[gmx-users] Distorted protein structure after MD simulation

[sonali dhindwal]

Hello All,
I have done one MD similation for 1 ns for my protein, having two ligands and 
one metal ion with GROMOS96 43a1 force field and  dodecahedron box as tge unit 
cell.
After simulation when i checked RMSD, it is increasing till 1ns and observing 
the .gro file in VMD, I have seen that, my protein structre is very much 
distorted,  intialy it had tim barell topolgy with 8 beeta sheets and 8 alpha 
sheets,,now only 7 sheets are remaing,one became coiled strucutre. What could b 
the possible reason ? 
Thanks in advance.

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Re: [gmx-users] NVE mdp

[Mark Abraham]

On 31/03/2010 2:51 PM, Ramachandran G wrote:

Dear gromacs users:
  I am using following mdp file as input for simulating the
system with NVE ensemble. But when i check the 'Total energy',
it doesn't seems to remain constant and keep decreasing. I am also


Thus, you are not yet in an NVE ensemble. Generating velocities is only 
an approximate process, and it takes at least several picoseconds for 
some observables to start converging to their ensemble-average values. 
So, equilibrate before you start collecting data!



giving some part of my output. Thanks for your help
Rama

title= Water box
DEFINE   = -DFLEXIBLE
constraints  = hbonds
constraint_algorithm = shake


Don't simulate with flexible water and bond constraints. It's inconsistent.

Mark


integrator = md
dt = 0.001   ;
nsteps = 150  ;
nstcomm= 100
nstlist= 10
ns_type= grid
nstenergy  = 5
nstlog = 0
nstvout= 5
nstxout= 5
nstxtcout = 0
xtc-precision  = 100
nstfout= 0
coulombtype= shift
fourierspacing = 0.135
pme_order  = 4
vdwtype= switch
rvdw   = 1.0
rlist  = 1.2
rcoulomb   = 1.0
pbc= xyz
fourier_nx  = 0.0
fourier_ny  = 0.0
fourier_nz  = 0.0
;Berendsen temperature coupling is on

Tcoupl  = no   ; temperature bath (yes, no)
tau_t   = 0.1
tc-grps = system
ref_t   = 200

;Berendsen Pressure coupling is on
pcoupl  = no ; pressure bath (yes, no)
pcoupltype  = isotropic
tau_p   = 0.5
compressibility = 4.5e-05
ref_p   = 1.0

;Generate velocities is on at 300K
gen_vel = yes   ; generate initial velocities
gen_temp= 300.0 ; initial temperature
gen_seed= 173529; random seed

Output:
"Total Energy"
 0.00  -59821.300781
 0.005000  -59806.011719
 0.01  -59790.937500
 0.015000  -59799.031250
 0.02  -59803.445312
 0.025000  -59799.058594
 0.03  -59803.445312
 0.035000  -59804.835938
 0.04  -59801.652344
 0.045000  -59803.144531
 0.05  -59804.605469
 0.055000  -59803.421875
 0.06  -59806.074219
 0.065000  -59805.125000
 0.07  -59803.632812
 0.075000  -59805.742188
 0.08  -59807.140625
 0.085000  -59806.539062
 0.09  -59806.328125
 0.095000  -59806.949219
 0.10  -59807.351562
 0.105000  -59806.531250
 0.11  -59806.894531
 0.115000  -59808.933594
 0.12  -59808.585938
 0.125000  -59807.019531
 0.13  -59808.171875
 0.135000  -59809.117188
 0.14  -59808.242188
 0.145000  -59808.820312
 0.15  -59808.75
 0.155000  -59806.507812
 0.16  -59808.839844
 0.165000  -59810.800781


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[gmx-users] NVE mdp

[Ramachandran G]

Dear gromacs users:
 I am using following mdp file as input for simulating the system
with NVE ensemble. But when i check the 'Total energy',
it doesn't seems to remain constant and keep decreasing. I am also giving
some part of my output. Thanks for your help
Rama

title= Water box
DEFINE   = -DFLEXIBLE
constraints  = hbonds
constraint_algorithm = shake
integrator = md
dt = 0.001   ;
nsteps = 150  ;
nstcomm= 100
nstlist= 10
ns_type= grid
nstenergy  = 5
nstlog = 0
nstvout= 5
nstxout= 5
nstxtcout = 0
xtc-precision  = 100
nstfout= 0
coulombtype= shift
fourierspacing = 0.135
pme_order  = 4
vdwtype= switch
rvdw   = 1.0
rlist  = 1.2
rcoulomb   = 1.0
pbc= xyz
fourier_nx  = 0.0
fourier_ny  = 0.0
fourier_nz  = 0.0
;Berendsen temperature coupling is on

Tcoupl  = no   ; temperature bath (yes, no)
tau_t   = 0.1
tc-grps = system
ref_t   = 200

;Berendsen Pressure coupling is on
pcoupl  = no ; pressure bath (yes, no)
pcoupltype  = isotropic
tau_p   = 0.5
compressibility = 4.5e-05
ref_p   = 1.0

;Generate velocities is on at 300K
gen_vel = yes   ; generate initial velocities
gen_temp= 300.0 ; initial temperature
gen_seed= 173529; random seed

Output:
"Total Energy"
0.00  -59821.300781
0.005000  -59806.011719
0.01  -59790.937500
0.015000  -59799.031250
0.02  -59803.445312
0.025000  -59799.058594
0.03  -59803.445312
0.035000  -59804.835938
0.04  -59801.652344
0.045000  -59803.144531
0.05  -59804.605469
0.055000  -59803.421875
0.06  -59806.074219
0.065000  -59805.125000
0.07  -59803.632812
0.075000  -59805.742188
0.08  -59807.140625
0.085000  -59806.539062
0.09  -59806.328125
0.095000  -59806.949219
0.10  -59807.351562
0.105000  -59806.531250
0.11  -59806.894531
0.115000  -59808.933594
0.12  -59808.585938
0.125000  -59807.019531
0.13  -59808.171875
0.135000  -59809.117188
0.14  -59808.242188
0.145000  -59808.820312
0.15  -59808.75
0.155000  -59806.507812
0.16  -59808.839844
0.165000  -59810.800781
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Re: [gmx-users] density tip3p

[nishap . patel]

Thanks. I will look up the manual again.

Quoting Sander Pronk :


Hi Nisha,

Looking at your .mdp, there are some issues that might lead to the   
behavior that you describe:
First: you should try to look up the published densities for tip3p   
water at 300K - they might actually be close to what you get.
Second: your neighbor list cut-off (rlist) might be too small to   
fully contain the charge groups (check the manual, section 7.3.11).
Third: You haven't enabled long-range mean field correction for the   
pressure or energy. Expect the pressure to be strongly dependent on   
cut-off (see the same section).


