
simulate with tau-t for CNT as 1.0 the system blows up for 300K. The output
temperatures (from g_energy) for CNT is about 150K for a ref-t of 300K.

 However, if a stronger coupling is used tau-t = 0.005, the system works
fine. Are there any artifacts for coupling the CNT group with such a low
tau-t?
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Re: Fwd: [gmx-users] SD integrator

2013-09-13 Thread Dr. Vitaly Chaban

Do you couple CNT as a separate T-group? It should be done so.

I think your systems blows up because of incorrectly defined bonded
parameters for the tube, not due to thermostatting. For instance, you might
not define all the valence angles and dihedrals.

See my papers for the parameters for CNT, if you need such...


Dr. Vitaly V. Chaban


On Fri, Sep 13, 2013 at 8:55 PM, HANNIBAL LECTER hanniballecte...@gmail.com
 wrote:

 However, even if position restraints are not used, the error can be
 reproduced. I am constraining the bonds in my CNTs though.

 I was wondering if you could point me to some parameters for CNT.


 On Fri, Sep 13, 2013 at 1:50 PM, HANNIBAL LECTER 
 hanniballecte...@gmail.com wrote:

 I am position restraining the CNT group. That affects the degrees of
 freedom.
 On Sep 13, 2013 1:43 PM, Dr. Vitaly Chaban vvcha...@gmail.com wrote:

 There must be some problem with degrees of freedom in your system...


 Dr. Vitaly V. Chaban


 -- Forwarded message --
 From: HANNIBAL LECTER hanniballecte...@gmail.com
 Date: Fri, Sep 13, 2013 at 7:15 PM
 Subject: [gmx-users] SD integrator
 To: Discussion list for GROMACS users gmx-users@gromacs.org


 Hi all,

 I have been posting for a while with my problems in simulating peptides
 inside CNTs. After a lot of trials it seems like simulating the CNT with
 bonds and angles seems like a wise thing to do.

 I am using the SD integrator + PR barostat. It seems like improper
 thermostatting can blow up the system. For example, when I am trying to
 simulate with tau-t for CNT as 1.0 the system blows up for 300K. The
 output
 temperatures (from g_energy) for CNT is about 150K for a ref-t of 300K.

  However, if a stronger coupling is used tau-t = 0.005, the system works
 fine. Are there any artifacts for coupling the CNT group with such a low
 tau-t?
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Re: [gmx-users] GaussView 4.0 and ITP adjuster

2013-09-09 Thread Dr. Vitaly Chaban

Hmmm

GaussView is a supplement to Gaussian to prepare input files and visualize
some (but far not all) results. Of course, it has nothing to do with
gromacs and its topologies.

Or, do I misunderstand you?


Dr. Vitaly V. Chaban


On Sun, Sep 8, 2013 at 1:29 PM, MUSYOKA THOMMAS 
mutemibiochemis...@gmail.com wrote:

 Dear Users,
 I am trying to run Protein-Ligand MD simulations using GROMACS. However, i
 seem to be lost in building correct ligand topologies. I came across an
 article explaining that the above mentioned softwares can be used to build
 a ligand topology file that can act as a guide in allocating correct
 charges and charge groups. Is there anyone who have used them before? If
 you have, would you kindly help me in finding my way especially in
 generating .out files using the GaussView.



 Thank you.
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Re: [gmx-users] GaussView 4.0 and ITP adjuster

2013-09-09 Thread Dr. Vitaly Chaban

First we built their 3D structures in the *.pdb format using Gauss View
4.0 and Frisch et al.
[30http://www.hindawi.com/journals/chem/2013/803151/#B30]
and submitted them to energy minimization with Frisch et al.
[30http://www.hindawi.com/journals/chem/2013/803151/#B30]
using the algorithm B3LYP/3-21G with charge chelpg, in order to generate
their *.out files.

What does this have to do with gromacs topologies?



Dr. Vitaly V. Chaban


On Mon, Sep 9, 2013 at 12:53 PM, MUSYOKA THOMMAS 
mutemibiochemis...@gmail.com wrote:

 Hi Dr,
 Check that link and see the role of GaussView in GROMACS.
 Thank you.
 http://www.hindawi.com/journals/chem/2013/803151/


 On Mon, Sep 9, 2013 at 12:46 PM, Dr. Vitaly Chaban vvcha...@gmail.comwrote:

 Hmmm

 GaussView is a supplement to Gaussian to prepare input files and visualize
 some (but far not all) results. Of course, it has nothing to do with
 gromacs and its topologies.

 Or, do I misunderstand you?


 Dr. Vitaly V. Chaban


 On Sun, Sep 8, 2013 at 1:29 PM, MUSYOKA THOMMAS 
 mutemibiochemis...@gmail.com wrote:

  Dear Users,
  I am trying to run Protein-Ligand MD simulations using GROMACS.
 However, i
  seem to be lost in building correct ligand topologies. I came across an
  article explaining that the above mentioned softwares can be used to
 build
  a ligand topology file that can act as a guide in allocating correct
  charges and charge groups. Is there anyone who have used them before? If
  you have, would you kindly help me in finding my way especially in
  generating .out files using the GaussView.
 
 
 
  Thank you.
  --
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  http://lists.gromacs.org/mailman/listinfo/gmx-users
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Re: [gmx-users] Re: periodic_molecule missing interactions

2013-08-30 Thread Dr. Vitaly Chaban

I think it is a dangerous practice to simulate with a cutoff of 0.5 nm.
Irrespectively of what you study.

Dr. Vitaly V. Chaban


On Fri, Aug 30, 2013 at 11:32 AM, Valentina valentina.erast...@durham.ac.uk
 wrote:

 Thank you for your reply.

 My box is quite small indeed, so my cut-offs are 0.5

 If I make a single layer, I would have to run quite a small system in
 z-direction.
 My residue box size:0.62840   0.54421   1.6   0.0   0.0
 -0.31420   0.0   0.0   0.0

 My suspect of the problem
 In my system I have Al, bonded to 6 OH, and Mg, that is non-bonded, so only
 LJ. My nrexcl is set to 2, as I don't have dihedrals. The Al and Mg form a
 mesh, that should be infinite in xy-

 I am guessing what I have to do is to artificially connect those Mg to OH
 with k=0 bonds  angles (?) and then include [ pairs ] of Mg O and Mg H to
 be calculated as LJ?

 I have a non usual FF, hence cannot figure out how to implement it yet.

 Thank you for help, V



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Re: [gmx-users] psf to tpr

2013-08-16 Thread Dr. Vitaly Chaban

No, it is not. But you can at least convert coordinates via VMD.

If you want to use gromacs trajectory analysis tools, it is easier to
convert NAMD trajectory to gromacs trajectory. Otherwise, I have no idea
why one may need to jump between codes.

Dr. Vitaly V. Chaban


On Fri, Aug 16, 2013 at 10:52 AM, Mark Abraham mark.j.abra...@gmail.comwrote:

 I doubt there's a useful script - there's too many details to even
 have a reliable psf-to-top converter. Google will know if anybody
 does!

 Mark

 On Fri, Aug 16, 2013 at 8:17 AM, Venkat Reddy venkat...@gmail.com wrote:
  Dear All,
  I would like to convert my NAMD psf file to GROMACS tpr file? First of
 all,
  is it possible? If so, is there any script available?
  Please help me in this regard.
 
  Thanks for your valuable time.
 
  --
  With Best Wishes
  Venkat Reddy Chirasani
  PhD student
  Laboratory of Computational Biophysics
  Department of Biotechnology
  IIT Madras
  Chennai
  INDIA-600036
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Re: [gmx-users] Lateral Diffusion of Lipids

2013-08-12 Thread Dr. Vitaly Chaban

Via an index file, I would guess... Or what do you mean exactly?

Dr. Vitaly V. Chaban


On Mon, Aug 12, 2013 at 5:26 AM, Kieu Thu Nguyen kieuthu2...@gmail.comwrote:

 Dear users,

 I want to use g_msd to measure diffusion coefficients of lipid bilayer. But
 i do not know how to choose the reference atom per lipid for an any type of
 lipid, such as POPC, DOPC,...
 Where i can get these references ?

 Thanks so much for any help !

 ~Thu
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Re: [gmx-users] Force Field for peptides and proteins

2013-08-12 Thread Dr. Vitaly Chaban

I like CHARMM.

Dr. Vitaly V. Chaban


On Mon, Aug 12, 2013 at 2:19 PM, Maria Astón Serrano 
m.aston.serr...@gmail.com wrote:

 Dear Gromacs users,

 We would like to know which is the Force Field which is customarily
 preferred for simulations of peptides and proteins.

 Thank you very much.

 Best regards,

 Maria
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Re: [gmx-users] GROMACS 4.6.3 Static Linking

2013-07-20 Thread Dr. Vitaly Chaban

Soneone said here that static versions are impossible for Cray...



Dr. Vitaly V. Chaban


On Fri, Jul 19, 2013 at 12:55 PM, Andrew R Turner a.tur...@epcc.ed.ac.ukwrote:

 Hi

 I am having problems creating static versions of the GROMACS binaries for
 a Cray XE6 (www.hector.ac.uk). The build process I am using is documented
 at:

 http://www.hector.ac.uk/**support/documentation/**
 software/gromacs/compiling_4-**6-1_phase3.phphttp://www.hector.ac.uk/support/documentation/software/gromacs/compiling_4-6-1_phase3.php

 and successfully produced static binaries for 4.6.1. Has something changed
 in the new version?

 In particular, I am setting:

 -DCMAKE_SKIP_RPATH=YES
 -DBUILD_SHARED_LIBS=OFF
 -DGMX_PREFER_STATIC_LIBS=ON
 -DCMAKE_C_FLAGS=-static -O3 -ftree-vectorize -ffast-math -funroll-loops
 -DCMAKE_CXX_FLAGS=-static -O3 -ftree-vectorize -ffast-math -funroll-loops

 but still get dynamic executables:

 gmx@hector-xe6-5:~/4.6.3-**phase3/bin ldd grompp
 linux-vdso.so.1 =  (0x7fff00da2000)
 libm.so.6 = /lib64/libm.so.6 (0x7f50dc58f000)
 libpthread.so.0 = /lib64/libpthread.so.0 (0x7f50dc371000)
 libAtpSigHandler.so.0 = /opt/cray/lib64/**libAtpSigHandler.so.0
 (0x7f50dc16b000)
 libgfortran.so.3 = /opt/gcc/4.7.2/snos/lib64/**libgfortran.so.3
 (0x7f50dbe54000)
 libscicpp_gnu.so.2 = /opt/cray/lib64/libscicpp_gnu.**so.2
 (0x7f50dbc4a000)
 libsci_gnu_mp.so.2 = /opt/cray/lib64/libsci_gnu_mp.**so.2
 (0x7f50d72ec000)
 libstdc++.so.6 = /opt/gcc/4.7.2/snos/lib64/**libstdc++.so.6
 (0x7f50d6fdf000)
 libfftw3_mpi.so.3 = /opt/cray/lib64/libfftw3_mpi.**so.3
 (0x7f50d6dc6000)
 libfftw3f_mpi.so.3 = /opt/cray/lib64/libfftw3f_mpi.**so.3
 (0x7f50d6bae000)
 libfftw3_threads.so.3 = /opt/cray/lib64/libfftw3_**threads.so.3
 (0x7f50d69a6000)
 libfftw3f_threads.so.3 = /opt/cray/lib64/libfftw3f_**threads.so.3
 (0x7f50d679d000)
 libfftw3.so.3 = /opt/cray/lib64/libfftw3.so.3 (0x7f50d63a2000)
 libfftw3f.so.3 = /opt/cray/lib64/libfftw3f.so.3
 (0x7f50d5f7c000)
 libmpich_gnu_47.so.1 = /opt/cray/lib64/libmpich_gnu_**47.so.1
 (0x7f50d5add000)
 libmpichf90_gnu_47.so.1 = /opt/cray/lib64/libmpichf90_**gnu_47.so.1
 (0x7f50d58da000)
 libmpl.so.0 = /opt/cray/lib64/libmpl.so.0 (0x7f50d56d5000)
 librt.so.1 = /lib64/librt.so.1 (0x7f50d54cb000)
 libxpmem.so.0 = /opt/cray/xpmem/default/lib64/**libxpmem.so.0
 (0x7f50d52c9000)
 libdmapp.so.1 = /opt/cray/dmapp/default/lib64/**libdmapp.so.1
 (0x7f50d5092000)
 libugni.so.0 = /opt/cray/ugni/default/lib64/**libugni.so.0
 (0x7f50d4e72000)
 libpmi.so.0 = /opt/cray/pmi/default/lib64/**libpmi.so.0
 (0x7f50d4c51000)
 libalpslli.so.0 = /usr/lib/alps/libalpslli.so.0
 (0x7f50d4a4e000)
 libalpsutil.so.0 = /usr/lib/alps/libalpsutil.so.0
 (0x7f50d4849000)
 libudreg.so.0 = /opt/cray/udreg/default/lib64/**libudreg.so.0
 (0x7f50d4641000)
 libgomp.so.1 = /opt/gcc/4.7.2/snos/lib64/**libgomp.so.1
 (0x7f50d4432000)
 libc.so.6 = /lib64/libc.so.6 (0x7f50d40d3000)
 libgcc_s.so.1 = /opt/gcc/4.7.2/snos/lib64/**libgcc_s.so.1
 (0x7f50d3ebd000)
 /lib/ld64.so.1 = /lib64/ld-linux-x86-64.so.2 (0x7f50dc812000)
 libquadmath.so.0 = /opt/gcc/4.7.2/snos/lib64/**libquadmath.so.0
 (0x7f50d3c87000)
 libcray_memcpy.so.0 = /opt/cray/lib64/libcray_**memcpy.so.0
 (0x7f50d3a84000)
 libopa.so.1 = /opt/cray/lib64/libopa.so.1 (0x7f50d3882000)
 librca.so.0 = /opt/cray/rca/default/lib64/**librca.so.0
 (0x7f50d367d000)
 libdl.so.2 = /lib64/libdl.so.2 (0x7f50d3479000)

 Any ideas?
 Andy


 ==**===
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  skype: aturner-epcc
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Re: [gmx-users] Chlorate ion force field

2013-07-16 Thread Dr. Vitaly Chaban

I am afraid you will need to derive it from scratch.


There should be some studies about perchlorate salts in literature. Make a
search.



Dr. Vitaly V. Chaban


On Tue, Jul 16, 2013 at 6:08 AM, Sushma Yadav sushc...@gmail.com wrote:

 Dear users,

 How do I get the force-field for ClO4- ion in the gromacs?

 Thanks in advance.
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Re: [gmx-users] snapshot

2013-07-15 Thread Dr. Vitaly Chaban

look for either -dt or -skip.