Sander


On Mar 30, 2010, at 22:47 , nishap.pa...@utoronto.ca wrote:

I have a box (3x3x3nm) of Tip3p water molecules ~900 and the   
density when I create the box using genbox is 997.177g/l. I did   
energy minimization run and the potential energy did converge   
smoothly, so I did NPT equilibration run of 100ps and I got the   
density value of 975g/l. Why does the density decrease after the   
run? these are the parameters that I used :


RUN CONTROL PARAMETERS
integrator   = md
tinit= 0
dt   = 0.002
nsteps   = 5
nstcomm  = 0
nstxout  = 0
nstvout  = 0
nstfout  = 0
nstlog   = 100
nstenergy= 100
nstxtcout= 0
xtc_precision= 1000
nstlist  = 5
ns-type  = Grid
pbc  = xyz
rlist= 1.1
coulombtype  = pme
rcoulomb = 1.1
epsilon-r= 1
vdw-type = switch
rvdw-switch  = 0.8
rvdw = 1.0
Tcoupl   = V-rescale
tc-grps  = System
tau_t= 0.1
ref_t= 300
Pcoupl   = berendsen
tau_p= 0.5
compressibility  = 4e-05
ref_p= 1.0
constraints  = all-bonds
constraint-algorithm = Lincs
unconstrained-start  = no
lincs-order  = 4
lincs-iter   = 1
lincs-warnangle  = 30

Am I missing something?
Thanks

Nisha Patel


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Nisha Patel
MSc Candidate
Leslie Dan Faculty of Pharmacy
Department of Pharmaceutical Sciences
144 College Street
Room 1172
Toronto, ON
M5S 3M2
Canada
Telephone: 416-978-1536

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Re: [gmx-users] density tip3p

[Sander Pronk]

Hi Nisha,

Looking at your .mdp, there are some issues that might lead to the behavior 
that you describe:
First: you should try to look up the published densities for tip3p water at 
300K - they might actually be close to what you get. 
Second: your neighbor list cut-off (rlist) might be too small to fully contain 
the charge groups (check the manual, section 7.3.11).
Third: You haven't enabled long-range mean field correction for the pressure or 
energy. Expect the pressure to be strongly dependent on cut-off (see the same 
section).

Sander


On Mar 30, 2010, at 22:47 , nishap.pa...@utoronto.ca wrote:

> I have a box (3x3x3nm) of Tip3p water molecules ~900 and the density when I 
> create the box using genbox is 997.177g/l. I did energy minimization run and 
> the potential energy did converge smoothly, so I did NPT equilibration run of 
> 100ps and I got the density value of 975g/l. Why does the density decrease 
> after the run? these are the parameters that I used :
> 
> RUN CONTROL PARAMETERS
> integrator   = md
> tinit= 0
> dt   = 0.002
> nsteps   = 5
> nstcomm  = 0
> nstxout  = 0
> nstvout  = 0
> nstfout  = 0
> nstlog   = 100
> nstenergy= 100
> nstxtcout= 0
> xtc_precision= 1000
> nstlist  = 5
> ns-type  = Grid
> pbc  = xyz
> rlist= 1.1
> coulombtype  = pme
> rcoulomb = 1.1
> epsilon-r= 1
> vdw-type = switch
> rvdw-switch  = 0.8
> rvdw = 1.0
> Tcoupl   = V-rescale
> tc-grps  = System
> tau_t= 0.1
> ref_t= 300
> Pcoupl   = berendsen
> tau_p= 0.5
> compressibility  = 4e-05
> ref_p= 1.0
> constraints  = all-bonds
> constraint-algorithm = Lincs
> unconstrained-start  = no
> lincs-order  = 4
> lincs-iter   = 1
> lincs-warnangle  = 30
> 
> Am I missing something?
> Thanks
> 
> Nisha Patel
> 
> 
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[gmx-users] density tip3p

[nishap . patel]

I have a box (3x3x3nm) of Tip3p water molecules ~900 and the density  
when I create the box using genbox is 997.177g/l. I did energy  
minimization run and the potential energy did converge smoothly, so I  
did NPT equilibration run of 100ps and I got the density value of  
975g/l. Why does the density decrease after the run? these are the  
parameters that I used :


 RUN CONTROL PARAMETERS
integrator   = md
tinit= 0
dt   = 0.002
nsteps   = 5
nstcomm  = 0
nstxout  = 0
nstvout  = 0
nstfout  = 0
nstlog   = 100
nstenergy= 100
nstxtcout= 0
xtc_precision= 1000
nstlist  = 5
ns-type  = Grid
pbc  = xyz
rlist= 1.1
coulombtype  = pme
rcoulomb = 1.1
epsilon-r= 1
vdw-type = switch
rvdw-switch  = 0.8
rvdw = 1.0
Tcoupl   = V-rescale
tc-grps  = System
tau_t= 0.1
ref_t= 300
Pcoupl   = berendsen
tau_p= 0.5
compressibility  = 4e-05
ref_p= 1.0
constraints  = all-bonds
constraint-algorithm = Lincs
unconstrained-start  = no
lincs-order  = 4
lincs-iter   = 1
lincs-warnangle  = 30

Am I missing something?
Thanks

Nisha Patel


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Re: [gmx-users] Pressure average problem

[nishap . patel]

Quoting Mark Abraham :


On 31/03/2010 5:19 AM, nishap.pa...@utoronto.ca wrote:

Hello,

I am simulating a box of water (TIP3P ) in a box of 3nm*3*3nm.My
simulations are 100ns each. I am using different cut-off. i.e
vdw-type = switch
rvdw-switch = 0.8
rvdw = 1.0, 1.2 and 1.3

and these are my parameters for Pressure coupling":
Pcoupl = Parrinello-Rahman
Pcoupltype = isotropic
tau_p = 2.0
compressibility = 4.5e-5
ref_p = 1.0

Now after my simulations, when I use g_energy to extract average
pressure I get different values for all three cut-offs.
For the cut-off of 1.0nm, the average value doesn't converge to 1.0atm
but it is rather ~2.1atm, for 1.2cut off the avg. pressure is ~1.7 and
for 1.3cut off avg. pressure is ~1.03. I don't understand why the
pressure is not converging to 1.0atm for the cut-off of 1.0nm.. All the
parameters are exactly the same, the only difference between these
simulations are the cut-off values. Could anyone please give me some
insight on how the pressure coupling works and if this behaviour seems
normal?


You've not told us critical information, like the rest of your .mdp
file, or how you equilibrated before running your simulation from which
you collected data. You could be doing all sorts of weird things and we
simply couldn't know. Your electrostatic treatment is far more
significant than your use of rvdw.

Haphazardly changing simulation parameters is not a desirable thing to
do. Find a suitable model of physics in a published calculation,
evaluate its applicability to your situation, test its performance
suitably, and then apply it.

Mark


Thanks Mark, I will look into it and hopefully it will make more sense then.

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Nisha Patel


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Re: [gmx-users] Using lennard jones and buckingham terms simultaneously

[Mark Abraham]

On 31/03/2010 1:40 AM, Gareth Tribello wrote:

Hello again

Still trying to get this carbonate forcefield to work with gromacs.  I
now know that the tables and so on are being read in correctly as I can
get gromacs to reproduce the energies that I get for the various terms
when I calculate them by hand/with a separate program.  There is stilla
a problem with the charge groups however.  As when I attempt to split up
the atoms in the water molecule the simulation fails.  Again checking
that I am doing this correctly I would replace:

;   at type   res nr  res name  at name   cg nr
charge mass
1   amber99_61  1   SOL  OW1   0
16.0
2   amber99_60  1   SOL HW21   0.52422
1.00800
3   amber99_60  1   SOL HW31   0.52422
1.00800
4   MW  1   SOL MW4   1
-1.04844   0.0

with

;   at type   res nr  res name  at name   cg nr
charge mass
1   amber99_61  1   SOL  OW1   0
16.0
2   amber99_60  1   SOL HW22   0.52422
1.00800
3   amber99_60  1   SOL HW33   0.52422
1.00800
4   MW  1   SOL MW4   4
-1.04844   0.0

The problem I get (even if I just run water without any
carbonate/tabulated potentials) if I do the above is that the settles
algorithm fails.


I'm surprised GROMACS even tries SETTLE with your modified water charge 
groups. Anyway, you can turn it off and try again and report back. You 
would have to think very carefully how any optimized water model 
interacts with your (probably) fundamentally broken model of physics.



I'm obviously missing something fundamental - I'm not even sure that cg
nr stands for the charge group.  Any help would be greatly appreciated.


"cg nr" == "charge group number"

You've heard my thoughts on possible fundamental problems twice before. 
It seems even more unlikely that your model physics was correctly 
parameterized to suit TIP4P than a simpler water model. If it had been 
correctly parameterized, you'd have a method in published literature to 
be following. Apparently, you think you know best, so I'm going to stop 
being helpful. :-)


Mark


On Thu, Mar 25, 2010 at 11:07 PM, Mark Abraham mailto:mark.abra...@anu.edu.au>> wrote:

On 26/03/2010 7:03 AM, Gareth Tribello wrote:

Hello again

I have tried to do as you suggest and use tables but I have a new
problem.  First let me describe my process and then you can let
me know
if there is anything wrong in the stages:

OK so first you include the following directives into the mdp file:

coulombtype = pme   (or whatever sort of coulomb interaction you
are using)
vdw-type = user

energygrps  = Ca CCA OCA OW HW
energygrp_table   = Ca OCA Ca CCA OCA OCA OCA OW OCA HW

Gromacs is then (at some stage) going to look for a series of
files called

table.xvg  -   which is the default 6-12 Lennard Jones that will
be used
for most of the atoms
table_Ca_OCA.xvg  - which are the Buckingham interactions
between your
various atom types.
table_Ca_CCA.xvg
table_OCA_OCA.xvg
table_OCA_OW.xvg
table_OCA_HW.xvg

These files have the format (and contents) described in section
6.7 of
the manual.  Finally, you define the various energy groups Ca,
OCA and
so on in your index.ndx file.

The problem is that grompp gives me the following error:

"atoms 1 and 2 in charge group 1 of molecule type 'SOL' are in
different
energy groups"

(incidentally these atoms 1 and 2 are OW and HW)

Does this mean that I cannot use different tabulated potentials for
different atoms in a molecules?  By which I mean that I can't use
different tabulated potentials for the OW Ca and HW Ca
interactions for
example?


Charge groups are the fundamental unit GROMACS uses in constructing
a simulation. Energy groups are the next "higher" layer in the data
structures, and these must be sets of whole charge groups. With some
electrostatics models, looping over charge groups whose charge is
preferably an integer is essential for modelling correct behaviour.
GROMACS does a complex sorting of all the interactions between
charge groups into lists that allow it to iterate over charge groups
and energy groups. A user table then gets applied to a whole intra-
or inter- energy-group loop. Thus your attempt violates this
precondition.

However, PME does not require the use of charge groups for accurate
results, since all inter-atomic electrostatic interactions get
treated, regardless of distance. So you could decompose your water

Re: [gmx-users] Pressure average problem

[Mark Abraham]

On 31/03/2010 5:19 AM, nishap.pa...@utoronto.ca wrote:

Hello,

I am simulating a box of water (TIP3P ) in a box of 3nm*3*3nm.My
simulations are 100ns each. I am using different cut-off. i.e
vdw-type = switch
rvdw-switch = 0.8
rvdw = 1.0, 1.2 and 1.3

and these are my parameters for Pressure coupling":
Pcoupl = Parrinello-Rahman
Pcoupltype = isotropic
tau_p = 2.0
compressibility = 4.5e-5
ref_p = 1.0

Now after my simulations, when I use g_energy to extract average
pressure I get different values for all three cut-offs.
For the cut-off of 1.0nm, the average value doesn't converge to 1.0atm
but it is rather ~2.1atm, for 1.2cut off the avg. pressure is ~1.7 and
for 1.3cut off avg. pressure is ~1.03. I don't understand why the
pressure is not converging to 1.0atm for the cut-off of 1.0nm.. All the
parameters are exactly the same, the only difference between these
simulations are the cut-off values. Could anyone please give me some
insight on how the pressure coupling works and if this behaviour seems
normal?


You've not told us critical information, like the rest of your .mdp 
file, or how you equilibrated before running your simulation from which 
you collected data. You could be doing all sorts of weird things and we 
simply couldn't know. Your electrostatic treatment is far more 
significant than your use of rvdw.


Haphazardly changing simulation parameters is not a desirable thing to 
do. Find a suitable model of physics in a published calculation, 
evaluate its applicability to your situation, test its performance 
suitably, and then apply it.


Mark
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[gmx-users] Pressure average problem

[nishap . patel]

Hello,

I am simulating a box of water (TIP3P ) in a box of 3nm*3*3nm.My  
simulations are 100ns each. I am using different cut-off. i.e

vdw-type = switch
rvdw-switch  = 0.8
rvdw = 1.0, 1.2 and 1.3

and these are my parameters for Pressure coupling":
Pcoupl   = Parrinello-Rahman
Pcoupltype   = isotropic
tau_p= 2.0
compressibility  = 4.5e-5
ref_p= 1.0

Now after my simulations, when I use g_energy to extract average  
pressure I get different values for all three cut-offs.
For the cut-off of 1.0nm, the average value doesn't converge to 1.0atm  
but it is rather ~2.1atm, for 1.2cut off the avg. pressure is ~1.7 and  
for 1.3cut off avg. pressure is ~1.03. I don't understand why the  
pressure is not converging to 1.0atm for the cut-off of 1.0nm.. All  
the parameters are exactly the same, the only difference between these  
simulations are the cut-off values. Could anyone please give me some  
insight on how the pressure coupling works and if this behaviour seems  
normal?



Thanks.
Nisha Patel


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Re: [gmx-users] Exploding box (in one dimension) Semi-isotropic pressure coupling?

[sapna sarupria]

Hi Sander

That helps quite a bit. Thanks so much!

Sapna

On Tue, Mar 30, 2010 at 12:50 PM, Sander Pronk  wrote:

> There *should* be no preference, but I seem to remember that one of the
> artifacts of using Ewald-style electrostatic treatment (such as PME) is that
> there may be dipole-coupling between periodic images, especially if one
> symmetry has already been broken.
> That doesn't mean you shouldn't use PME, though: you're a long way off from
> the thermodynamic limit, so you can't rely on fluctuations being slow. The
> situation you're describing will always happen, and with a small number of
> particles (i.e. less than you can see with the naked eye) it will happen
> sooner rather than later.
>
> Sander
>
>
> On Mar 30, 2010, at 18:00 , sapna sarupria wrote:
>
> Hi Sander
> Thanks for your response. Is there then a preference for z-dimension to
> expand (other than the way the system is setup in terms of semi-isotropic
> coupling). Would one see an expansion in any one direction if I had the same
> system setup with independent pressure coupling for each dimension
> (anisotropic)?
>
> Thanks,
> Sapna
>
> On Tue, Mar 30, 2010 at 11:53 AM, Sander Pronk  wrote:
>
>> It sounds like the normal thing that would happen if you have a system
>> that has no shear elastic constant, like a fluid.
>> In that case, there are no restoring forces against growth of system size
>> in one coordinate with a concomitant decrease in the other coordinates, so
>> eventually this should happen (unless I misunderstand the nature of your
>> system).
>>
>> Sander
>>
>>
>> On Mar 30, 2010, at 17:47 , sapna sarupria wrote:
>>
>> Hello all,
>>
>> I have a simulation running for a hydrate (with CO2) and water in contact
>> with each other. I run the simulation at 280K at which the hydrate melts and
>> finally the system is just liquid water with CO2 in it. However, as the
>> simulation proceeds the box begins to expand in the z-direction and
>> decreases in the x-y direction considerably. Initially the box has
>> 4.8x4.8x9.6 nm^3 dimensions. After the hydrate melts (the volume fluctuates
>> more) and is fine for another 10 ns but after that the dimensions in the x-y
>> direction decrease to 2.5 nm and z-dimension increases to 35 nm. At this
>> point the simulation crashes since my cut-off distance are 1.2 nm.
>>
>> I am using semi-isotropic pressure coupling but the pressure in the x-y
>> direction and z-direction are the same (=30.5 bar) and so is the
>> compressibility (=4.5e-5). I am using Parrinello-Rahman pressure coupling
>> and Nose-Hoover thermostat. The CO2 and water molecules are rigid and shake
>> is used to maintain their geometry. The simulation time step is 2 fs. Can
>> someone tell me why such a thing happens? I have pasted my mdp file for
>> completeness. I am using Gromacs  4.0.5 and I run the simulations in
>> parallel using 4 processors. Values related to domain decomposition etc are
>> unchanged and the default values are used.
>>
>> Any insights will be helpful. Thanks for the help.
>>
>> MDP File:
>> title   =  CO2 hydrate + water  ; a string
>> cpp =  /lib/cpp ; c-preprocessor
>> dt  =  0.002; time step
>> nsteps   =  2500; number of steps
>> nstcomm   =  10   ; reset c.o.m. motion
>> nstxout  =  2; write coords
>> nstvout  =  2; write velocities
>> nstlog=  25000; print to logfile
>> nstenergy  =  500   ; print energies
>> xtc_grps=  OW_HW1_HW2_CO2
>> nstxtcout   =  500
>> nstlist =  10   ; update pairlist
>> ns_type  =  grid ; pairlist method
>> coulombtype   =  PME
>> rvdw=  1.2  ; cut-off for vdw
>> rcoulomb =  1.2  ; cut-off for coulomb
>> rlist  =  1.2  ; cut-off for coulomb
>> DispCorr  =  EnerPres
>> Tcoupl  =  Nose-Hoover
>> ref_t =  300
>> tc-grps =  System
>> tau_t =  0.5
>> Pcoupl  =  Parrinello-Rahman
>> Pcoupltype   =  semiisotropic; pressure geometry
>> tau_p   =  1.0   1.0; p-coupling time
>> compressibility =  4.5e-5  4.5e-5   ; compressibility
>> ref_p   =  30.5  30.5   ; ref pressure
>> gen_vel =  yes  ; generate initial vel
>> gen_temp=  200  ; initial temperature
>> gen_seed=  372340   ; random seed
>> constraint_algorithm = shake
>> constraints =  all-bonds
>>
>>
>>
>> Thanks a lot
>>  Sapna
>>
>>
>>
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[gmx-users] Parallel pulling with Gromacs 4.0.7: COMM mode problem

[Chris Neale]

Dear Aykut:

1. Did you see the log file message:

"comm-mode angular will give incorrect results when the comm group 
partially crosses a periodic boundary"


2. You say "Actually you might be right about the domain decomposition", 
but it seems like you didn't run it on gmx 4 in serial or with particle 
decomposition.


I wish you the best of luck, I'm out of ideas here.

Chris.

-- original message --

Hi

Actually you might be right about the domain decomposition


G3 pull.pdo output file on single machine

focus on the 2nd and 3rd columns which are x and y positions of the
surface: almost *unchanged* as expected for COMM_grps=surface option
*
2.00 3.149521 1.576811 5.770928
7.149521 1.874820 1.676811
2.201172 3.149521 1.576812 5.761463
7.149541 1.880746 1.676812
2.400391 3.149520 1.576813 5.771702
7.149560 1.867692 1.676813
2.601562 3.149519 1.576813 5.797871
7.149579 1.879650 1.676813
2.800781 3.149518 1.576812 5.794115
7.149598 1.887728 1.676812
20001.00 3.149517 1.576813 5.778761
7.149617 1.870823 1.676813
20001.201172 3.149518 1.576815 5.783334
7.149638 1.849283 1.676815
20001.400391 3.149517 1.576815 5.780031
7.149658 1.877158 1.676815
.
.
3.402344 3.149799 1.576911 2.249830
9.149739 1.604563 1.676911
3.601562 3.149797 1.576911 2.209385
9.149757 1.622380 1.676911
3.800781 3.149792 1.576911 2.215503
9.149773 1.653246 1.676911
4.00 3.149791 1.576912 2.221903
9.149791 1.659781 1.676912



G4 pull.xvg output (in parellel), 2nd and 3rd columns which are x and y
positions of the surface: *changing*, contradiction to COMM_grps=surface
option

*
0.4000 3.1498 2.997 -0.391131 -0.331925
0.8000 3.14903 2.99499 -0.391976 -0.346309
1.2000 3.14753 2.99846 -0.372158 -0.407621
1.6000 3.14635 3.00695 -0.337084 -0.422437
2. 3.14465 3.00585 -0.306999 -0.474991
2.4000 3.14365 3.00408 -0.30164 -0.48047
2.8000 3.14338 3.00447 -0.285076 -0.483861
3.2000 3.14361 3.00119 -0.226717 -0.460955

..
2838. 3.20024 0.662325 1.7185 0.986139
2838.4000 3.19435 0.661913 1.74023 1.0404
2838.8000 3.18835 0.666171 1.8073 1.02766
2839.2000 3.18264 0.658261 1.81687 0.999429
2839.6000 3.17766 0.668439 1.82782 1.05693


here is the log file for G4 (pulling) run in parallel


Initializing Domain Decomposition on 32 nodes
Dynamic load balancing: auto
Will sort the charge groups at every domain (re)decomposition
Initial maximum inter charge-group distances:
two-body bonded interactions: 0.507 nm, LJ-14, atoms 5186 5197
multi-body bonded interactions: 0.507 nm, Proper Dih., atoms 5186 5197
Minimum cell size due to bonded interactions: 0.557 nm
Maximum distance for 5 constraints, at 120 deg. angles, all-trans: 0.200 nm
Estimated maximum distance required for P-LINCS: 0.200 nm
Guess for relative PME load: 0.20
Will use 24 particle-particle and 8 PME only nodes
This is a guess, check the performance at the end of the log file
Using 8 separate PME nodes
Scaling the initial minimum size with 1/0.8 (option -dds) = 1.25
Optimizing the DD grid for 24 cells with a minimum initial size of 0.697 nm
The maximum allowed number of cells is: X 9 Y 4 Z 9
Domain decomposition grid 4 x 2 x 3, separate PME nodes 8

comm-mode angular will give incorrect results when the comm group
partially crosses a periodic boundary
Interleaving PP and PME nodes
This is a particle-particle only node

Domain decomposition nodeid 0, coordinates 0 0 0

Table routines are used for coulomb: TRUE
Table routines are used for vdw: FALSE
Will do PME sum in reciprocal space.

  --- Thank You ---  
Using a Gaussian width (1/beta) of 0.25613 nm for Ewald
Cut-off's: NS: 0.8 Coulomb: 0.8 LJ: 0.8
System total charge: -0.000
Generated table with 3600 data points for Ewald.
Tabscale = 2000 points/nm
Generated table with 3600 data points for LJ6.
Tabscale = 2000 points/nm
Generated table with 3600 data points for LJ12.
Tabscale = 2000 points/nm
Generated table with 3600 data points for 1-4 COUL.
Tabscale = 2000 points/nm
Generated table with 3600 data points for 1-4 LJ6.
Tabscale = 2000 points/nm
Generated table with 3600 data points for 1-4 LJ12.
Tabscale = 2000 points/nm

Enabling SPC water optimization for 3021 molecules.