Dr. Vitaly V. Chaban


On Mon, Jul 15, 2013 at 2:03 AM, Rama ramkishn...@gmail.com wrote:

 Hi,

 How to get a snapshots in equal intervals of time (250ps) from production
 MD
 trajectory. I'm using -sep , -t0, -timestep but output came only one .gro
 file.



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Re: [gmx-users] How to calculate enthalpy

2013-07-15 Thread Dr. Vitaly Chaban

Sure, you can.



Dr. Vitaly V. Chaban


On Mon, Jul 15, 2013 at 8:38 AM, pooja_gu...@nccs.res.in wrote:

 Hi

 I want calculate the enthalpy of water molecule corresponding to protein
 folded and unfolded state.
 How much a single water molecule (enthalpy and free energy) contribute in
 folding ?
 Can we calculate enthapy from g_energy?



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Re: [gmx-users] How to calculate enthalpy

2013-07-15 Thread Dr. Vitaly Chaban

H = U +pV, all these terms are available through g_energy.

Your resulting values will be per mole, so I would perform no additional
normalization.

Personally, I would simulate all cases (folded, unfolded, etc) with the
same number of waters -- to avoid any possible artifacts.



Dr. Vitaly V. Chaban




On Mon, Jul 15, 2013 at 9:34 AM, pooja_gu...@nccs.res.in wrote:

 Thanks Vitaly

 but how??

 let's say the difference between unfolded to folded protein is 100 water
 molecules. What is the correct procedure to calculate (theoretically) the
 entrapy correspond to single water molecule for stabilizing/destabilizing
 the protein.

 help me

  Sure, you can.
 
 
 
  Dr. Vitaly V. Chaban
 
 
  On Mon, Jul 15, 2013 at 8:38 AM, pooja_gu...@nccs.res.in wrote:
 
  Hi
 
  I want calculate the enthalpy of water molecule corresponding to protein
  folded and unfolded state.
  How much a single water molecule (enthalpy and free energy) contribute
  in
  folding ?
  Can we calculate enthapy from g_energy?
 
 
 
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Re: [gmx-users] Mass in GMX topology

2013-07-13 Thread Dr. Vitaly Chaban

On Thu, Jul 11, 2013 at 1:17 PM, Steven Neumann s.neuman...@gmail.comwrote:

 Thank you. Another question: Does RDF depends on the mass of the atom? On
 the one hand it gives different value of the force in equation of motion
 but on the other hand velocities are rescaled with a thermostat.



It does not. Provided that ergodicity applies to your calculation/system.

No different value of the force, just of the acceleration.


Dr. Vitaly V. Chaban






 Steven


 On Thu, Jul 11, 2013 at 12:57 PM, Justin Lemkul jalem...@vt.edu wrote:

 
 
  On 7/11/13 7:54 AM, Steven Neumann wrote:
 
  Dear Users,
 
  Can you please write me where gromacs does read the mass of each atom:
 Is
  that the [atoms] under [moleculetype] or from [atomtypes] ? I wish to
  assign different mass for two different beads of the same type in my
  topology.
 
 
  It is taken from [atoms].  The entries for mass in [atomtypes] are only
  used if the mass field is blank in the [atoms] directive, IIRC.  Easy to
  check, of course, with gmxdump :)
 
  -Justin
 
  --
  ==**
 
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  Postdoctoral Associate
 
  Department of Pharmaceutical Sciences
  School of Pharmacy
  Health Sciences Facility II, Room 601
  University of Maryland, Baltimore
  20 Penn St.
  Baltimore, MD 21201
 
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 | (410)
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Re: [gmx-users] Xe atom

2013-07-11 Thread Dr. Vitaly Chaban

Indeed.


So, go to your main topology file and define a new atom type Xe under an
appropriate section. Then just add sigma and epsilon in the non-bonded
section and you are ready to explore the binding.




Dr. Vitaly V. Chaban


On Wed, Jul 10, 2013 at 12:04 PM, Divya Sunil divyasunilku...@gmail.comwrote:

 ya.. but there is experimental data to confirm the presence. can you help
 me to solve this problem


 On 9 July 2013 11:54, Dr. Vitaly Chaban vvcha...@gmail.com wrote:

 Is this, http://en.wikipedia.org/wiki/Xenon, your Xe ? If so, it will
 obviously not sit in the binding site


 Dr. Vitaly V. Chaban


 On Tue, Jul 9, 2013 at 10:39 AM, Divya Sunil divyasunilku...@gmail.com
 wrote:

  thanks for the reply.. I am planning to place Xe in the protein binding
  site ( just like a metal atom). I made a topology file with xe charge
 and
  mass. I have two options to implement the simulation. 1. like
  protein-ligand simulation. 2. replacing a number of solvent (water)
  molecules with xe in the cubic system. for these purposes what is the
  correct procedure?... do I need to simply add the xe parameters to .gro
  file and topol file?  or may i need to make changes in forcefield?  pls
 help
 
  Thanking you
  Divya
 
 
  On 8 July 2013 19:16, Dr. Vitaly Chaban vvcha...@gmail.com wrote:
 
  I am a too curious person not to ask WHY Xe is of interest in
 connection
  with the protein..?
 
 
  Dr. Vitaly V. Chaban
 
 
  On Mon, Jul 8, 2013 at 6:45 PM, Justin Lemkul jalem...@vt.edu wrote:
 
  
  
   On 7/8/13 9:21 AM, divyasunil wrote:
  
   Hello,
  
   Please help me to add Xe atom to GROMOS96 53a6 force field. I need
 to
   carry
   out a protein-Xe simulation . I tried myself but failed.
  
  
  
  
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  Germany
  ##
 
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 ##
 Dr. Divya G. Nair
 Post Doctoral Fellow
 Institute of Biophysics and Physical Biochemistry
 University of Regensburg
 Regensburg-93040
 Germany
 ##

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Re: [gmx-users] Cyclohexane as a solvent

2013-07-11 Thread Dr. Vitaly Chaban

if you prepare a separate ITP for each solvent, you will save some nerves
in the long term

Dr. Vitaly V. Chaban

On Thu, Jul 11, 2013 at 7:14 PM, Justin Lemkul jalem...@vt.edu wrote:

On 7/11/13 8:59 AM, Shima Arasteh wrote:

Dear all,

I see cyclohexane parameters in top par CGenFF files. Would it be
correct if I add this molecule to the rtp file in charmm and then use it as
a solvent rather than for example water?

The .rtp mechanism is generally used for building blocks of larger
molecules, for which topologies are built with pdb2gmx. There's nothing
wrong with building an .rtp, but it's probably about the same work as
building an .itp, and then you have to run pdb2gmx and modify the topology
it gives you (from .top to .itp). Save some work and just write the .itp
file, especially since you already have all the parameters.

Generally, how is it possible to add a new solvent to the charmm ff
simulations?

Like you would any other standalone molecule - write an .itp for it.

-Justin

--
==**

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Postdoctoral Associate

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

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Re: [gmx-users] Xe atom

2013-07-09 Thread Dr. Vitaly Chaban

Is this, http://en.wikipedia.org/wiki/Xenon, your Xe ? If so, it will
obviously not sit in the binding site


Dr. Vitaly V. Chaban


On Tue, Jul 9, 2013 at 10:39 AM, Divya Sunil divyasunilku...@gmail.comwrote:

 thanks for the reply.. I am planning to place Xe in the protein binding
 site ( just like a metal atom). I made a topology file with xe charge and
 mass. I have two options to implement the simulation. 1. like
 protein-ligand simulation. 2. replacing a number of solvent (water)
 molecules with xe in the cubic system. for these purposes what is the
 correct procedure?... do I need to simply add the xe parameters to .gro
 file and topol file?  or may i need to make changes in forcefield?  pls help

 Thanking you
 Divya


 On 8 July 2013 19:16, Dr. Vitaly Chaban vvcha...@gmail.com wrote:

 I am a too curious person not to ask WHY Xe is of interest in connection
 with the protein..?


 Dr. Vitaly V. Chaban


 On Mon, Jul 8, 2013 at 6:45 PM, Justin Lemkul jalem...@vt.edu wrote:

 
 
  On 7/8/13 9:21 AM, divyasunil wrote:
 
  Hello,
 
  Please help me to add Xe atom to GROMOS96 53a6 force field. I need to
  carry
  out a protein-Xe simulation . I tried myself but failed.
 
 
 
 
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 ##
 Dr. Divya G. Nair
 Post Doctoral Fellow
 Institute of Biophysics and Physical Biochemistry
 University of Regensburg
 Regensburg-93040
 Germany
 ##

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Re: [gmx-users] Xe atom

2013-07-08 Thread Dr. Vitaly Chaban

I am a too curious person not to ask WHY Xe is of interest in connection
with the protein..?


Dr. Vitaly V. Chaban


On Mon, Jul 8, 2013 at 6:45 PM, Justin Lemkul jalem...@vt.edu wrote:



 On 7/8/13 9:21 AM, divyasunil wrote:

 Hello,

 Please help me to add Xe atom to GROMOS96 53a6 force field. I need to
 carry
 out a protein-Xe simulation . I tried myself but failed.




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Re: [gmx-users] new forcefield not appear in slave node pdb2gmx list

2013-07-06 Thread Dr. Vitaly Chaban

I think this question is for the developers of your operating system ...



Dr. Vitaly V. Chaban


On Sat, Jul 6, 2013 at 6:10 PM, Hari Pandey hariche...@yahoo.com wrote:

 Hi all gromacs users,
 I have new forcefield and I have this folder in my working directory as
 well as in  /share/gromacs/top.  When I run pdb2gmx from head node this
 forcefield appears in list but when I run from slave nodes it do not appear
 in pdb2gmx list. could somebody tell me how do resolve this problem

 thanks in advance
 hari
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Re: [gmx-users] Re: g_velacc

Use this command line:

-- g_velacc -nonormalize -acflen 2001
-- g_integrate -f vac.xvg -integrate
-- Multiply the resulting value by 333.333, the result will be
self-diffusion coefficient expressed as result * 10^(-9) m^2/s.

The velocities should be written down at least every 10fs during MD. The
required trajectory depends on system viscosity. The higher it is, the
longer trajectory (and larger acflen) is necessary for relevant results.

Dr. Vitaly V. Chaban

On Fri, Jul 5, 2013 at 11:10 AM, David van der Spoel
sp...@xray.bmc.uu.sewrote:

On 2013-07-05 10:50, Ishwor wrote:

I have taken the fit for 2ns in Einsteins curve to calculate the diffusion
coefficient but when i take the values up to 100 ps for velocity auto
correlation i get the matching result...Is it good to do such thing? i
will
be happy if you guide me.
I have attached the graph of VAC herewith.
Thanks
http://gromacs.5086.x6.**nabble.com/file/n5009582/vac.**jpeghttp://gromacs.5086.x6.nabble.com/file/n5009582/vac.jpeg

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The graph does not show the tradition ripples. If this is for water the
result could be ok with 100 ps, but you still need to have decent sampling
(e.g. 20 fs) of the velocities since they change rapidly.

--
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Dept. of Cell Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
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Re: [gmx-users] Re: g_velacc

g_integrate should be g_analyze below. Sorry.



On Fri, Jul 5, 2013 at 12:20 PM, Dr. Vitaly Chaban vvcha...@gmail.comwrote:

 Use this command line:

 -- g_velacc -nonormalize -acflen 2001
 -- g_integrate -f vac.xvg -integrate
 -- Multiply the resulting value by 333.333, the result will be
 self-diffusion coefficient expressed as result * 10^(-9) m^2/s.

 The velocities should be written down at least every 10fs during MD. The
 required trajectory depends on system viscosity. The higher it is, the
 longer trajectory (and larger acflen) is necessary for relevant results.

 Dr. Vitaly V. Chaban


 On Fri, Jul 5, 2013 at 11:10 AM, David van der Spoel sp...@xray.bmc.uu.se
  wrote:

 On 2013-07-05 10:50, Ishwor wrote:

 I have taken the fit for 2ns in Einsteins curve to calculate the
 diffusion
 coefficient but when i take the values up to 100 ps for velocity auto
 correlation i get the matching result...Is it good to do such thing? i
 will
 be happy if you guide me.
 I have attached the graph of VAC herewith.
 Thanks 
 http://gromacs.5086.x6.**nabble.com/file/n5009582/vac.**jpeghttp://gromacs.5086.x6.nabble.com/file/n5009582/vac.jpeg
 



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 com/g-velacc-**tp5009541p5009582.htmlhttp://gromacs.5086.x6.nabble.com/g-velacc-tp5009541p5009582.html
 Sent from the GROMACS Users Forum mailing list archive at Nabble.com.

  The graph does not show the tradition ripples. If this is for water the
 result could be ok with 100 ps, but you still need to have decent sampling
 (e.g. 20 fs) of the velocities since they change rapidly.

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

In which case can the determinant not be computed?


Dr. Vitaly V. Chaban


On Thu, Jul 4, 2013 at 10:53 AM, Sergey gandalfg...@yandex.ru wrote:

 Dear users,

 I'm trying to run MD with SWM4-DP model (data from
 http://virtualchemistry.org), but I always have error:
 Can not invert matrix, determinant =.

 I did energy minimization etc. but it don't help...

 May be someone have complete stuff of files for
 shell MD, including .mdp file ?

 Sergey
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Re: [gmx-users] shell MD

The was a bug report on this error a few years ago,
http://redmine.gromacs.org/issues/332

Can your problem correlate with that discussion, perhaps?




Dr. Vitaly V. Chaban


On Fri, Jul 5, 2013 at 1:58 PM, Sergey gandalfg...@yandex.ru wrote:

 In case of MD run. Minimization procedure was successful.

 05.07.2013, 14:48, Dr. Vitaly Chaban vvcha...@gmail.com:
  In which case can the determinant not be computed?
 
  Dr. Vitaly V. Chaban
 
  On Thu, Jul 4, 2013 at 10:53 AM, Sergey gandalfg...@yandex.ru wrote:
 
   Dear users,
 
   I'm trying to run MD with SWM4-DP model (data from
   http://virtualchemistry.org), but I always have error:
   Can not invert matrix, determinant =.
 
   I did energy minimization etc. but it don't help...
 
   May be someone have complete stuff of files for
   shell MD, including .mdp file ?
 
   Sergey
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Re: [gmx-users] shell MD

Vitaly saw this problem while running gromacs/mopac interface about 4 years
ago... The impression was that the problem is related to incorrectly
computed forces.

I would file a bug report.




Dr. Vitaly V. Chaban


On Fri, Jul 5, 2013 at 2:43 PM, Sergey gandalfg...@yandex.ru wrote:

 Possibly, can :)
 I will have to run shell MD in NAMD, though it will be slower a bit.
 Seemingly, only Vitaly see my problem :).


 05.07.2013, 16:31, Dr. Vitaly Chaban vvcha...@gmail.com:
  The was a bug report on this error a few years ago,
  http://redmine.gromacs.org/issues/332
 
  Can your problem correlate with that discussion, perhaps?
 