Configuring nonbonded kernels...


Removing pbc first time

Will apply umbrella COM pulling in geometry 'position'
between a reference group and 1 group
Pull group 0: 5181 atoms, mass 56947.551
Pull group 1: 13 atoms, mass 116.120

Initializing Parallel LINear Constraint Solver



Linking all bonded interactions to atoms
There are 85833 inter charge-group exclusions,
will use an extra communication step for exclusion forces for PME

The initial number of communication pulses is: X 1 Y 1 Z 1
The initial domain decomposition cell size is: X 1.58 nm Y 1.58 nm Z 2.23 nm

The maximum allowed distance for charge groups involved in interactions is:
non-bonded interactions 0.800 nm
(the following are initial values, th

Re: [gmx-users] Exploding box (in one dimension) Semi-isotropic pressure coupling?

[Sander Pronk]

There *should* be no preference, but I seem to remember that one of the 
artifacts of using Ewald-style electrostatic treatment (such as PME) is that 
there may be dipole-coupling between periodic images, especially if one 
symmetry has already been broken. 
That doesn't mean you shouldn't use PME, though: you're a long way off from the 
thermodynamic limit, so you can't rely on fluctuations being slow. The 
situation you're describing will always happen, and with a small number of 
particles (i.e. less than you can see with the naked eye) it will happen sooner 
rather than later.

Sander


On Mar 30, 2010, at 18:00 , sapna sarupria wrote:

> Hi Sander
> Thanks for your response. Is there then a preference for z-dimension to 
> expand (other than the way the system is setup in terms of semi-isotropic 
> coupling). Would one see an expansion in any one direction if I had the same 
> system setup with independent pressure coupling for each dimension 
> (anisotropic)? 
> 
> Thanks,
> Sapna
> 
> On Tue, Mar 30, 2010 at 11:53 AM, Sander Pronk  wrote:
> It sounds like the normal thing that would happen if you have a system that 
> has no shear elastic constant, like a fluid. 
> In that case, there are no restoring forces against growth of system size in 
> one coordinate with a concomitant decrease in the other coordinates, so 
> eventually this should happen (unless I misunderstand the nature of your 
> system).
> 
> Sander
> 
> 
> On Mar 30, 2010, at 17:47 , sapna sarupria wrote:
> 
>> Hello all,
>> 
>> I have a simulation running for a hydrate (with CO2) and water in contact 
>> with each other. I run the simulation at 280K at which the hydrate melts and 
>> finally the system is just liquid water with CO2 in it. However, as the 
>> simulation proceeds the box begins to expand in the z-direction and 
>> decreases in the x-y direction considerably. Initially the box has 
>> 4.8x4.8x9.6 nm^3 dimensions. After the hydrate melts (the volume fluctuates 
>> more) and is fine for another 10 ns but after that the dimensions in the x-y 
>> direction decrease to 2.5 nm and z-dimension increases to 35 nm. At this 
>> point the simulation crashes since my cut-off distance are 1.2 nm. 
>> 
>> I am using semi-isotropic pressure coupling but the pressure in the x-y 
>> direction and z-direction are the same (=30.5 bar) and so is the 
>> compressibility (=4.5e-5). I am using Parrinello-Rahman pressure coupling 
>> and Nose-Hoover thermostat. The CO2 and water molecules are rigid and shake 
>> is used to maintain their geometry. The simulation time step is 2 fs. Can 
>> someone tell me why such a thing happens? I have pasted my mdp file for 
>> completeness. I am using Gromacs  4.0.5 and I run the simulations in 
>> parallel using 4 processors. Values related to domain decomposition etc are 
>> unchanged and the default values are used.
>> 
>> Any insights will be helpful. Thanks for the help.
>> 
>> MDP File:
>> title   =  CO2 hydrate + water  ; a string
>> cpp =  /lib/cpp ; c-preprocessor
>> dt  =  0.002; time step
>> nsteps   =  2500; number of steps
>> nstcomm   =  10   ; reset c.o.m. motion
>> nstxout  =  2; write coords
>> nstvout  =  2; write velocities
>> nstlog=  25000; print to logfile
>> nstenergy  =  500   ; print energies
>> xtc_grps=  OW_HW1_HW2_CO2
>> nstxtcout   =  500
>> nstlist =  10   ; update pairlist
>> ns_type  =  grid ; pairlist method
>> coulombtype   =  PME
>> rvdw=  1.2  ; cut-off for vdw
>> rcoulomb =  1.2  ; cut-off for coulomb
>> rlist  =  1.2  ; cut-off for coulomb
>> DispCorr  =  EnerPres
>> Tcoupl  =  Nose-Hoover
>> ref_t =  300
>> tc-grps =  System
>> tau_t =  0.5
>> Pcoupl  =  Parrinello-Rahman
>> Pcoupltype   =  semiisotropic; pressure geometry
>> tau_p   =  1.0   1.0; p-coupling time
>> compressibility =  4.5e-5  4.5e-5   ; compressibility
>> ref_p   =  30.5  30.5   ; ref pressure
>> gen_vel =  yes  ; generate initial vel
>> gen_temp=  200  ; initial temperature
>> gen_seed=  372340   ; random seed
>> constraint_algorithm = shake
>> constraints =  all-bonds
>> 
>> 
>> 
>> Thanks a lot
>> Sapna
>> 
>> 
> 
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Re: [gmx-users] water box with prescribed volume and density

[Justin A. Lemkul]

grivet wrote:

Thank you for your quick and detailed answer.

First, begin by using the right genbox flags :)  The -nmol flag is for insertion 
of extra molecules (specified in -ci).  This operation is not what you want.  If 
you wish to cap the number of solvent molecules, you want the -maxsol option.



By the way, I notice that the number of molecules in topol.top is not
updated; is that normal ?
Given your commands, yes.  You are not passing your topology to genbox using -p. 
  If you do, it will happily update it for you.


I followed your prescriptions with succes. 

Also understand that the number of water molecules present in the box is 
dependent upon other species (i.e., solute).  If you are trying to compare 
results with some other system (with a different solute), the space available 
for solvent may be different, and really is an irrelevant consideration. 
Provided you have a reasonable unit cell that does not violate the minimum image 
convention, and you use the same run parameters, then the comparison should be 
legitimate.  If you simply wish to run a new simulation from a previous 
configuration, there is no need to re-build the system; just start a new 
simulation with different starting velocities.


No, I simply want to simulate a box of water and compare results with
those obained with GROMOS and spc water.

Having cleared the first hurdle, I ran mdrun for steepest descent (5832
molecules). The program stopped after 2067 steps, with maximum force =
1.58E02 on atom 4870. How important is that warning?



What warning?  This one?

http://www.gromacs.org/Documentation/Errors#Stepsize_too_small.2c_or_no_change_in_energy._Converged_to_machine_precision.2c_but_not_to_the_requested_precision


Anyway, I started mdrun again for a dynamics run (0.5 fs step, 25 ps
long, temperature and pressure cooupling with Berendsen thermostats).
How can I judge the quality of results ?



Evaluate the resulting observable parameters and compare them to what is 
expected, either experimentally or from other simulations.  See the manual for a 
list of analysis tools and what they can do.



The temperature quickly evolved from 300K to the prescribed 270 K and
then fluctuated by 2-3 K. (One would think that velocities are generated
according to the reference temperature, 270K?)



The initial temperature will depend on the quality of the initial configuration 
(i.e., if two particles are extremely close, they may spin off a bit from each 
other, causing a small temperature spike), application of constraints, etc.