  Dr. Vitaly V. Chaban
 
  On Fri, Jul 5, 2013 at 1:58 PM, Sergey gandalfg...@yandex.ru wrote:
 
   In case of MD run. Minimization procedure was successful.
 
   05.07.2013, 14:48, Dr. Vitaly Chaban vvcha...@gmail.com:
   In which case can the determinant not be computed?
 
   Dr. Vitaly V. Chaban
 
   On Thu, Jul 4, 2013 at 10:53 AM, Sergey gandalfg...@yandex.ru
 wrote:
Dear users,
 
I'm trying to run MD with SWM4-DP model (data from
http://virtualchemistry.org), but I always have error:
Can not invert matrix, determinant =.
 
I did energy minimization etc. but it don't help...
 
May be someone have complete stuff of files for
shell MD, including .mdp file ?
 
Sergey
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Re: [gmx-users] Re: Re: Lennard-Jones potential for protons

2013-07-04 Thread Dr. Vitaly Chaban

why not to pick up a QM technique to study the interaction?

Dr. Vitaly V. Chaban


On Thu, Jul 4, 2013 at 3:58 AM, Jong Wha Lee jongwh...@postech.ac.krwrote:

 Thank you Mark and Vitaly.



 I understand that simulation of protons in the solution phase is
 unphysical.
 Though I haven't mentioned beforehand, I'm actually trying to simulate
 noncovalent interaction between a proton and a carbonyl oxygen in the gas
 phase. Could you give me any ideas how I may simulate this?



 Thank you very much





 Jong Wha

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Re: [gmx-users] Re: g_velacc

2013-07-04 Thread Dr. Vitaly Chaban

It would be nice to see plotted velocity autocorrelation function, VACF,
which you integrate?

The resulting diffusion constant looks crazy large, so there must be
something rotten in the VACF.



Dr. Vitaly V. Chaban


On Thu, Jul 4, 2013 at 8:32 AM, Ishwor ishwor.poudya...@gmail.com wrote:

 I have really tried to calculate diffusion coefficient using both commands
 but i cant find the comparable results.
 i have my *.mdp file as
 ;PREPROCESSING parameters
 tinit   = 0
 integrator  = md
 dt  =.002
 nsteps  = 1
 nstcomm = 1

 ;OUPUT CONTROL parameters.
 nstxout =  500
 nstvout =  500
 nstfout =  500
 nstlog  =  500
 nstenergy   =  500
 nstxtcout   =  500
 energygrps  =  system
 ;NEIGHBOUR SEARCHING parameters.
 nstlist =  10
 ns_type =  grid
 rlist   =  1.0
 ;ELECTROSTATIC and VdW parameters.
 rcoulomb=  1.0
 rvdw=  1.0
 epsilon-r   =  1
 ;BERENDSEN TEMPERATURE COUPLING is on in two groups
 Tcoupl  =  berendsen
 tc-grps =  system
 tau_t   =  0.1
 ref_t   =  303

 ;PRESSURE COUPLING is on
 Pcoupl  =  no
 gen_vel =  no;
 ;BONDS parameters
 constraints = all-bonds
 constraint-algorithm = shake
 unconstrained-start  = yes
 pbc  = xyz
 i have calculated the diffusion coefficient using Einsteins law and found
 2.40*10^-5 cm^2/s. I have used 2 ns time to fit the curve.
 To calculate the diffusion coefficient using g_velacc i used the command
  g_velacc -f nvt.trr -s nvt.tpr -n index.ndx -o vac.xvg -nonormalize
 -acflen
 2001 -mol
 and integrate using g_analyze -f vac.xvg -integrate
 but i found the result
 Calculating the integral using the trapezium rule
 Integral 1 0.11915  +/-0.0
   std. dev.relative deviation of
standard   -   cumulants from those of
 set  average   deviation  sqrt(n-1)   a Gaussian distribition
   cum. 3   cum. 4
 SS1   1.262569e-04   5.975760e-03   1.336220e-04  27.976   664.233

 I guess the required integral value is 0.11915 and to find diffusion
 coefficient i divide the result by 3 but get the result not matching with
 the one found using g_msd. i guess the value 0.11915 is in unit nm^2/ps.
 I dont know whether i am in the correct path or there is some problems with
 my doings.
 i am waiting for the suggestions
 Thanks




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Re: [gmx-users] Lennard-Jones potential for protons

2013-07-03 Thread Dr. Vitaly Chaban

I am also not aware of the force field parameters for hydrated/solvated
proton, but maybe I am just wrong here.

An attempt to describe proton with Newtonian dynamics will unlikely give
you anything similar to reality. Lennard-Jones parameters play no role
here, by the way, some force fields assign zero sigma and zero epsilon to
hydrogen, for instance, in water molecule.

If you construct a particle, such as H3O+ or H5O2+, etc, it might work
somehow. But you definitely need to run some QM calculations on these
particles beforehand.


Dr. Vitaly V. Chaban




On Wed, Jul 3, 2013 at 10:00 AM, Mark Abraham mark.j.abra...@gmail.comwrote:

 One does not have a free proton in a condensed phase simulation, which
 is what all those force fields target. And even if you do, a
 classical-mechanics description of it will probably be poor at best.

 Mark

 On Wed, Jul 3, 2013 at 9:35 AM, Jong Wha Lee jongwh...@postech.ac.kr
 wrote:
  Dear Gromacs Users,
 
 
 
  Hi, I'm trying to simulate a system with a free proton included.
 However, I
  wasn't able to find Lennard-Jones parameters for free protons in charmm,
  amber, and opls ff. On the other hand, there are parameters for other
  cations such as Na, K, etc.
 
  Is there any reason why parameters for free protons are not included? Or
 is
  there any way I may find appropriate parameters?
 
 
 
  Thank you very much in advance,
 
 
 
  Jong Wha
 
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Re: [gmx-users] Atomtype OWT3 not found during EM step

2013-07-03 Thread Dr. Vitaly Chaban

I would guess the new atom type should be in the ITP file. And of course,
you are expected to define bonded and nonbonded terms for all applicable
pairs, triples... of atoms.

Good luck.


Dr. Vitaly V. Chaban


On Wed, Jul 3, 2013 at 6:41 PM, Juganta K. Roy juganta...@yahoo.com wrote:

 Dear all,

 I am a new user of GOMACS. My system contains Polymer and Water. I used
 gromos53a6 force field and spc water model, it ran nicely.

 But now I want to use TIP3P water model with the same force
 field (gromos53a6), in that case, I am getting a error message from the
 'grompp' during energy minimization step - Fatal error: Atomtype OWT3 not
 found.

 From GMX users Forum I got some information to resolve this problem. Such
 that, I added OWT3 at the bottom of the  .atp file of the related force
 field and also edited the nonbonded.itp file. But I couldn't get rid of
 such kind of error.

 Would you please give me suggestion to fix it?

 Thanks in advance for the help.


 Jugnata
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Re: [gmx-users] System expansion

2013-06-20 Thread Dr. Vitaly Chaban

Hi Oliver -

Hmm. Did you try to start from (a little bit) different configurations
on the problematic machine? Or re-install gromacs there, perhaps?

Dr. Vitaly Chaban

On Thu, Jun 20, 2013 at 3:44 PM, Oliver Schillinger
o.rus...@fz-juelich.dewrote:

Dear Gromacs users,

I experience a very strange problem.
I have a well equilibrated system consisting of a protein, a ligand, ions
and water. On most machines I run my simulations on, everything is just
fine. Except for one compute cluster, where the system undergoes an extreme
expansion when I use the md-vv integrator for an NPT-simulation. To give
you an impression I uploaded a short video showing the first 100
picoseconds of the run to my Dropbox:
https://www.dropbox.com/s/**d1ef94bbns0hasr/explode.mpghttps://www.dropbox.com/s/d1ef94bbns0hasr/explode.mpg

The system expands so heavily that it consists mainly of vacuum.
If I switch the integrator from md-vv to md, everything is fine again.
The same simulation (same .mdp file, same starting positions and
velocities from previous simulation) runs fine with the md-vv integrator on
our GPU-cluster.

The .mdp file can be downloaded here:
https://www.dropbox.com/s/**k9it6eiqb259o59/explode.mdphttps://www.dropbox.com/s/k9it6eiqb259o59/explode.mdp

I have no idea if it is me who is doing something wrond, a bug in Gromacs,
a problem with the cluster or something else.
Any suggestions and ideas are appreciated.

Regards,
Oliver

--
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52425 Juelich | Germany

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Re: [gmx-users] shall we use double precision?

It is *desirable*.

In many cases of free energy calculations, single precision is still
reliable.

Dr. Vitaly Chaban






On Tue, Jun 11, 2013 at 7:35 AM, Albert mailmd2...@gmail.com wrote:

 Hello :

  I am going to use Gromacs with PLUMD plugin to perform Metadynamics.
 Since this methods involved in free energy calculations, I am just
 wondering is it necessary to introduce double precision Gromacs?

 thank you very much

 Albert
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Re: [gmx-users] Constraints of distance

I think all is correct.

Why are you asking? People normally report problems.

Dr. Vitaly Chaban






On Tue, Jun 11, 2013 at 12:30 PM, Steven Neumann s.neuman...@gmail.comwrote:

 Dear Gmx Users,

 I am running CG simulation and I wish my beads to be constraint - one away
 from each other of 0.4 nm. I wan to use Lincs for this purpose. I do not
 have any bonds in my topology or rtp entry. I just add:

 [ constraints ]
 1 2  1  0.4
 2 3  1  0.4
 ...
 31   32 1  0.4

 constraints = none
 constraint_algorithm = Lincs


 Is that correct? I used function 1, is that right?

 Shall I specify something else?


 Steven
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Re: [gmx-users] A charge group moved too far between two domain decomposition steps

This problem indeed happens from time to time. With versions 4.5+ it is
more frequent than with versions up to 4.0.7. It is not always connected to
blowing up in the sense of bad contacts, positive potential energy, etc.
The more cores you use per job, the more likely this error to appear. The
larger *spatially) system you simulate, the more likely it to appear.

The simple advice is to reduce the time-step, but it is not to be
understood as a universal treatment.

Of course, you can reinitialize your charge groups, as this is better
connected with the below error message.

Dr. Vitaly Chaban

On Tue, Jun 11, 2013 at 12:54 PM, Justin Lemkul jalem...@vt.edu wrote:

On 6/11/13 1:30 AM, Souilem Safa wrote:

Dear Gromacs users,
I tried to do the simulation of a single molecule in cyclohexane, I'm
using
gromos 53a6 force field for both molecules.
i did all the minimization steps. After npt, I runned for 25 000 000
steps.
just after around 100 000 steps, the system stops and i got this fatal
error:

Fatal error:
A charge group moved too far between two domain decomposition steps
This usually means that your system is not well equilibrated

Then I back again to npt step to equilibrate for longer time as the error
message said to me, I equilibrate for 500 000 steps instead of 25
steps
setted in the mdp file, but again I got the same error.

What should I do to overcome this problem?

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

There are plenty of possible problems within your topology or .mdp
settings. Unfortunately, you provided neither, but everything there is to
say is fairly well summarized in the link.

-Justin

--
==**==

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Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
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Re: [gmx-users] stay at some temperature during annealing

On Tue, Jun 11, 2013 at 12:52 PM, Justin Lemkul jalem...@vt.edu wrote:



 On 6/11/13 1:11 AM, mu xiaojia wrote:

 Hi guys,

 I am using simulated annealing for my protein+water+Ion system, I tried to
 let the system stay at some temperature for a while, e.g.: stay at 600k
 from 3000ps to 1 ps, then gradually cool it down to 298k, so my mdp is
 like:

 annealing_time = 0 3000 1 2 0 3000 1 2 0 3000 1 2
 annealing_temp = 298 600 600 298 298 600 600 298  298 600 600 298


 however, error message is:

 Found 12 annealing_time values, wanter 9

 apparently, the 600 600 does not work, does anyone have any suggestion,
 or I could only separate the simulation? Thanks very much!




There is a problem with the number of temperature coupling groups. You have
defined less than you expect, as the program requests only 9 values. So,
refer to the number of points to T annealing, which you do not list here.


Dr. Vitaly Chaban
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Re: [gmx-users] A charge group moved too far between two domain decomposition steps

On Tue, Jun 11, 2013 at 3:52 PM, Justin Lemkul jalem...@vt.edu wrote:

On 6/11/13 9:27 AM, Dr. Vitaly Chaban wrote:

This problem indeed happens from time to time. With versions 4.5+ it is
more frequent than with versions up to 4.0.7. It is not always connected
to
blowing up in the sense of bad contacts, positive potential energy, etc.
The more cores you use per job, the more likely this error to appear. The
larger *spatially) system you simulate, the more likely it to appear.

People generally reported more crashes in 4.5.x than in 4.0.x that we
determined arise from nsttcouple and nstpcouple being set incorrectly.
There's a thread somewhere about it, but in general, the same principles
are always true - adequate equilibration and sensible .mdp settings should
lead to stable integration later on.

I can send you a couple of systems, which spontaneously crash. Not at the
beginning and not at the end, just unpredictably every few dozens of
nanoseconds. The systems are not strictly in the thermodynamic equilibrium
state, but they are not exploding in the common sense of this term. Another
coordinate files, executed with the same MDP file, never crash, however. I
do not really know the reason, but it is not as simple as good or bad set
of MD parameters. Maybe, something is connected with (deprecated) versions
of external libraries, since at my workstation, where I control everything,
crashes occur more rarely than at the cluster.

The simple advice is to reduce the time-step, but it is not to be
understood as a universal treatment.

Of course, you can reinitialize your charge groups, as this is better
connected with the below error message.

What does this mean? Charge groups are a fixed element of the force
field; how would you propose adjusting them to make the error go away?

Really? How many force fields can you enumerate, where the developers say
how we should distribute atoms among the charge groups?

Not all MD codes use charge group mechanism, by the way.

Anyways, this is not my thread. Perhaps, the starter really has a simple
problem with blowing up.

Dr. Vitaly Chaban

-Justin

--
==**==

==**==

Re: [gmx-users] Constraints of distance

Steven -

I probably know nothing about function #2, but function 1 is used just
everywhere. It does constrain intramolecular distances.

Good luck. Vitaly


Dr. Vitaly Chaban


On Tue, Jun 11, 2013 at 4:46 PM, Steven Neumann s.neuman...@gmail.comwrote:

 I was not sure about the fucntion type (1 or 2). Once in manual it is
 stated that function 1 is only for exclusions and another time it can be
 used to miimc bonds. Both functions are working though.  Thanks anyway.

 Steven


 On Tue, Jun 11, 2013 at 2:18 PM, Dr. Vitaly Chaban vvcha...@gmail.comwrote:

 I think all is correct.

 Why are you asking? People normally report problems.