The pressure fluctuated a lot and is -179 at the end of the run; what is
the significance of this result?



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

The end value is far less significant than the average value.  See the link for 
notes on what dictates instantaneous pressure.



The volume and density evolved rather smoothly to reasonable values. I
have two values for the density; according to the .log file, it is
0.9937E03 and according to g_energy, it is 1.015E03; which should I
believe?



Probably g_energy.  See the manual, Appendix C.  How many values in the .log 
file are you looking at?  Anything printed there is just an instantaneous value, 
and may not represent the actual average over the simulation.



Can I consider my system to be fully equilibrated? Since the run lasted
50 mn on a signle node, I cans easily extend the equilibration. A last
point is not clear; which file should I start from to extend the
computation: .cpt, .trr, or .xtc?



http://www.gromacs.org/Documentation/How-tos/Extending_Simulations

The exact time necessary will depend on how well-converged all of your desired 
observables are.  For pure water, this shouldn't take long, maybe a few hundred 
ps at most.


-Justin


Thank you again for taking pains with an ignorant user
JP Grivet




--


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


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Re: [gmx-users] Exploding box (in one dimension) Semi-isotropic pressure coupling?

[sapna sarupria]

Hi Sander
Thanks for your response. Is there then a preference for z-dimension to
expand (other than the way the system is setup in terms of semi-isotropic
coupling). Would one see an expansion in any one direction if I had the same
system setup with independent pressure coupling for each dimension
(anisotropic)?

Thanks,
Sapna

On Tue, Mar 30, 2010 at 11:53 AM, Sander Pronk  wrote:

> It sounds like the normal thing that would happen if you have a system that
> has no shear elastic constant, like a fluid.
> In that case, there are no restoring forces against growth of system size
> in one coordinate with a concomitant decrease in the other coordinates, so
> eventually this should happen (unless I misunderstand the nature of your
> system).
>
> Sander
>
>
> On Mar 30, 2010, at 17:47 , sapna sarupria wrote:
>
> Hello all,
>
> I have a simulation running for a hydrate (with CO2) and water in contact
> with each other. I run the simulation at 280K at which the hydrate melts and
> finally the system is just liquid water with CO2 in it. However, as the
> simulation proceeds the box begins to expand in the z-direction and
> decreases in the x-y direction considerably. Initially the box has
> 4.8x4.8x9.6 nm^3 dimensions. After the hydrate melts (the volume fluctuates
> more) and is fine for another 10 ns but after that the dimensions in the x-y
> direction decrease to 2.5 nm and z-dimension increases to 35 nm. At this
> point the simulation crashes since my cut-off distance are 1.2 nm.
>
> I am using semi-isotropic pressure coupling but the pressure in the x-y
> direction and z-direction are the same (=30.5 bar) and so is the
> compressibility (=4.5e-5). I am using Parrinello-Rahman pressure coupling
> and Nose-Hoover thermostat. The CO2 and water molecules are rigid and shake
> is used to maintain their geometry. The simulation time step is 2 fs. Can
> someone tell me why such a thing happens? I have pasted my mdp file for
> completeness. I am using Gromacs  4.0.5 and I run the simulations in
> parallel using 4 processors. Values related to domain decomposition etc are
> unchanged and the default values are used.
>
> Any insights will be helpful. Thanks for the help.
>
> MDP File:
> title   =  CO2 hydrate + water  ; a string
> cpp =  /lib/cpp ; c-preprocessor
> dt  =  0.002; time step
> nsteps   =  2500; number of steps
> nstcomm   =  10   ; reset c.o.m. motion
> nstxout  =  2; write coords
> nstvout  =  2; write velocities
> nstlog=  25000; print to logfile
> nstenergy  =  500   ; print energies
> xtc_grps=  OW_HW1_HW2_CO2
> nstxtcout   =  500
> nstlist =  10   ; update pairlist
> ns_type  =  grid ; pairlist method
> coulombtype   =  PME
> rvdw=  1.2  ; cut-off for vdw
> rcoulomb =  1.2  ; cut-off for coulomb
> rlist  =  1.2  ; cut-off for coulomb
> DispCorr  =  EnerPres
> Tcoupl  =  Nose-Hoover
> ref_t =  300
> tc-grps =  System
> tau_t =  0.5
> Pcoupl  =  Parrinello-Rahman
> Pcoupltype   =  semiisotropic; pressure geometry
> tau_p   =  1.0   1.0; p-coupling time
> compressibility =  4.5e-5  4.5e-5   ; compressibility
> ref_p   =  30.5  30.5   ; ref pressure
> gen_vel =  yes  ; generate initial vel
> gen_temp=  200  ; initial temperature
> gen_seed=  372340   ; random seed
> constraint_algorithm = shake
> constraints =  all-bonds
>
>
>
> Thanks a lot
>  Sapna
>
>
>
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Re: [gmx-users] Exploding box (in one dimension) Semi-isotropic pressure coupling?

[Sander Pronk]

It sounds like the normal thing that would happen if you have a system that has 
no shear elastic constant, like a fluid. 
In that case, there are no restoring forces against growth of system size in 
one coordinate with a concomitant decrease in the other coordinates, so 
eventually this should happen (unless I misunderstand the nature of your 
system).

Sander


On Mar 30, 2010, at 17:47 , sapna sarupria wrote:

> Hello all,
> 
> I have a simulation running for a hydrate (with CO2) and water in contact 
> with each other. I run the simulation at 280K at which the hydrate melts and 
> finally the system is just liquid water with CO2 in it. However, as the 
> simulation proceeds the box begins to expand in the z-direction and decreases 
> in the x-y direction considerably. Initially the box has 4.8x4.8x9.6 nm^3 
> dimensions. After the hydrate melts (the volume fluctuates more) and is fine 
> for another 10 ns but after that the dimensions in the x-y direction decrease 
> to 2.5 nm and z-dimension increases to 35 nm. At this point the simulation 
> crashes since my cut-off distance are 1.2 nm. 
> 
> I am using semi-isotropic pressure coupling but the pressure in the x-y 
> direction and z-direction are the same (=30.5 bar) and so is the 
> compressibility (=4.5e-5). I am using Parrinello-Rahman pressure coupling and 
> Nose-Hoover thermostat. The CO2 and water molecules are rigid and shake is 
> used to maintain their geometry. The simulation time step is 2 fs. Can 
> someone tell me why such a thing happens? I have pasted my mdp file for 
> completeness. I am using Gromacs  4.0.5 and I run the simulations in parallel 
> using 4 processors. Values related to domain decomposition etc are unchanged 
> and the default values are used.
> 
> Any insights will be helpful. Thanks for the help.
> 
> MDP File:
> title   =  CO2 hydrate + water  ; a string
> cpp =  /lib/cpp ; c-preprocessor
> dt  =  0.002; time step
> nsteps   =  2500; number of steps
> nstcomm   =  10   ; reset c.o.m. motion
> nstxout  =  2; write coords
> nstvout  =  2; write velocities
> nstlog=  25000; print to logfile
> nstenergy  =  500   ; print energies
> xtc_grps=  OW_HW1_HW2_CO2
> nstxtcout   =  500
> nstlist =  10   ; update pairlist
> ns_type  =  grid ; pairlist method
> coulombtype   =  PME
> rvdw=  1.2  ; cut-off for vdw
> rcoulomb =  1.2  ; cut-off for coulomb
> rlist  =  1.2  ; cut-off for coulomb
> DispCorr  =  EnerPres
> Tcoupl  =  Nose-Hoover
> ref_t =  300
> tc-grps =  System
> tau_t =  0.5
> Pcoupl  =  Parrinello-Rahman
> Pcoupltype   =  semiisotropic; pressure geometry
> tau_p   =  1.0   1.0; p-coupling time
> compressibility =  4.5e-5  4.5e-5   ; compressibility
> ref_p   =  30.5  30.5   ; ref pressure
> gen_vel =  yes  ; generate initial vel
> gen_temp=  200  ; initial temperature
> gen_seed=  372340   ; random seed
> constraint_algorithm = shake
> constraints =  all-bonds
> 
> 
> 
> Thanks a lot
> Sapna
> 
> 
> 
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[gmx-users] Exploding box (in one dimension) Semi-isotropic pressure coupling?