 Dr. Vitaly Chaban






 On Tue, Jun 11, 2013 at 12:30 PM, Steven Neumann s.neuman...@gmail.com
 wrote:

  Dear Gmx Users,
 
  I am running CG simulation and I wish my beads to be constraint - one
 away
  from each other of 0.4 nm. I wan to use Lincs for this purpose. I do not
  have any bonds in my topology or rtp entry. I just add:
 
  [ constraints ]
  1 2  1  0.4
  2 3  1  0.4
  ...
  31   32 1  0.4
 
  constraints = none
  constraint_algorithm = Lincs
 
 
  Is that correct? I used function 1, is that right?
 
  Shall I specify something else?
 
 
  Steven
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Re: [gmx-users] Membrane Equilibration

what happens to your energy before the observed crash? does the crash
happen at the same time-step each time?


Dr. Vitaly Chaban


On Tue, Jun 11, 2013 at 5:22 PM, Neha nshafi...@wesleyan.edu wrote:

 Hi everybody,

 I am trying to simulate a lipid bilayer and wanted to use Parrinello Rahman
 coupling. However, I read that Parinello-Rahman is not great for
 equilibration so I thought I would do a small run using the Berendsen
 barostat to decrease the chances of large oscillations. I then used the
 .gro
 file obtained from that run to start a new run using Parrinello-Rahman. I
 am
 not sure if that's the correct way to go about doing what I want to do.

 My Parrinello run also terminated a little while in, with the error that 2
 of my atoms have moved further apart than the cut-off distance. A part of
 my
 mdp file is pasted below and I was wondering if anyone had any suggestions
 as to stop that from happening. My time step is 0.02 ps and I thought
 increasing tau-p might work. I am using the compressibility from the map
 file on the Martini website and am worried that might be too large. Any
 help
 will be super useful! Let me know if you need any more information.


 ; OPTIONS FOR WEAK COUPLING ALGORITHMS =
 ; Temperature coupling   =
 tcoupl   = nose-hoover
 ; Groups to couple separately =
 tc-grps  = DPPC W
 ; Time constant (ps) and reference temperature (K) =
 tau_t= 1.0 1.0
 ref_t= 320 320
 nsttcouple   = 1
 ; Pressure coupling  =
 Pcoupl   = Parrinello-Rahman
 Pcoupltype   = semiisotropic
 ; Time constant (ps), compressibility (1/bar) and reference P (bar) =
 tau_p= 5.0  5.0
 compressibility  = 3e-4 3e-4
 ref_p= 0.0  0.0
 nstpcouple   = 5

 ; GENERATE VELOCITIES FOR STARTUP RUN =
 gen_vel  = yes
 gen_temp = 105
 gen_seed = 473529



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Re: [gmx-users] System does not heat up to 300K.

According to your MD parameters, your system should attain T=300K at the 300th
nanosecond.

Since you have run only for 50 * 0.002 ps = 1ns, you got T=1K, since
temperature elevates linearly, based on your setup.


Dr. Vitaly Chaban




On Tue, Jun 11, 2013 at 8:07 PM, Marc Hömberger hoe...@gmail.com wrote:

 Hi,

 I have a system setup (minimized etc.) and wanted to heat this system
 gradually with simulated annealing. I set up the mdp file as you can see
 below (simulated annealing part is marked bold). But when the heating is
 finished, the log file tells me that the temperature of the system is only
 1K (see below).

 Can someone tell me what I am doing wrong?


 Best,
 Marc

 ; PREPROCESSING *
 ;include=
 ;define =
 ; RUN CONTROL ***
 dt  = 0.002 ; timestep, 2 fs
 integrator  = md; leap-frog integrator
 nsteps  = 50 ; 2 * 50 = 1000 ps
 tinit   = 0 ; starting time, ps
 init_step   = 0 ; starting step
 comm-mode   = linear; remove COM translation
 nstcomm = 10; freq steps comm-mode
 comm-grps   = system; groups COM removal ; protein
 nstcalcenergy   = -1; freq calc ener; default = nstlist
 ; DYNAMICS **
 ;### Initial velocity assignment
 gen_vel = yes   ; assign velocities from Maxwell
 distribution
 gen_temp= 300   ; temperature for Maxwell
 distribution
 gen_seed= -1; random generator seed; -1 from
 job ID
 ; OUTPUT CONTROL 
 ;### xtc
 nstxtcout   = 2500  ; .xtc freq write coor
 xtc-precision   = 1000  ; .xtc precision
 xtc_grps= system; .xtc saved groups
 ;### trr
 nstxout = 50; .trr freq write coor
 nstvout = 50; .trr freq write vel
 nstfout = 0 ; .trr freq write forces
 ;### log
 nstlog  = 2500  ; .log freq write ener
 ;### edr
 nstenergy   = 2500  ; .edr freq write ener; =
 i*nstcalcenergy
 energygrps  = protein non-protein   ; .edr saved groups
 ; NON-BONDED INTERACTIONS ***
 ns_type = grid  ; search neighbor grid cells
 nstlist = 10; freq update NB list

 vdwtype = switch; switching function for VdW
 coulombtype = PME   ; PME for long-range electrostatics
 rvdw_switch = 0.9   ; switching dist VdW
 rvdw= 1.0   ; cutoff VdW
 rcoulomb= 1.2   ; cutoff elec
 rlist   = 1.2   ; cutoff NB list; must = rcoulomb
 when PME

 epsilon-r   = 1 ; dielectric const
 DispCorr= EnerPres  ; Long-range VdW dispersion
 correction

 ;### PME  Ewald
 ewald_rtol  = 1.0e-5; direct space tolerance;
 1.0e-6/2.2e-5
 fourierspacing  = 0.12  ; max grid spacing for FFT
 pme_order   = 6 ; interpolation order; depends on
 cutoff
 ewald_geometry  = 3d; Ewald in 3d
 epsilon_surface = 0 ; dipole correction for 3d Ewald
 optimize_fft= yes   ; start-up FFT grid optimization
 ; BOUNDARY CONTROL **
 pbc = xyz   ; 3-D PBC
 ; CONSTRAINTS CONTROL ***
 constraints = all-bonds ; all bonds (even heavy atom-H
 bonds) constrained
 continuation= no; constraints applied to initial
 conf
 constraint_algorithm = lincs; holonomic constraints
 lincs_iter  = 1 ; accuracy of LINCS
 lincs_order = 4 ; also related to accuracy
 lincs_warnangle = 30; max allowed bond angle before
 warning
 ; TEMPERATURE CONTROL ***
 tcoupl  = nose-hoover   ; Nose-Hoover T-coupling; v-rescale
 tc-grps = system; two coupling groups - more
 accurate
 tau_t   = 0.6   ; coupling time constant at equil,
 in ps
 ref_t   = 300   ; reference temperature, one for
 each group, in K
 ; PRESSURE CONTROL **
 pcoupl  = Parrinello-Rahman ; Pressure coupling on in
 NPT
 pcoupltype  = isotropic

Re: [gmx-users] Can we connect two boxes together for the simulation?

2013-06-04 Thread Dr. Vitaly Chaban

editconf is a nice tool to create vacuum in your box. You can then insert
one of your box into another box using cat box1.gro box2.gro, just remove
the very last line in box1.gro.

Dr. Vitaly Chaban









On Tue, Jun 4, 2013 at 2:46 PM, Bao Kai paeanb...@gmail.com wrote:

 Hi, all,

 I want to do NPT simulations with different compositions first. Then I want
 to connect the two boxes to continue the NPT simulation.

 I mean, after simulations, we get two boxes with different compositions.

 Can we do that with gromacs? or how can we do that?

 Thanks.

 Best,
 Kai
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Re: [gmx-users] Can we connect two boxes together for the simulation?

2013-06-04 Thread Dr. Vitaly Chaban

Nohow.

Numbers in GRO files serve exclusively decorative function.


Dr. Vitaly Chaban





On Tue, Jun 4, 2013 at 4:12 PM, Bao Kai paeanb...@gmail.com wrote:

 Hi,


 I guess the renumbering of the atoms and molecules will be a problem,
 especially when the two boxes contain the same type of the molecules.


 How can we handle that?


 Thanks.


 Best,

 Kai




 editconf is a nice tool to create vacuum in your box. You can then insert
 one of your box into another box using cat box1.gro box2.gro, just remove
 the very last line in box1.gro.

 Dr. Vitaly Chaban









 On Tue, Jun 4, 2013 at 2:46 PM, Bao Kai paeanball at gmail.com
 http://lists.gromacs.org/mailman/listinfo/gmx-users wrote:

 * Hi, all, I want to do NPT simulations with different compositions
 first. Then I want** to connect the two boxes to continue the NPT
 simulation. I mean, after simulations, we get two boxes with
 different compositions. Can we do that with gromacs? or how can we do
 that? Thanks. Best,** Kai** --** gmx-users mailing list
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Re: [gmx-users] ngmx not installed in gmx4.6.1

2013-06-04 Thread Dr. Vitaly Chaban

I do not know about the newest versions, but in older ones ngmx was missed
when you did not have the lesstif library installed.


Dr. Vitaly Chaban







On Tue, Jun 4, 2013 at 5:55 PM, Chandan Choudhury iitd...@gmail.com wrote:

 Dear gmx users,

 I had installed gromacs 4.6.1 using cmake. All the binaries are installed,
 but surprisingly I do not find ngmx executable. Can anyone guide me how do
 I install ngmx using cmake.

 Chandan
 --
 Chandan kumar Choudhury
 NCL, Pune
 INDIA
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Re: [gmx-users] .GRO Formatting

2013-05-30 Thread Dr. Vitaly Chaban

In GRO file, the atom numbers do not really matter. Just use any number you
like. It will work correctly.

mdrun will renumber atoms from 9, as it likes, automatically.

Dr. Vitaly Chaban






On Thu, May 30, 2013 at 4:57 AM, Phil pmcho...@syr.edu wrote:

 I'm working on a .GRO file and have come across a formatting error.

 In the manual, it states that the spacing for each column in the .GRO file
 is:

 residue number (5 positions, integer)
 residue name (5 characters)
 atom name (5 characters)
 atom number (5 positions, integer)
 position (in nm, x y z in 3 columns, each 8 positions with 3 decimal
 places)
 velocity (in nm/ps (or km/s), x y z in 3 columns, each 8 positions with 4
 decimal places)

 In my .GRO file, the atom number exceeds 5 positions. How should I reformat
 the .GRO file to account for this?



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Re: [gmx-users] Difference between the electrostatic treatments PME/Cut-offs and Reaction Field

2013-05-30 Thread Dr. Vitaly Chaban

Hmmm...

And what does the observed difference look like, numerically?





On Thu, May 30, 2013 at 10:14 AM, Mark Abraham mark.j.abra...@gmail.comwrote:

 No charges = no problem. You can trivially test this yourself with mdrun
 -rerun ;-)  Manual 4.1.4 talks about what RF is doing.

 Mark


 On Thu, May 30, 2013 at 6:38 AM, Dallas Warren dallas.war...@monash.edu
 wrote:

  In a system that has no charges, should we observe a difference between
  simulations using PME/Cut-offs or Reaction Field?
 
  From my understanding there should not be, since there are no charges
  which treatment you use shouldn't' make a difference.
 
  However, it does and I am trying to work out why.
 
  Any suggestions on the reason?
 
  What is it that Reaction Field is doing, does it influence anything other
  than long range charge interactions?
 
  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.
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Re: [gmx-users] Continue simulation from the specific time

If the frame was saved to the trajectory file, just extract it with

trjconv -dump $timeframe -o conf.gro

and continue your MD.

No need for any additional energy minimizations, of course.

Dr. Vitaly Chaban






On Wed, May 29, 2013 at 12:45 PM, Андрей Гончар gontc...@gmail.com wrote:

 Hello, I've got a question. Is there a way to continue MD simulation, not
 from last state but from specific time of MD? Say we have made a MD, have
 analysed it and have found an interresting molecule conformation at
 specific frame. Can we continue from this point or we should extract this
 frame, make all minimisations etc.?

 --
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 Андрей Гончар
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Re: [gmx-users] Continue simulation from the specific time

Aside from original question, you will probably want to initialize
velocities (gen_vel) in order to evolve a different trajectory rather than
repeating previous one.

Dr. Vitaly Chaban






On Wed, May 29, 2013 at 1:00 PM, Dr. Vitaly Chaban vvcha...@gmail.comwrote:

 If the frame was saved to the trajectory file, just extract it with

 trjconv -dump $timeframe -o conf.gro

 and continue your MD.

 No need for any additional energy minimizations, of course.

 Dr. Vitaly Chaban






 On Wed, May 29, 2013 at 12:45 PM, Андрей Гончар gontc...@gmail.comwrote:

 Hello, I've got a question. Is there a way to continue MD simulation, not
 from last state but from specific time of MD? Say we have made a MD, have
 analysed it and have found an interresting molecule conformation at
 specific frame. Can we continue from this point or we should extract this
 frame, make all minimisations etc.?

 --
 Andrew Gonchar
 Андрей Гончар
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[gmx-users] Re: choice of force field -reg

If you want to observe H-bond dynamics and do it with an atomistic
precision than, of course, you need an all-atom representation. United
atoms will still *effectively* account for H-bonding, if you are happy with
reduced precision.

Dr. Vitaly Chaban




On Wed, May 29, 2013 at 8:01 AM, Revthi Sanker revthi.san...@yahoo.comwrote:

 Dear Sir,
 I would like to express my deepest gratitude for patiently reading my
 query. I am simulating the cholesteryl ester transfer protein ( the crystal
 structure has 4 bound lipids). I propose to study the inhibitor induced
 changes in the conformation of protein and the bound lipids. I am assuming
 unless I perform an all-atom  simulation, I will be missing out some
 crucial interactions like H-bond formation and breaking. Kindly let me if
 my understanding is wrong.
 Thank you so much once again for the reply,
 Revathi

 --- On *Tue, 28/5/13, Dr. Vitaly Chaban vvcha...@gmail.com* wrote:


 From: Dr. Vitaly Chaban vvcha...@gmail.com
 Subject: Re: choice of force field -reg
 To: Revthi Sanker revthi.san...@yahoo.com, gmx-users@gromacs.org
 Date: Tuesday, 28 May, 2013, 4:14 PM

 without knowing full details of your simulated system and the goals you
 pose, I cannot advise anything more definite than I did before.

 if I were you and my system were yours, I would start with MARTINI FF.

 I wish you a success in your endeavor.

 Dr. Vitaly Chaban




 On Tue, May 28, 2013 at 6:11 PM, Revthi Sanker 
 revthi.san...@yahoo.comhttp://mc/compose?to=revthi.san...@yahoo.com
  wrote:



 Dear Sir,
 Thank you so much for your reply. To be specific, my system has only four
 lipid moities- 2 cholesteryl oleates and 2 phosphotidyl cholines. But I was
 not able to get all atom paramters for these lipids from the lipid book(
 only united atom parameters were available). So I had resorted to using
 united atom for the whole system. But I am afraid if I am missing out on
 some crucial protein-drug interactions because of this united atom
 consideration.
 Kindly guide me in this regard.
 Thank you so much once again.