[sapna sarupria]

Hello all,

I have a simulation running for a hydrate (with CO2) and water in contact
with each other. I run the simulation at 280K at which the hydrate melts and
finally the system is just liquid water with CO2 in it. However, as the
simulation proceeds the box begins to expand in the z-direction and
decreases in the x-y direction considerably. Initially the box has
4.8x4.8x9.6 nm^3 dimensions. After the hydrate melts (the volume fluctuates
more) and is fine for another 10 ns but after that the dimensions in the x-y
direction decrease to 2.5 nm and z-dimension increases to 35 nm. At this
point the simulation crashes since my cut-off distance are 1.2 nm.

I am using semi-isotropic pressure coupling but the pressure in the x-y
direction and z-direction are the same (=30.5 bar) and so is the
compressibility (=4.5e-5). I am using Parrinello-Rahman pressure coupling
and Nose-Hoover thermostat. The CO2 and water molecules are rigid and shake
is used to maintain their geometry. The simulation time step is 2 fs. Can
someone tell me why such a thing happens? I have pasted my mdp file for
completeness. I am using Gromacs  4.0.5 and I run the simulations in
parallel using 4 processors. Values related to domain decomposition etc are
unchanged and the default values are used.

Any insights will be helpful. Thanks for the help.

MDP File:
title   =  CO2 hydrate + water  ; a string
cpp =  /lib/cpp ; c-preprocessor
dt  =  0.002; time step
nsteps   =  2500; number of steps
nstcomm   =  10   ; reset c.o.m. motion
nstxout  =  2; write coords
nstvout  =  2; write velocities
nstlog=  25000; print to logfile
nstenergy  =  500   ; print energies
xtc_grps=  OW_HW1_HW2_CO2
nstxtcout   =  500
nstlist =  10   ; update pairlist
ns_type  =  grid ; pairlist method
coulombtype   =  PME
rvdw=  1.2  ; cut-off for vdw
rcoulomb =  1.2  ; cut-off for coulomb
rlist  =  1.2  ; cut-off for coulomb
DispCorr  =  EnerPres
Tcoupl  =  Nose-Hoover
ref_t =  300
tc-grps =  System
tau_t =  0.5
Pcoupl  =  Parrinello-Rahman
Pcoupltype   =  semiisotropic; pressure geometry
tau_p   =  1.0   1.0; p-coupling time
compressibility =  4.5e-5  4.5e-5   ; compressibility
ref_p   =  30.5  30.5   ; ref pressure
gen_vel =  yes  ; generate initial vel
gen_temp=  200  ; initial temperature
gen_seed=  372340   ; random seed
constraint_algorithm = shake
constraints =  all-bonds



Thanks a lot
 Sapna
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Re: [gmx-users] gmx_fatal.c, line: 481

[Sander Pronk]

The reason grompp is failing is because there are some things it warns about 
(that's quite clear from your error message), and by default it will refuse to 
continue unless you explicitly tell it to. 
Without the actual warning there is very little we can do to help you.

Sander



On Mar 30, 2010, at 16:18 , carolsil...@cantv.net wrote:

> Carolina and Javier wrote:
> 
>  
> We have the same error that Nitu sharma and Wara Boon. We have successfully 
> installed the gromacs 4.0.7, on Redhad 4 and 5 but the problem is the same. 
> we review all, every step of the installation, but continued the error.
>  
> This program run on Redhad ?
> 
> Who can help me to solve this problem?
>  
>  
> nitu sharma wrote: 
> (http://www.mail-archive.com/gmx-users@gromacs.org/msg19562.html)
>  
> I have successfully installed the gromacs 4.0.3 it is working but the problem 
> is when I want to run the gromacs demo during processing when I put the 
> command "grompp -v" the output like this:
> 
>  
> There were 2 notes
>  
> There was 1 warning
>  
> ---
> Program grompp, VERSION 4.0.3
> Source code file: gmx_fatal.c, line: 481
>  
> Fatal error:
> Too many warnings (1), grompp terminated.
> If you are sure all warnings are harmless, use the -maxwarn option.
>  
>  
> in these condition, gromacs generate "mdout.mdp" file but no generate
> > "topol.tpr" file.
> > 
> > 
> > when I used this options:grompp -v -maxwarn 1
> > the pre-processing is done and the topol.tpr file is constracted.
> > 
> > Is it possible and correct to use of "-maxwarn 1" for run these
> > tutorial example or not?!?
>  
> wara boon wrote: 
> http://oldwww.gromacs.org/pipermail/gmx-users/2009-June/042751.html
>  
> I pull molecule into membrane by MD simulations but it error about
> Program grompp_mpi, VERSION 4.0.2
> > 
> > Source code file: gmx_fatal.c, line: 481
> > 
> >  
> > 
> > Fatal error:
> > 
> > Too many warnings (1), grompp_mpi terminated.
> > 
> > If you are sure all warnings are harmless, use the -maxwarn option.
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Re: [gmx-users] Using lennard jones and buckingham terms simultaneously

[Matthew Watkins]

Hi Gareth,

Gareth Tribello wrote:

Hello again

Still trying to get this carbonate forcefield to work with gromacs.  I 
now know that the tables and so on are being read in correctly as I can 
get gromacs to reproduce the energies that I get for the various terms 
when I calculate them by hand/with a separate program.  There is stilla 
a problem with the charge groups however.  As when I attempt to split up 
the atoms in the water molecule the simulation fails.  Again checking 
that I am doing this correctly I would replace:


;   at type   res nr  res name  at name   cg nr 
charge mass
1   amber99_61  1   SOL  OW1   0
16.0
2   amber99_60  1   SOL HW21   0.52422   
1.00800
3   amber99_60  1   SOL HW31   0.52422   
1.00800
4   MW  1   SOL MW4   1  
-1.04844   0.0


with

;   at type   res nr  res name  at name   cg nr 
charge mass
1   amber99_61  1   SOL  OW1   0
16.0
2   amber99_60  1   SOL HW22   0.52422   
1.00800
3   amber99_60  1   SOL HW33   0.52422   
1.00800
4   MW  1   SOL MW4   4  
-1.04844   0.0


The problem I get (even if I just run water without any 
carbonate/tabulated potentials) if I do the above is that the settles 
algorithm fails.


extract from *.top file for TIP4P_2005 water, below.  I think you can 
use two charge groups - one with OW and one with HW + MW - both groups 
are then neutral, which might be beneficial.


You then need an index group with a HW and MW group (or whatever you 
call them).  Something like below in you *.mdp.


"
energygrps   = F Ca OW HW_AND_T_MW
energygrp_table  = OW OW F F F Ca Ca OW F OW F HW_AND_T_MW
"

I am not sure that settles likes the split charge group, I'm using lincs 
at the moment.