 Yours sincerely,
 Revathi
 M.S.Research Scholar
 Indian Institute of Technology Madras
 India



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Re: [gmx-users] How to choose bd_fric value in brownian dynamics

According to my understanding, setting friction coefficient is quite a
personal thing. The higher is bd-fric, the smaller are velocities.

Why not to set bd-fric = 0 in order to start with? See manual for details
of how this trick works.

Dr. Vitaly Chaban





On Wed, May 29, 2013 at 11:48 AM, Mohan maruthi sena maruthi.s...@gmail.com
 wrote:

 Hi all,
  I want to perform brownian dynamics simulations  using gromacs
 4.5.5 for  a system containing  protein in water. What is the basis to
 select the bd_fric value for this system.  I came to know through previous
 posts that a value of 3000 would be fine for a time step less than 4fs. My
 question is on what basis we choose the value for bd_fric ? How does high
 bd_fric value impact  a simulation when compared to slow bd_fric value ?


 Thanks for  a reply in advance,
 Mohan
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Re: [gmx-users] How to choose bd_fric value in brownian dynamics

Hello Mohan -

I do not use Brownian dynamics code routinely to have exact values for
various cases, but if I were you, I would start with smaller value and then
increase, until your simulation runs fine. The time-step depends not on the
method, but on characteristic oscillations (bond lengths, etc) in your
system, so maybe 2fs is just too much for your case. Although one, in
principle, can scale the force and apply a large time-step, it will not
bring any performance gain at the very end.

It is my impression that there are very few people in the community,  who
use BD engine in GROMACS. Why don't you want to use molecular dynamics?

Dr. Vitaly Chaban




On Wed, May 29, 2013 at 4:10 PM, Mohan maruthi sena
maruthi.s...@gmail.comwrote:

 Hello Sir ,
 Thanks for your quick reply. I have used bd_fric =0 and then my
 simulation is blowing up. I have used a time step of 0.002ps, Hence i
 thought if i  can use some other value rather than zero  but I do not know
 which value to use. Can you suggest   any general value for protein water
 simulations.

 Thanks,
 Mohan


 On Wed, May 29, 2013 at 4:46 PM, Dr. Vitaly Chaban vvcha...@gmail.comwrote:

 According to my understanding, setting friction coefficient is quite a
 personal thing. The higher is bd-fric, the smaller are velocities.

 Why not to set bd-fric = 0 in order to start with? See manual for details
 of how this trick works.

 Dr. Vitaly Chaban





 On Wed, May 29, 2013 at 11:48 AM, Mohan maruthi sena 
 maruthi.s...@gmail.com
  wrote:

  Hi all,
   I want to perform brownian dynamics simulations  using gromacs
  4.5.5 for  a system containing  protein in water. What is the basis to
  select the bd_fric value for this system.  I came to know through
 previous
  posts that a value of 3000 would be fine for a time step less than 4fs.
 My
  question is on what basis we choose the value for bd_fric ? How does
 high
  bd_fric value impact  a simulation when compared to slow bd_fric value ?
 
 
  Thanks for  a reply in advance,
  Mohan
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Re: [gmx-users] Extending simualtions

On Wed, May 29, 2013 at 3:14 PM, Fábio Filippi Matioli 
fabiof...@hotmail.com wrote:

 Hello, I have a problem.
 I try to extending my simulation. I made this steps.

 tpbconv -s previous.tpr -extend timetoextendby -o next.tpr
 mdrun -s next.tpr -cpi previous.cpt

 I need to put more things on mdrun, or only this? because my first mdrun
 had 4 or 5 outputs, or the extending recognize de outputs from the first
 time?



Checkpoint file contains everything you need to go on.




 I cant run, and gromcs give me this error

 File appending requested, but only 2 of the 4 output files are present

 Tnks




I believe the idea is that you should have trajectory file, energy file,
logfile, etc, so that gromacs could append them. If they have non-default
name, you probably should specify them explicitly in the invocation line.


Dr. Vitaly Chaban













 Fábio Filippi MatioliGraduando em Física MédicaUNESP-BotucatuTel (19)
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Re: [gmx-users] pulling simulations

The force should not probably exceed kT product too much...

Dr. Vitaly Chaban


On Wed, May 29, 2013 at 3:19 PM, Sathish Kumar sathishk...@gmail.comwrote:

 Dear Sir,
  In pulling simulations how to set pull_rate and
 pull_k .On which basis we can set these values.
 --
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[gmx-users] Re: Extending simulations

I do not remember all the keys.

Rename your files to their default names and you will have nothing to
specify except

mdrun -cpi




On Wed, May 29, 2013 at 6:31 PM, Fábio Filippi Matioli 
fabiof...@hotmail.com wrote:

 Hello, i'm who asked about extending simulations.
 You sad for me pen teh checkpoint file, u say the file .cpt?
 But its a binary file... Can you give a example of extending simulation if
 my first mdrun its this:

 mdrun -v -s full -o full -e full -c after_full -np 8 -gflog full.job

 Tnks

 *Fábio Filippi Matioli*
 Graduando em Física Médica
 UNESP-Botucatu
 Tel (19) 9291.6738

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[gmx-users] Re: Extending simulations

perhaps mdrun -cpi -deffnm full

will also do the job in your case



On Wed, May 29, 2013 at 6:36 PM, Dr. Vitaly Chaban vvcha...@gmail.comwrote:

 I do not remember all the keys.

 Rename your files to their default names and you will have nothing to
 specify except

 mdrun -cpi




 On Wed, May 29, 2013 at 6:31 PM, Fábio Filippi Matioli 
 fabiof...@hotmail.com wrote:

 Hello, i'm who asked about extending simulations.
 You sad for me pen teh checkpoint file, u say the file .cpt?
 But its a binary file... Can you give a example of extending simulation
 if my first mdrun its this:

 mdrun -v -s full -o full -e full -c after_full -np 8 -gflog full.job

 Tnks

 *Fábio Filippi Matioli*
 Graduando em Física Médica
 UNESP-Botucatu
 Tel (19) 9291.6738



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Re: [gmx-users] Gromacs for Non biological systems

2013-05-28 Thread Dr. Vitaly Chaban

Look for my papers. At least, two dozens of them are about non-biophysical
stuff.

Gromacs can. The question is whether you can provide an adequate
Hamiltonian to describe your systems involving Al-surface.

Dr. Vitaly Chaban




On Mon, May 27, 2013 at 10:59 PM, Jeya vimalan jeyavimala...@gmail.comwrote:

 Dear Collegues,
 I was pointed to Gromacs to make it work
 on the non biological systems.
 My aim is to understand the interaction
 of Hf precursors on Gamma Alumina surface.
 But, i do not know yet if gromacs can efficiently handle this.
 Can someone help me fiding some papers where GROMACS have been used for the
 non biological system.
 jeya
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Re: [gmx-users] choice of forcefield

2013-05-28 Thread Dr. Vitaly Chaban

In my mind, MARTINI is a decent option to build your particular topology
upon.

Dr. Vitaly Chaban


On Tue, May 28, 2013 at 8:22 AM, Revthi Sanker revthi.san...@yahoo.comwrote:

 Dear all,
 I am a beginner to performing simulations and my system consists of
 protein+ cholesteryl ester +phospholipid and drug. Papers involving lipids
 are in general united atom, while those involving drug-protein systems are
 all-atom mostly. Kindly suggest me which of these, all-atom or united atom
 should I be using for my system.

 Thanks for your help in advance
 Yours sincerely,
 Revathi
 M.S. Research Scholar
 Indian Institute of Technology,Madras
 India
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[gmx-users] Re: choice of force field -reg

2013-05-28 Thread Dr. Vitaly Chaban

without knowing full details of your simulated system and the goals you
pose, I cannot advise anything more definite than I did before.

if I were you and my system were yours, I would start with MARTINI FF.

I wish you a success in your endeavor.

Dr. Vitaly Chaban




On Tue, May 28, 2013 at 6:11 PM, Revthi Sanker revthi.san...@yahoo.comwrote:



 Dear Sir,
 Thank you so much for your reply. To be specific, my system has only four
 lipid moities- 2 cholesteryl oleates and 2 phosphotidyl cholines. But I was
 not able to get all atom paramters for these lipids from the lipid book(
 only united atom parameters were available). So I had resorted to using
 united atom for the whole system. But I am afraid if I am missing out on
 some crucial protein-drug interactions because of this united atom
 consideration.
 Kindly guide me in this regard.
 Thank you so much once again.

 Yours sincerely,
 Revathi
 M.S.Research Scholar
 Indian Institute of Technology Madras
 India


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Re: [gmx-users] how to get the epsilon and sigma values of CO

2013-05-27 Thread Dr. Vitaly Chaban

if there are many values in the literature, what do you want?


On Mon, May 27, 2013 at 4:29 PM, Ishwor Poudyal ishwor_p...@hotmail.comwrote:

 Dear all.I want to study simulation of  carbonmonoxide in water...I get
 different values of force constant partial charge while searching for those
 constants. Can anyone help me providing the values of partial charge (of
 CO), force constant and lennard jones parameter epsilon and sigma used in
 the simulation processThanks --
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Re: [gmx-users] Why the shape of the molecules changed?

2013-05-25 Thread Dr. Vitaly Chaban

Of course, you can simulate what you like, but I would personally use an
all-atom representation for long hydrocarbons. I think explicit hydrogens
matter for conformations.


V.V. Chaban




On Thu, May 23, 2013 at 5:16 PM, Bao Kai paeanb...@gmail.com wrote:

 Hi, all,

 I finally wrote a decane topology file. I used it to some simple
 simulation.

 The energy minimization works, while after a simple nvt equilibration,
 the shape of the molecules changed.

 Please find the images before and after the nvt equilibration from the
 following links.
 https://www.dropbox.com/s/qcfgipchnus3vcb/before_nvt.png
 https://www.dropbox.com/s/nvbxbs6tofdc0ol/after_nvt.png



 The following is the topology part for the decane molecule.   Please
 help to check if there is anything wrong.   C2 and C3 are CH2 and CH3
 respectively.

 [ defaults ]
 ; nbfunccomb-rule   gen-pairs   fudgeLJ fudgeQQ
 1  3  yes 0.50.5

 [ atomtypes ]
 ;   type  at.nummasschargeptypesigmaepsilon
   C2   6 14.02700.0  A0.3740.4301
   C3   6 15.035  0.0  A0.3740.6243
 [ moleculetype ]
 ; Namenrexcl
 D10 3

 [ atoms ]
 ;   nr   type  resnr residue  atom   cgnr charge   mass
 typeBchargeB  massB
  1C3  1D10 1C3  1   0.0 15.035
  ; qtot -0.18
  2C2  1D10 1C2  2  0.0  14.027
   ; qtot -0.3
  3C2  1D10 2C2  3  0.0  14.027
   ; qtot -0.42
  4C2  1D10 3C2  4  0.0  14.027
   ; qtot -0.54
  5C2  1D10 4C2  5  0.0  14.027
   ; qtot -0.66
  6C2  1D10 5C2  6  0.0  14.027
   ; qtot -0.78
  7C2  1D10 6C2  7  0.0  14.027
   ; qtot -0.9
  8C2  1D10 7C2  8  0.0  14.027
   ; qtot -1.02
  9C2  1D10 8C2  9  0.0  14.027
   ; qtot -1.14
 10C3  1D10 2C3  10 0.0  15.035
   ; qtot -1.32


 [ bonds ]
 ;  aiaj functc0c1c2c3
 1 2 1  1.53e-01  543  1.53e-01  543
 2 3 1  1.53e-01  543  1.53e-01  543
 3 4 1  1.53e-01  543  1.53e-01  543
 4 5 1  1.53e-01  543  1.53e-01  543
 5 6 1  1.53e-01  543  1.53e-01  543
 6 7 1  1.53e-01  543  1.53e-01  543
 7 8 1  1.53e-01  543  1.53e-01  543
 8 9 1  1.53e-01  543  1.53e-01  543
 910 1  1.53e-01  543  1.53e-01  543

 [ pairs ]
 ;  aiaj functc0c1c2c3
 1 4 1
 2 5 1
 3 6 1
 4 7 1
 5 8 1
 6 9 1
 710 1

 [ angles ]
 ;  aiajak functc0c1c2
c3
 1 2 3 2  1.11e+02  4.00e+02  1.11e+02
  4.00e+02
 2 3 4 2  1.11e+02  4.00e+02  1.11e+02
  4.00e+02
 3 4 5 2  1.11e+02  4.00e+02  1.11e+02
  4.00e+02
 4 5 6 2  1.11e+02  4.00e+02  1.11e+02
  4.00e+02
 5 6 7 2  1.11e+02  4.00e+02  1.11e+02
  4.00e+02
 6 7 8 2  1.11e+02  4.00e+02  1.11e+02
  4.00e+02
 7 8 9 2  1.11e+02  4.00e+02  1.11e+02
  4.00e+02
 8 910 2  1.11e+02  4.00e+02  1.11e+02
  4.00e+02

 [ dihedrals ]
 ;  aiajakal functc0c1
 c2c3c4c5
 1 2 3 4 3  0.00e+00 5.00e+00  3.00e+00
  0.00e+00 5.00e+00  3.00e+00
 2 3 4 5 3  0.00e+00 5.00e+00  3.00e+00
  0.00e+00 5.00e+00  3.00e+00
 3 4 5 6 3  0.00e+00 5.00e+00  3.00e+00
  0.00e+00 5.00e+00  3.00e+00
 4 5 6 7 3  0.00e+00 5.00e+00  3.00e+00
  0.00e+00 5.00e+00  3.00e+00
 5 6 7 8 3  0.00e+00 5.00e+00  3.00e+00
  0.00e+00 5.00e+00  3.00e+00
 6 7 8 9 3  0.00e+00 5.00e+00  3.00e+00
  0.00e+00 5.00e+00  3.00e+00
 7 8 910 3  0.00e+00 5.00e+00  3.00e+00
  0.00e+00 5.00e+00  3.00e+00


 [system]
 sparkling water
 [molecules]
 D10 208

 Thank you very much.

 Best Regards,
 Kai
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[gmx-users] DD fails

2013-05-19 Thread Dr. Vitaly Chaban

any ideas what the below error message can indicate?

Step 350755:
The charge group starting at atom 44257 moved than the distance allowed by
the domain decomposition (2.745686) in direction Z
distance out of cell 32.799423
Old coordinates:4.7944.2994.356
New coordinates:  -72.747  -69.851   38.291
Old cell boundaries in direction Z:2.7465.491
New cell boundaries in direction Z:2.7465.491


The system is reasonably equilibrated. It is NOT a gas phase. The listed
displacement is NOT possible, according to conventional wisdom. The
question is what can make mdrun say that it happens?


Thank you. Dr. Vitaly Chaban
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[gmx-users] Re: DD fails

2013-05-19 Thread Dr. Vitaly Chaban

UPD: the version of gromacs exhibiting this marvellous behavior is 4.5.5.



On Mon, May 20, 2013 at 8:11 AM, Dr. Vitaly Chaban vvcha...@gmail.comwrote:

 any ideas what the below error message can indicate?

 Step 350755:
 The charge group starting at atom 44257 moved than the distance allowed by
 the domain decomposition (2.745686) in direction Z
 distance out of cell 32.799423
 Old coordinates:4.7944.2994.356
 New coordinates:  -72.747  -69.851   38.291
 Old cell boundaries in direction Z:2.7465.491
 New cell boundaries in direction Z:2.7465.491


 The system is reasonably equilibrated. It is NOT a gas phase. The listed
 displacement is NOT possible, according to conventional wisdom. The
 question is what can make mdrun say that it happens?


 Thank you. Dr. Vitaly Chaban

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Re: [gmx-users] Charmm27 potential energies.

2013-05-09 Thread Dr. Vitaly Chaban

The positive charge on the alpha-carbon should be expected. Many methods
(not only DFT) will predict tiny non-zero charges even on more remote
carbons, if you consider deprotonated form.

Protonated form is a neutral molecule. So, alpha -CH2- may be acceptably
described as having a a zero charge in total. You can distribute the +1e
charge throughout COOH (for instance, uniformly with respect to what you
have in COO(-)) to make it also neutral in total.

On a related note, it is not very time consuming to calculate electronic
structures of CH3-COOH(0e) and CH3-COO(-1e) and derive better electrostatic
charges for each site.


Dr. Vitaly Chaban





On Thu, May 9, 2013 at 11:33 PM, Eric Stokes es...@uw.edu wrote:

 Hello,

 I am attempting to generate force-field parameters for a fatty acid
 molecule that contains a carboxilic acid head group. I decided to use the
 parameters for stearic acid as the base for my molecule, since they contain
 similar structures with the only major change being a shorter hydrophobic
 tail. I noticed that the charge on stearic acid, and other molecules that
 have a carboxilic head group, is spread out with -0.9 residing on the head
 group and -0.1 on the second carbon. I need to use the protonated from of
 my molecule for my simulation, as well as the deprotonated form. I looked
 into the parameters for the COOH replacement in the Charmm27 force-field
 and used that to form the head group of the protonated form of my molecule.
 The problem that I am facing is that this left behind a charge of -0.1 that
 resides on the second carbon. Is there any way to find acceptable partial
 charges without doing the full Gaussian calculations? I would also
 appreciate it if someone could explain why the charges were split onto the
 second carbon in the first place.

 Thanks in advance,
 Eric Stokes
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Re: [gmx-users] Usage of g_spatial

2013-05-07 Thread Dr. Vitaly Chaban

I think you can process the trajectories without generating TPR.

Dr. Vitaly Chaban


On Tue, May 7, 2013 at 12:12 PM, Venkat Reddy venkat...@gmail.com wrote:

 Dear gromacs users,

 I am analyzing trajectories of an ionic liquid system generated using AMBER
 MD package. The force field parameters are typical of this IL system and
 not from the existing libraries. Hence, it is difficult for me to generate
 a tpr file. I understand that running the g_spatial command needs
 pre-processing of the coordinates (Steps 1 and 2 in g_spatial help) but I
 need tpr file for that. So there is  no way of doing g_spatial without a
 tpr file is it? Then how do I generate tpr file for my system?

 Thanks for all the help
 --
 With Best Wishes
 Venkat Reddy Chirasani
 PhD student
 Laboratory of Computational Biophysics
 Department of Biotechnology
 IIT Madras
 Chennai
 INDIA-600036
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Re: [gmx-users] simulation single molecule in water

2013-05-07 Thread Dr. Vitaly Chaban

Your problem has nothing to do with barostat.

There is such thing as DispCorr. I am unsure whether if should be turned on
or off in case of your model. It does influence density to certain extent.


Dr. Vitaly Chaban







 -Original Message-
 From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org]
 On Behalf Of Souilem Safa
 Sent: Tuesday, 7 May 2013 4:38 PM
 To: Discussion list for GROMACS users
 Subject: [gmx-users] simulation single molecule in water

 Dear gromacs users,
 I'm simulating a single molecule in spc water. I'm using a cubic water box
 which has 3.4 nm size.
 I got the toplogy of my molecule via PRODRG.
 After running minimization, NVT , NPT and MD for 10 ns , I checked the
 density of water ,it was less than the real value (1000 kg m\S-3\N)
 ,actually I got around 950.
 I have checked my mdp file in the NPT step and I was wondering about tau_p
 that I should use. First I used 2.0 ps with Parrinello-Rahman coupling.
 After checking in gromacs archive, I found it is better to use 0.5 ps, I
 have changed tau-p ,but I still have density value less than 1000.
 Details of my  mdp file are below :
  Run parameters
 integrator= md; leap-frog integrator
 nsteps= 500; 2 * 500 = 1 ps, 1 ns
 dt= 0.002; 2 fs
 ; Output control
 nstxout= 1000; save coordinates every 2 ps
 nstvout= 1000; save velocities every 2 ps
 nstxtcout= 1000; xtc compressed trajectory output every 2 ps
 nstenergy= 1000; save energies every 2 ps
 nstlog= 1000; update log file every 2 ps
 ; Bond parameters
 continuation= yes; Restarting after NPT
 constraint_algorithm = lincs; holonomic constraints
 constraints= all-bonds; all bonds (even heavy atom-H bonds)
 constrained
 lincs_iter= 1; accuracy of LINCS
 lincs_order= 4; also related to accuracy
 ; Neighborsearching
 ns_type= grid; search neighboring grid cells
 nstlist= 5; 10 fs
 rlist= 1.0; short-range neighborlist cutoff (in nm)
 rcoulomb= 1.0; short-range electrostatic cutoff (in nm)
 rvdw= 1.0; short-range van der Waals cutoff (in nm)
 ; Electrostatics
 coulombtype= PME; Particle Mesh Ewald for long-range
 electrostatics
 pme_order= 4; cubic interpolation
 fourierspacing= 0.16; grid spacing for FFT
 ; Temperature coupling is on
 tcoupl= V-rescale; modified Berendsen thermostat
 tc-grps= system; two coupling groups - more accurate
 tau_t= 0.1; time constant, in ps
 ref_t= 300 ; reference temperature, one for each group, in
 K
 ; Pressure coupling is on
 pcoupl= Parrinello-Rahman; Pressure coupling on in NPT
 pcoupltype= isotropic; uniform scaling of box vectors
 tau_p= 0.50; time constant, in ps
 ref_p= 1.0; reference pressure, in bar
 compressibility = 4.5e-5; isothermal compressibility of water, bar^-1
 ; Periodic boundary conditions
 pbc= xyz; 3-D PBC
 ; Dispersion correction
 DispCorr= EnerPres; account for cut-off vdW scheme
 ; Velocity generation
 gen_vel= no; Velocity generation is off

 What should be the origin of this density difference?
 looking forward to your advise
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Re: [gmx-users] where can be obtain circled lipids bilayer?

2013-05-02 Thread Dr. Vitaly Chaban

On Thu, May 2, 2013 at 6:32 PM, Albert mailmd2...@gmail.com wrote:

 Hello:

  I've got a question about where can be obtain circled lipids bilayer?


 like shown here:

 http://wwwuser.gwdg.de/~**ggroenh/membed/vesicle.pnghttp://wwwuser.gwdg.de/~ggroenh/membed/vesicle.png



1) When packing parameter of the the lipid is large enough.

2) When concentration of lipids in the box is reasonably low.

Dr. Vitaly Chaban









 thank you very much
 Albert
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Re: [gmx-users] vacum simulation

2013-05-02 Thread Dr. Vitaly Chaban

LINCS doesn't like your system... or your system doesn't like LINCS...

You can decrease the time-step as the simplest action.

Dr. Vitaly Chaban








On Thu, May 2, 2013 at 2:40 PM, Souilem Safa safasouil...@gmail.com wrote:

 Dear Gromacs users ,
  I did the simulation of a single molecule in vacum. I have choosed 10 ns
 which corresponds to 500 steps. I was checking the .log file
 frequently.
 I have noticed that the number of steps from 1938900 didn't increases.
 When I open a new tab with the top option, I see mdrun still existing.
 I have attached here the .log file and also some warnings that I saw when
 steps stop at 1938900

 Step 1938969, time 3877.94 (ps)  LINCS WARNING
 relative constraint deviation after LINCS:
 rms 12871303501.643789, max 33207281664.00 (between atoms 3 and 6)
 bonds that rotated more than 30 degrees:
  atom 1 atom 2  angle  previous, current, constraint length
  46 47   98.80.1406 3889.8669  0.1000
  45 46   79.4  10193.8799 10564.2393  0.1440
  43 44   79.60.1033 631.2256  0.1000
  42 45   80.1  10193.9062 11014.6123  0.1520
  42 43   93.50.1851 4970.4243  0.1440
  40 41   76.50.1009 184.9659  0.1000
  39 42   90.40.1819 5231.5186  0.1520
  39 40  100.00.1502 624.0559  0.1440
  37 38   97.10.1001 592.4050  0.1000
  36 37   81.40.1469 828.7896  0.1430
  35 39   88.60.1742 8071.4395  0.1520
  35 36   94.70.1861 8093.3452  0.1530
  35 34   92.9  8046.3804 17904.5762  0.1440
  33 45   78.0  26093.2402 332765.5000  0.1520
  33 34   94.6  26065.5371 330302.5625  0.1440
  29 30   74.4  190965.5938 1213272.  0.1360
  27 28   91.2  85465.0547 294693.5000  0.1430
  25 27   85.7  126649.9141 1143663.7500  0.1360
  25 26  107.7  116051.3750 805165.8125  0.1230
  24 29  102.8  1939418.3750 1702562.5000  0.1390
  24 25  101.0  1963544.3750 1402288.3750  0.1390
  22 23   97.9  345568.0625 1364901.  0.1530
  31 21  109.7  1948370.1250 7003795.5000  0.1390
  21 22  101.2  2108572.2500 6662917.5000  0.1390
  20 24   89.4  8876732. 68351760.  0.1390
  20 21   89.1  8780558. 67941296.  0.1390
  20 19   88.5  39924512. 280068256.  0.1530
  17 19   92.9  371385600. 509824768.  0.1530
  17 18   96.4  394707616. 358144416.  0.1230
  17 16   90.0  446916736. 883243840.  0.1360
  15 16   98.9  1051905920. 370290400.  0.1430
  14 15  100.8  520221760. 522257472.  0.1530
  13 14  128.2  1139173888. 3275473920.  0.1390
  13 11  155.0  2786396928. 3396753920.  0.1390
  11 12  151.7  1220930176. 2911329792.  0.1090
   9 11  161.5  369404096. 342864.  0.1390
   9 10  135.8  2190610944. 1502276608.  0.1090
   7  8   91.7  148944928. 1389486464.  0.1000
   6  9  150.6  497182528. 4613532672.  0.1390
   6  7  168.3  1652069120. 3562507776.  0.1360
   4  5  165.5  55138408. 449667456.  0.1000
   3  6  169.0  1702803200. 4615812096.  0.1390
   3  4  124.7  198457328. 2500093184.  0.1360
  13  1  158.1  1042088320. 3730094848.  0.1390
 Wrote pdb files with previous and current coordinates
 Please I need your help what should I do in this case?
 Best regards,
 Safa
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Re: [gmx-users] g_msd for many molecules

2013-05-01 Thread Dr. Vitaly Chaban

The resulting MSD will correspond to the average from individual atoms.

Calculating MSD of an individual atom and ascribing it to a [small]
molecule, which this atom belongs to, is reasonable. Assuming that averaged
MSD from atoms correspond to the cluster they form is not.


Dr. Vitaly Chaban




On Wed, May 1, 2013 at 2:40 PM, George Patargias g...@bioacademy.gr wrote:

 Hello

 I am trying to calculate the MSD of 8 molecules in a lipid bilayer with
 g_msd. If I include the atoms of all these 8 molecules as a single group
 in the index file, will g_msd calculate the MSD of the center of mass of
 them or it will average over all atoms?


 Thanks
 George


 Dr. George Patargias
 Postdoctoral Researcher
 Biomedical Research Foundation
 Academy of Athens
 4, Soranou Ephessiou
 115 27
 Athens
 Greece

 Office: +302106597568






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Re: [gmx-users] Martini with PME, temp two low

2013-04-25 Thread Dr. Vitaly Chaban

Hmmm

Aren't the keywords here charged system + PME?


Dr. Vitaly Chaban



On Thu, Apr 25, 2013 at 1:34 PM, XAvier Periole x.peri...@rug.nl wrote:


 Did you visualise the system? T in function of time? Epot in function of
 time?

 As a side note (not relevant for PME) the mix of nstlist = 10 and the
 rlist = 1.0 is pretty bad! You want at least rlist=1.2 when nstlist=5 and
 rlist=1.4 if nstlist =10.

 On Apr 25, 2013, at 1:10 PM, ABEL Stephane 175950 stephane.a...@cea.fr
 wrote:

  Hello all,
 
  I am trying to test the martini force field with PME for a charged
 system that contains na+, water, surfactant, octane molecules at 298K and
 P=0.1MPa. My system works well, if i use the standard shift parameters
 (correct temp, and pressure). But for for the simulation with PME , the
 temp of the system decrease to  290 K. Below my *.mdp parameters for a NPT
 equil at 298K
 
 
  integrator   = md
  dt   = 0.020
  nsteps   = 1 ; 200ps
  nstcomm  = 10
  comm-grps=
  ;refcoord_scaling = com
 
  nstxout  = 0
  nstvout  = 0
  nstfout  = 0
  nstlog   = 1000
  nstenergy= 100
  ;nstxtcout= 1000
  xtc_precision= 100
  ;xtc-grps =
  energygrps   = AOT W ION OCT
 
  nstlist  = 10
  ns_type  = grid
  pbc  = xyz
  rlist= 1.
 
  ; PME parameters
  coulombtype  = PME
  rcoulomb = 1.2
  rvdw = 1.2
  fourierspacing   = 0.12
  fourier_nx   = 0
  fourier_ny   = 0
  fourier_nz   = 0
  pme_order= 4
 
  tcoupl   = v-rescale
  tc-grps  = AOT_W_ION OCT
  tau_t= 1.0 1.0
  ref_t= 298 298
  Pcoupl   = berendsen
  Pcoupltype   = isotropic
  tau_p= 1.0
  compressibility  = 4.5e-5
  ref_p= 1.0
 
  ;gen_vel  = no
  ;gen_temp = 0
  ;gen_seed = 473529
 
 
  ; MARTINI and CONSTRAINTS
  ; for ring systems and stiff bonds constraints are defined
  ; which are best handled using Lincs.
 
  constraints  = none
  constraint_algorithm = Lincs
  unconstrained_start  = no
  lincs_order  = 4
  lincs_warnangle  = 3
 
 
  Results obtained with W/ PME
 
Statistics over 10001 steps using 1001 frames
 
Energies (kJ/mol)
Bond   G96AngleLJ (SR)   Coulomb (SR)   Coul.
 recip.
 1.63789e+041.25195e+03   -4.02093e+05   -8.22079e+03
 -4.86843e+04
   PotentialKinetic En.   Total EnergyTemperature Pressure
 (bar)
-4.41367e+057.81801e+04   -3.63187e+052.90373e+02
 -1.76470e+01
 T-AOT_W_ION  T-OCT
 2.90629e+022.90357e+02
 
  Results W:o PME
 
Energies (kJ/mol)
Bond   G96AngleLJ (SR)   Coulomb (SR)
  Potential
 1.60482e+041.24820e+03   -3.34608e+05   -7.33665e+02
 -3.18046e+05
 Kinetic En.   Total EnergyTemperature Pressure (bar)
 8.02685e+04   -2.3e+052.98129e+02   -3.07123e+01
 
   Box-X  Box-Y  Box-Z
 1.52926e+011.52926e+011.52926e+01
 
 
 T-AOT_W_ION  T-OCT
 2.98141e+022.98129e+02
 
 
  Did I miss something ?
 
 
  Note that for the moment i do not use the polarizable water model.
 
  Thanks for your help
 
  Stephane
 
 
 
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Re: [gmx-users] Problem with gromacs in Cluster

2013-04-25 Thread Dr. Vitaly Chaban

The salvation is to use:

mdrun -cpi state.cpt


Dr. Vitaly Chaban




On Thu, Apr 25, 2013 at 2:37 PM, Justin Lemkul jalem...@vt.edu wrote:



 Can any body tell me  how do it split script i such  that i will get all
 20ns simulation


 You specified a given time limit for the job, and the run exceeded it.
  Either specify more run time (if allowed) or run your job in shorter
 intervals that will finish within the maximum time limit.

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

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Re: [gmx-users] Martini with PME, temp two low

2013-04-25 Thread Dr. Vitaly Chaban

PME should NOT be used with charged systems, for obvious reasons.


On Thu, Apr 25, 2013 at 4:00 PM, ABEL Stephane 175950
stephane.a...@cea.frwrote:

 And ? sorry but i do not understand...

 Stephane

 --

 Message: 2
 Date: Thu, 25 Apr 2013 15:39:12 +0200
 From: Dr. Vitaly Chaban vvcha...@gmail.com
 Subject: Re: [gmx-users] Martini with PME, temp two low
 To: Discussion list for GROMACS users gmx-users@gromacs.org
 Message-ID:
 CAPXdD+bDiuQWG_3eWZ_0yb=
 aynlaaf08vt46usel4wk_bjg...@mail.gmail.com
 Content-Type: text/plain; charset=ISO-8859-1

 Hmmm

 Aren't the keywords here charged system + PME?


 Dr. Vitaly Chaban



 On Thu, Apr 25, 2013 at 1:34 PM, XAvier Periole x.peri...@rug.nl wrote:

 
  Did you visualise the system? T in function of time? Epot in function of
  time?
 
  As a side note (not relevant for PME) the mix of nstlist = 10 and the
  rlist = 1.0 is pretty bad! You want at least rlist=1.2 when nstlist=5 and
  rlist=1.4 if nstlist =10.
 
  On Apr 25, 2013, at 1:10 PM, ABEL Stephane 175950 stephane.a...@cea.fr
  wrote:
 
   Hello all,
  
   I am trying to test the martini force field with PME for a charged
  system that contains na+, water, surfactant, octane molecules at 298K and
  P=0.1MPa. My system works well, if i use the standard shift parameters
  (correct temp, and pressure). But for for the simulation with PME , the
  temp of the system decrease to  290 K. Below my *.mdp parameters for a
 NPT
  equil at 298K
  
  
   integrator   = md
   dt   = 0.020
   nsteps   = 1 ; 200ps
   nstcomm  = 10
   comm-grps=
   ;refcoord_scaling = com
  
   nstxout  = 0
   nstvout  = 0
   nstfout  = 0
   nstlog   = 1000
   nstenergy= 100
   ;nstxtcout= 1000
   xtc_precision= 100
   ;xtc-grps =
   energygrps   = AOT W ION OCT
  
   nstlist  = 10
   ns_type  = grid
   pbc  = xyz
   rlist= 1.
  
   ; PME parameters
   coulombtype  = PME
   rcoulomb = 1.2
   rvdw = 1.2
   fourierspacing   = 0.12
   fourier_nx   = 0
   fourier_ny   = 0
   fourier_nz   = 0
   pme_order= 4
  
   tcoupl   = v-rescale
   tc-grps  = AOT_W_ION OCT
   tau_t= 1.0 1.0
   ref_t= 298 298
   Pcoupl   = berendsen
   Pcoupltype   = isotropic
   tau_p= 1.0
   compressibility  = 4.5e-5
   ref_p= 1.0
  
   ;gen_vel  = no
   ;gen_temp = 0
   ;gen_seed = 473529
  
  
   ; MARTINI and CONSTRAINTS
   ; for ring systems and stiff bonds constraints are defined
   ; which are best handled using Lincs.
  
   constraints  = none
   constraint_algorithm = Lincs
   unconstrained_start  = no
   lincs_order  = 4
   lincs_warnangle  = 3
  
  
   Results obtained with W/ PME
  
 Statistics over 10001 steps using 1001 frames
  
 Energies (kJ/mol)
 Bond   G96AngleLJ (SR)   Coulomb (SR)   Coul.
  recip.
  1.63789e+041.25195e+03   -4.02093e+05   -8.22079e+03
  -4.86843e+04
PotentialKinetic En.   Total EnergyTemperature Pressure
  (bar)
 -4.41367e+057.81801e+04   -3.63187e+052.90373e+02
  -1.76470e+01
  T-AOT_W_ION  T-OCT
  2.90629e+022.90357e+02
  
   Results W:o PME
  
 Energies (kJ/mol)
 Bond   G96AngleLJ (SR)   Coulomb (SR)
   Potential
  1.60482e+041.24820e+03   -3.34608e+05   -7.33665e+02
  -3.18046e+05
  Kinetic En.   Total EnergyTemperature Pressure (bar)
  8.02685e+04   -2.3e+052.98129e+02   -3.07123e+01
  
Box-X  Box-Y  Box-Z
  1.52926e+011.52926e+011.52926e+01
  
  
  T-AOT_W_ION  T-OCT
  2.98141e+022.98129e+02
  
  
   Did I miss something ?
  
  
   Note that for the moment i do not use the polarizable water model.
  
   Thanks for your help
  
   Stephane
  
  
  

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Re: [gmx-users] using CHARMM force field for organic molecule

2013-04-22 Thread Dr. Vitaly Chaban

a simple way is x2top

Dr. Vitaly Chaban


On Mon, Apr 22, 2013 at 1:38 PM, aixintiankong aixintiank...@126.comwrote:

 Dear ,
  I want to use charmm force field to simulate the protein and ligand
 system. The protein can selcet charmm27 in gromacs, but i don't konw how to
 get the charmm force field for the ligand. could tell me a simple way to
 get the to Topology file for the organic molecule .
 thank you !
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[gmx-users] Re: Water spreading on graphene!

2013-04-21 Thread Dr. Vitaly Chaban

Yes, the water droplet should remain a droplet on graphene.

Since you have a droplet, I assume you have much vacuum in the system. I
would not use PME for such system, but would rather compensate it by
using larger cutoffs.

If you need a simple advice, it is -- enlarge the box to avoid any
interactions, which you would not have had in real experiment.

I also expect a specific behavior, if your droplet is very small.

Maybe, I would simulate this system without PBC at all.


Dr. Vitaly Chaban







 I have a graphene like surface (carbons on a hexagonal lattice with zero
 partial charges and some LJ parameters) with a drop of water placed on it.
 In principle, this is a hydrophobic surface and the drop should remain a
 droplet on it. However, surprisingly I am seeing that the drop is spreading
 within a 1 ns of the simulation. In the past I have done some similar
 simulations (with a different structure but basically zero partial charge
 surface and LJ) on which the drop remains a drop.

 Does any body have any ideas of what I may be doing wrong? Pasted below is
 my mdp and top file. Briefly, I am doing NVT simulation, PME for
 electrostatics, TIP3P water model, the surface is frozen and intra-surface
 interactions are excluded, the cut-off distances are 1 nm, velocity rescale
 thermostat (I tried both with the entire system coupled to the same
 thermostat and with sheet and water being coupled to different
 thermostats).
 Any suggestions are welcome.

 My analysis suggests this comes from the long range electrostatics because
 we have tested the same thing in LAMMPS. When we turn off PPPM and use
 cut-off based Coulomb (~5 nm) in LAMMPS (yes now we have changed the
 software) we don't see the drop spreading.

 I have done so many simulations and to have this problem stumps me!! Thanks
 for being helpful always.

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[gmx-users] Re: Viscosity calculation using cos_acceleration

2013-04-16 Thread Dr. Vitaly Chaban

Alternatively, has anyone else reproduced the viscosity calculation, or

 tried to?
 If anyone would be so kind as to forward their input files, that might help
 me narrow down the problem with my own input files.

 Thank you.

 James

 On 11 April 2013 16:55, James Cannon jamesresearch...@gmail.com wrote:

  Dear Gromacs users,
 
  This question seems to come up periodically in the mailing list, but none
  of the previous answers seem helpful in my case.
 
  I'm trying to reproduce the viscosity calculation of SPC water by Berk
  Hess (JCP 116, 2002) using cos_acceleration in Gromacs. The answer I get
 is
  2 orders of magnitude out.
 
  My topology file and parameter file is appended at the bottom of this
  email.
 
  I run g_energy and get
 
  Energy  Average   Err.Est.   RMSD  Tot-Drift
 
 
 ---
  1/Viscosity 23.4689   0.132.39126  -0.255371  (m
  s/kg)
 
  which gives a viscosity of 0.04 kg/(m s), or 40 mPa.s
 
  The value quoted in the paper is about 0.4 mPa.s which is around the
  correct value for water, give or take a bit.
 
  So my question is, where is my missing factor of 100?




Non-equilibrium method for viscosity heavily depends on the acceleration
value. Your selection looks reasonable for me, but try to decrease the
value. Ideal acceleration depends on the particular collective dynamics
in each system, of course.

I can soothe you ability a workability of the utility. It has been tried
many times and works really perfectly.


Dr. Vitaly Chaban
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Re: [gmx-users] Re: RDF output has no data

So there is a problem with your trajectory file. Try to understand what
kind of problem it is.

I can recollect that I experienced something like that why translating CPMD
trajectory to GROMACS. Maybe, it does not write time for each frame at the
right place -- just a guess.

Dr. Vitaly Chaban




On Tue, Apr 9, 2013 at 7:44 AM, Venkat Reddy venkat...@gmail.com wrote:

 Sir

 I tried g_msd, after asking for group selection the program appears not to
 read the frames as it remains stuck at reading frame 0, time 0.00.

 What to do?

 Thanks




 On Mon, Apr 8, 2013 at 11:16 PM, Dr. Vitaly Chaban vvcha...@gmail.comwrote:

 Do you experience this problem with g_rdf only, or with all gromacs
 analysis utilities?


 On Mon, Apr 8, 2013 at 7:33 PM, Venkat Reddy venkat...@gmail.com wrote:

 Sir

 I loaded the trajectory. There doesn't seem to be anything wrong with
 it. Have no clue whats going wrong

 Thanks


 On Mon, Apr 8, 2013 at 5:28 PM, Dr. Vitaly Chaban vvcha...@gmail.comwrote:

 I believe the problem is in the way which you used to convert AMBER
 trajectory to the GROMACS trajectory

 I would suggest to try gmxdump and see what your trajectory looks like.
 Oe
 maybe even better - try to visualize it in VMD to see if the format is
 correct.

 Dr. Vitaly Chaban



 Sir
 
  I was using an old version. Now I used 4.5.5, it still gives me the
 same
  blank output file.
 
  Kindly suggest how to go about solving this
 
  Thanks
 
 
  On Sat, Apr 6, 2013 at 2:26 PM, Mark Abraham 
 mark.j.abra...@gmail.com
  wrote:
 
   On Sat, Apr 6, 2013 at 7:19 AM, Venkat Reddy venkat...@gmail.com
  wrote:
  
There was no fatal error preceding the output. After selecting the
  groups
following are the output on the screen
Reading frame   1 time0.100
Warning: can not make broken molecules whole without a run input
 file,
 don't worry, mdrun doesn't write broken molecules
   
  
   This message is from a prehistoric version of g_rdf. Please get a
 new
  one.
  
   Mark
  
  
   
Reading frame2000 time  200.000
   
   
gcq#69: The Wheels On the Bus Go Round and Round (J. Richman)
   
And the rdf.xvg file looks like this
   
#This file was created Sat Apr  6 10:54:13 2013
# by the following command:
# g_rdf -f 6md.trr -s ../../6md.pdb -n rdf.ndx -o rdf.xvg
#
# g_rdf is part of G R O M A C S:
#
# GROningen MAchine for Chemical Simulation
#
@title Radial Distribution
@xaxis  label r
@yaxis  label 
@TYPE xy
@ subtitle O21-H2__CAT
 0.001  1
~
   
Whats going wrong? Please help.
 
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 --
 With Best Wishes
 Venkat Reddy Chirasani
 PhD student
 Laboratory of Computational Biophysics
 Department of Biotechnology
 IIT Madras
 Chennai
 INDIA-600036





 --
 With Best Wishes
 Venkat Reddy Chirasani
 PhD student
 Laboratory of Computational Biophysics
 Department of Biotechnology
 IIT Madras
 Chennai
 INDIA-600036

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Re: [gmx-users] Re: How to set the sigma and epsilon for Cu2+ in OPLS-AA/L

On Tue, Apr 9, 2013 at 9:39 AM, fantasticqhl fantastic...@gmail.com wrote:

  Dear Dr. Vitaly Chaban,

 Thanks very much for your patient and detailed suggestions on this
 problem. Actually, I am doing what your suggested now.
 I optimized the copper-ligand complex using QM method, and then did some
 QM scannings to derive the bond and angle force constants.
 Right now, I am doing the MM scanning using the same coordinates which
 were used in the QM scanning. What we want is that the MM curves
 can reproduce the QM curves.



I think it is simply impossible in your case to reproduce the QM curves.
You neglect charge transfer from copper to the ligand, resulting a chemical
bond formation, you neglect finite T effect in your MD. If you want to
remain in the framework of LJ+Coulomb, the best think you can get is
reproduction of ion-ligand binding energy and more or less adequate
distance ion-closest atom of the ligand




 But some of them agreed well, some of them did not. So I try to tune the
 sigma of the liganded atoms, however,
 it is a little complicated to tune many liganded atoms at the same time. I
 am still trying to work it out.



Start from the sigma for ion-closest atom of the ligand. All other atoms
will adjust automatically, since they are connected all together within the
ligand.

My personal viewpoint, which you may share or not, is not to do anything
with sigmas of other atoms of the ligand. It is best for future portability
to limit refinement to the ion only.




  It seems that you have much experience on such problems, could you please
 give me some suggestions on tuning the sigmas of atoms again?
 Thanks very much in advance!


 All the best,
 Qinghua Liao



 On 04/08/2013 03:51 PM, Dr. Vitaly Chaban wrote:


  On Mon, Apr 8, 2013 at 3:36 PM, fantasticqhl fantastic...@gmail.comwrote:

  Dear Dr. Vitaly Chaban,

 Thanks very much for your patient explanation. Yeah, you are right, that
 is what I want to know: how you tuned this parameter?

 Since then, if I want to set a new atom type and I know its vdw radius,
 so how should I set the sigma for it based on the vdw radius,



  You cannot set the sigma based ONLY on the VDW radius.



  which should be in agreement with OPLS-AA/L force filed? Could you give
 me some suggestions?
 I guess that I have to tune it by myself this time, right? Thanks in
 advance!



  I would do the following:

  1) Optimize ion-ligand complex using ab initio. Write down binding
 energy and optimal distance;
 2) Construct topology for classical MD using approximate sigma;
 3) Calculate energy and distance from classical MD;
 4) Compare them to distance and energy from ab initio;
  5) If you are not satisfied, adjust your sigma;
 6) Repeat classical MD until the difference between ion-ligand distance in
 classical MD becomes reasonably similar to that in ab initio.

  To preserve compatibility with OPLS, use the same level of theory in ab
 initio, which they used when derived OPLS. Keep in mind that their original
 level of theory is not so perfect...


  Dr. Vitaly Chaban




 All the best,
 Qinghua Liao






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Re: [gmx-users] Re: How to set the sigma and epsilon for Cu2+ in OPLS-AA/L

On Tue, Apr 9, 2013 at 11:03 AM, fantasticqhl fantastic...@gmail.comwrote:

  Dear Dr. Vitaly Chaban,

 Thanks very much again. I am sorry for the unclear, charge transfer was
 also taken into account for the complex, I did not mentioned in the last
 e-mail.

 What do you mean by finite T effect in MD? Kinetics?



I mean thermal motion. You have an optimal structure/energy at 0K in QM. In
MD you want to simulate at higher T, I guess. The optimal structures in
both cases may be very similar, but may be not so similar. I am just saying
that you should not expect ideal coincidence of energy vs. distance curves.



 For the reproduction of binding energy, I guess I know how to do it using
 QM method. Simply, I just need to do three single point calculations for
 complex,
 ligands and ion, respectively.



And correct for BSSE.



 For MM method, it is similar, however, I am not sure I get get the MM
 energy for just one ion.



This energy is zero within classical MD, since you do not consider
electrons and nucleus, as you do in QM.

Only one calculation is needed for MM. You define the charge groups, such
as ion and ligand and look at the interaction between them (g_energy).







  Is my understanding right?

 Thanks for all your explanations and suggestions on this problems!

 All the best,
 Qinghua Liao


 On 04/09/2013 10:03 AM, Dr. Vitaly Chaban wrote:




 On Tue, Apr 9, 2013 at 9:39 AM, fantasticqhl fantastic...@gmail.comwrote:

  Dear Dr. Vitaly Chaban,

 Thanks very much for your patient and detailed suggestions on this
 problem. Actually, I am doing what your suggested now.
 I optimized the copper-ligand complex using QM method, and then did some
 QM scannings to derive the bond and angle force constants.
 Right now, I am doing the MM scanning using the same coordinates which
 were used in the QM scanning. What we want is that the MM curves
 can reproduce the QM curves.



  I think it is simply impossible in your case to reproduce the QM curves.
 You neglect charge transfer from copper to the ligand, resulting a chemical
 bond formation, you neglect finite T effect in your MD. If you want to
 remain in the framework of LJ+Coulomb, the best think you can get is
 reproduction of ion-ligand binding energy and more or less adequate
 distance ion-closest atom of the ligand




  But some of them agreed well, some of them did not. So I try to tune
 the sigma of the liganded atoms, however,
 it is a little complicated to tune many liganded atoms at the same time.
 I am still trying to work it out.



  Start from the sigma for ion-closest atom of the ligand. All other
 atoms will adjust automatically, since they are connected all together
 within the ligand.

  My personal viewpoint, which you may share or not, is not to do anything
 with sigmas of other atoms of the ligand. It is best for future portability
 to limit refinement to the ion only.




  It seems that you have much experience on such problems, could you
 please give me some suggestions on tuning the sigmas of atoms again?
 Thanks very much in advance!


 All the best,
 Qinghua Liao



 On 04/08/2013 03:51 PM, Dr. Vitaly Chaban wrote:


  On Mon, Apr 8, 2013 at 3:36 PM, fantasticqhl fantastic...@gmail.comwrote:

  Dear Dr. Vitaly Chaban,

 Thanks very much for your patient explanation. Yeah, you are right, that
 is what I want to know: how you tuned this parameter?

 Since then, if I want to set a new atom type and I know its vdw radius,
 so how should I set the sigma for it based on the vdw radius,



  You cannot set the sigma based ONLY on the VDW radius.



  which should be in agreement with OPLS-AA/L force filed? Could you
 give me some suggestions?
 I guess that I have to tune it by myself this time, right? Thanks in
 advance!



  I would do the following:

  1) Optimize ion-ligand complex using ab initio. Write down binding
 energy and optimal distance;
 2) Construct topology for classical MD using approximate sigma;
 3) Calculate energy and distance from classical MD;
 4) Compare them to distance and energy from ab initio;
  5) If you are not satisfied, adjust your sigma;
 6) Repeat classical MD until the difference between ion-ligand distance
 in classical MD becomes reasonably similar to that in ab initio.

  To preserve compatibility with OPLS, use the same level of theory in ab
 initio, which they used when derived OPLS. Keep in mind that their original
 level of theory is not so perfect...


  Dr. Vitaly Chaban




 All the best,
 Qinghua Liao








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[gmx-users] Re: Lipid membrane partially broken and create huge voids

 My complex heterogenous system has DPPC+ Protein+ligand. I have packed
 lipids around protein and ligand using Inflategro method, (APL: 0.79 nm2
 got
 after 24th iteration) followed by adding solvent and neutralize the system
 by adding CL35  NA 39, since my system has -3.999 non zero total charge.
 Then the minimized system has the energy -2.8989 with Max force= 9.58
 converged normally in step 464 step.

 I used lipid constraints in the file DPOSRES_LIPID.itp before NVT


 There is no grompp error and no problem till NVT, after this
 equillibration,
 half of the DPPC along with SOL is no showing in VMD. Could any suggestions
 on this behavior.



I think your particles are still there...

Try to adjust VMD settings.

Dr. Vitaly Chaban
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[gmx-users] Re: Simulating a large system

 Hi, is it possible to instruct gromacs to only perform the dynamics on
 half of the system or protein while ignoring the rest?

 thanks



Would you explain to us why you need so exotic setup?

Dr. Vitaly Chaban
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[gmx-users] Re: can we use GPU from another machine for calculation?

 I've got two GPU workstation both of which have two GTX690 GPU. Now
 I am planning to run Gromacs GPU version and I am just wondering can we
 submit a single GPU jobs in one machine and evoke all GPU resources from
 both machine?


If I were you, I would insert both cards into the same block...

I am not an expert in this question, but intuitively the bandwidth between
your two workstations will likely kill most of the anticipated performance
gain.

Dr. Vitaly Chaban
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[gmx-users] Re: Simulating a large system

If you do not care about the atoms, which are too far away from the region
of interest, is it not reasonable just to cut that useless part? Also,
you may want to look towards implicit solvent simulations.

Dr. Vitaly Chaban


On Mon, Apr 8, 2013 at 11:35 AM, Juan Antonio Raygoza Garay 
raygo...@psu.edu wrote:

 Sure, it's basically improving minimization time. if i can focus all my
 resources in simulating or minimizing a portion of the system while
 ignoring other parts that are too far away from the selected portion, it
 can also be possible to run some simulations without the need of a big
 cluster and sort of obtaining about the same results. This goes to my
 interest of harnessing small computing systems for doing all these tasks.
 There are systems like rna molecules where i could get the fine grained
 structure first and then running the entire molecule to obtain the coarser
 structure.

 As someone says it might not improve time but at least having the ability
 to run portions only on my small desktop overnight or just leave it there
 running a lot of this could be accomplished. I do have access to a cluster
 but having to wait in the queue is time that can be used to getting
 somewhere, maybe slower but you're moving.


 On Apr 8, 2013, at 5:20 AM, Dr. Vitaly Chaban wrote:

 Vitaly Chaban



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Re: [gmx-users] Re: How to set the sigma and epsilon for Cu2+ in OPLS-AA/L

Dear Qinghua Liao -

In that case, I am just wishing you luck with the copper containing systems.

Are you going to simulate copper-ligand interactions using Coulomb+LJ
potential only? I would guess it is a chemical bonding case. Maybe the
Morse potential (additionally) can be of better service?


Dr. Vitaly Chaban




On Mon, Apr 8, 2013 at 1:09 PM, fantasticqhl fantastic...@gmail.com wrote:

  Dear Dr. Vitaly Chaban,

 Thanks very much for your explanation. I guess that I get what you mean
 now! Thanks!

 All the best,
 Qinghua Liao

 On 04/07/2013 11:35 AM, Dr. Vitaly Chaban wrote:

 The equation is a direct consequence of LJ-12-6 equation. This equation is
 used in OPLS and most other force fields.

  The difference you found originate from the fact that, besides LJ
 potential, there is much stronger Coulomb potential in the copper-ion case.
 If you run simulations, you will see that copper-ligand distance is smaller
 than the sum of their sigmas multiplied by pow (2, 1/6).


  Dr. Vitaly Chaban






  On Sun, Apr 7, 2013 at 11:28 AM, fantasticqhl fantastic...@gmail.comwrote:

  Dear Dr. Vitaly Chaban,

 Thanks for the explanation. I know this equation. However, the van der
 Waals radius and its counterpart sigma in OPLS-AA/L force field files do
 not follow this equation.

 For example, the vdw radius of copper ion is 1.4 angstrom, and its sigma
 is  2.08470e-01 (I guess the unit is nm). pow(2, 1/6) is more than 1, so
 obviously this equation
 does not work with copper. So do other atoms. I guess that there might be
 an additional coefficient for this equation in gromacs. That's the purpose
 for asking. Thanks very much!


 All the best,
 Qinghua

 On 04/07/2013 10:48 AM, Dr. Vitaly Chaban wrote:

 Dear Qinghua -

  The formal relation is diameter = pow (2, 1/6) * sigma, provided that
 you have only LJ potential in your interacting subsystem.

  If this is not the case, an optimal sigma can only be found iteratively.


  Dr. Vitaly Chaban





 On Sun, Apr 7, 2013 at 10:36 AM, fantasticqhl fantastic...@gmail.comwrote:

 Dear Dr. Vitaly Chaban,

 Thanks very much for your reply. My question is the relationship between
 van der Waals radius and sigma in the OPLS-AA/L force filed files of
 Gromacs.

 Of course I did ab initio optimizations of my system, but I do not know
 there is some relation between the optimal bond length (copper--atom of the
 ligand) and sigma.
 Could you please be more clear and give a little detailed explanation?
 Thanks very much!

 All the best,
 Qinghua

 On 04/06/2013 06:07 PM, Dr. Vitaly Chaban wrote:

 In systems of such kind, everything will depend on the atom of the
 ligand,
 which coordinated by copper ion.

 Perform ab initio geometry optimization and find the optimal distance.
 Then
 adjust sigma(s).

 Dr. Vitaly Chaban







 There is a copper ion with four ligands in my system. I am going to

 study this system using MD simulations.
 For the vdW parameters, R*=1.74 angstrom and epsilon=1.14 kcal.mol from
 one paper will be used in our
 simulations. I already found the parameters of copper ion (Cu2+) in the
 OPLS-AA/L force field files:
 sigma= 2.08470e-01, epsilon=4.76976e+00, which are for Cu2+ without
 ligands. The two epsilon are the same,
 just with different units.

 My question is that I do not know how to convert the vdW radius to
 sigma. I found that the vdw radius of copper is
 1.4 angstrom, and the sigma in the force field file is 2.08470e-01.
 Could someone tell me how to do the converting?

 Thanks very much!








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[gmx-users] Re: RDF output has no data

I believe the problem is in the way which you used to convert AMBER
trajectory to the GROMACS trajectory

I would suggest to try gmxdump and see what your trajectory looks like. Oe
maybe even better - try to visualize it in VMD to see if the format is
correct.

Dr. Vitaly Chaban



Sir

 I was using an old version. Now I used 4.5.5, it still gives me the same
 blank output file.

 Kindly suggest how to go about solving this

 Thanks


 On Sat, Apr 6, 2013 at 2:26 PM, Mark Abraham mark.j.abra...@gmail.com
 wrote:

  On Sat, Apr 6, 2013 at 7:19 AM, Venkat Reddy venkat...@gmail.com
 wrote:
 
   There was no fatal error preceding the output. After selecting the
 groups
   following are the output on the screen
   Reading frame   1 time0.100
   Warning: can not make broken molecules whole without a run input file,
don't worry, mdrun doesn't write broken molecules
  
 
  This message is from a prehistoric version of g_rdf. Please get a new
 one.
 
  Mark
 
 
  
   Reading frame2000 time  200.000
  
  
   gcq#69: The Wheels On the Bus Go Round and Round (J. Richman)
  
   And the rdf.xvg file looks like this
  
   #This file was created Sat Apr  6 10:54:13 2013
   # by the following command:
   # g_rdf -f 6md.trr -s ../../6md.pdb -n rdf.ndx -o rdf.xvg
   #
   # g_rdf is part of G R O M A C S:
   #
   # GROningen MAchine for Chemical Simulation
   #
   @title Radial Distribution
   @xaxis  label r
   @yaxis  label 
   @TYPE xy
   @ subtitle O21-H2__CAT
0.001  1
   ~
  
   Whats going wrong? Please help.

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Re: [gmx-users] Re: How to set the sigma and epsilon for Cu2+ in OPLS-AA/L