Cheers,

Matt

"
[moleculetype]
; name nrexcl
water  1

[atoms]
; nr type resnr residu atom cgnr charge
1 OW   1 OW  OW   1 0  15.994
2 HW   1 HW  HW   2 0.55641.008
3 HW   1 HW  HW   2 0.55641.008
4 MW   1 MW  MW   2-1.11280.0

[constraints]
;i j funct doh  dhh
1   2   1   0.09572
1   3   1   0.09572
2   3   1   0.15139

[exclusions]
1   2   3   4
2   1   2   3
3   1   2   4
4   1   2   3

"



I'm obviously missing something fundamental - I'm not even sure that cg 
nr stands for the charge group.  Any help would be greatly appreciated.


Gareth

On Thu, Mar 25, 2010 at 11:07 PM, Mark Abraham > wrote:


On 26/03/2010 7:03 AM, Gareth Tribello wrote:

Hello again

I have tried to do as you suggest and use tables but I have a new
problem.  First let me describe my process and then you can let
me know
if there is anything wrong in the stages:

OK so first you include the following directives into the mdp file:

coulombtype = pme   (or whatever sort of coulomb interaction you
are using)
vdw-type = user

energygrps  = Ca CCA OCA OW HW
energygrp_table   = Ca OCA Ca CCA OCA OCA OCA OW OCA HW

Gromacs is then (at some stage) going to look for a series of
files called

table.xvg  -   which is the default 6-12 Lennard Jones that will
be used
for most of the atoms
table_Ca_OCA.xvg  - which are the Buckingham interactions
between your
various atom types.
table_Ca_CCA.xvg
table_OCA_OCA.xvg
table_OCA_OW.xvg
table_OCA_HW.xvg

These files have the format (and contents) described in section
6.7 of
the manual.  Finally, you define the various energy groups Ca,
OCA and
so on in your index.ndx file.

The problem is that grompp gives me the following error:

"atoms 1 and 2 in charge group 1 of molecule type 'SOL' are in
different
energy groups"

(incidentally these atoms 1 and 2 are OW and HW)

Does this mean that I cannot use different tabulated potentials for
different atoms in a molecules?  By which I mean that I can't use
different tabulated potentials for the OW Ca and HW Ca
interactions for
example?


Charge groups are the fundamental unit GROMACS uses in constructing
a simulation. Energy groups are the next "higher" layer in the data
structures, and these must be sets of whole charge groups. With some
electrostatics models, looping over charge groups whose charge is
preferably an integer is essential for modelling correct behaviour.
GROMACS does a complex sorting of all the interactions between
charge 

[gmx-users] gmx_fatal.c, line: 481

[carolsil...@cantv.net]

Carolina and Javier wrote:   We have the same error that Nitu sharma and Wara Boon. We have successfully installed the gromacs 4.0.7, on Redhad 4 and 5 but the problem is the same. we review all, every step of the installation, but continued the error.     This program run on Redhad ?  Who can help me to solve this problem?        nitu sharma wrote: (http://www.mail-archive.com/gmx-users@gromacs.org/msg19562.html)     I have successfully installed the gromacs 4.0.3 it is working but the problem is when I want to run the gromacs demo during processing when I put the command "grompp -v" the output like this:     There were 2 notes There was 1 warning ---Program grompp, VERSION 4.0.3Source code file: gmx_fatal.c, line: 481 Fatal error:Too many warnings (1), grompp terminated.  If you are sure all warnings are harmless, use the -maxwarn option.    in these condition, gromacs generate "mdout.mdp" file but no generate> "topol.tpr" file.> > > when I used this options:    grompp -v -maxwarn 1> the pre-processing is done and the topol.tpr file is constracted.> > Is it possible and correct to use of "-maxwarn 1" for run these> tutorial example or not?!? wara boon wrote: http://oldwww.gromacs.org/pipermail/gmx-users/2009-June/042751.html I pull molecule into membrane by MD simulations but it error aboutProgram grompp_mpi, VERSION 4.0.2> > Source code file: gmx_fatal.c, line: 481> >  > > Fatal error:> > Too many warnings (1), grompp_mpi terminated.> > If you are sure all warnings are harmless, use the -maxwarn option.
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Re: [gmx-users] mean force.

[Jochen Hub]

lammps lammps wrote:
> Hi everyone,
> I use umbrella sample and g_wham to get potential of mean force.
> However, I also want to compute the mean force. How can I deal with
> this? Can I get it through calculating the average of data in
> pullf.xvg file?

In principle, yes. But note that the position of the particle fluctuates
within the umbrella window during your simulation. A more well-defined
force would be computed by using

pull = constraint

and then by averaging the pullf.xvg output. In theory, you should then
get the same PMF by either integrating the mean force or by using wham
on the umbrella ouput.

Best,

Jochen

> Thanks in advance.
> Wende
> --
> ;spring point is equal to ref_group0+pull_init+time*pull_rate*pull_vec，
> pull = Umbrella ;umbrella,constraint
> pull_geometry = Distance ;distance ,direction,cylinder,position
> pull_dim = Y Y Y
> pull_group0 = DEN1
> pull_group1 = DEN2
> pull_nstxout = 500
> pull_nstfout = 50
> pull_init1 = 5.7
> pull_k1 = 1000
> ---
> # This file was created Thu Feb 4 00:51:24 2010
> # by the following command:
> # mdrun_mpi -rdd 1.4 -s npt.tpr -c npt.gro
> #
> # mdrun_mpi is part of G R O M A C S:
> #
> # Groningen Machine for Chemical Simulation
> #
> @ title "Pull force"
> @ xaxis label "Time (ps)"
> @ yaxis label "Force (kJ/mol/nm)"
> @TYPE xy
> 0. -28.8555
> 1.6000 -19.2897
> 3.2000 -18.59
> 4.8000 -20.7866
> 6.4000 -26.1605
> 8. -42.8572
> 9.6000 -50.7524
> 11.2000 -73.9647
> 12.8000 -74.2521
> 14.4000 -102.284
> 16. -96.5184
>
> -- 
> wende


-- 
---
Dr. Jochen Hub
Molecular Biophysics group
Dept. of Cell & Molecular Biology
Uppsala University. Box 596, 75124 Uppsala, Sweden.
Phone: +46-18-4714451 Fax: +46-18-511755
---

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Re: [gmx-users] water box with prescribed volume and density

[grivet]

Thank you for your quick and detailed answer.

> First, begin by using the right genbox flags :)  The -nmol flag is for 
> insertion 
> of extra molecules (specified in -ci).  This operation is not what you want.  
> If 
> you wish to cap the number of solvent molecules, you want the -maxsol option.
> 
> > By the way, I notice that the number of molecules in topol.top is not
> > updated; is that normal ?
> 
> Given your commands, yes.  You are not passing your topology to genbox using 
> -p. 
>   If you do, it will happily update it for you.
> 
I followed your prescriptions with succes. 

> Also understand that the number of water molecules present in the box is 
> dependent upon other species (i.e., solute).  If you are trying to compare 
> results with some other system (with a different solute), the space available 
> for solvent may be different, and really is an irrelevant consideration. 
> Provided you have a reasonable unit cell that does not violate the minimum 
> image 
> convention, and you use the same run parameters, then the comparison should 
> be 
> legitimate.  If you simply wish to run a new simulation from a previous 
> configuration, there is no need to re-build the system; just start a new 
> simulation with different starting velocities.

No, I simply want to simulate a box of water and compare results with
those obained with GROMOS and spc water.

Having cleared the first hurdle, I ran mdrun for steepest descent (5832
molecules). The program stopped after 2067 steps, with maximum force =
1.58E02 on atom 4870. How important is that warning?

Anyway, I started mdrun again for a dynamics run (0.5 fs step, 25 ps
long, temperature and pressure cooupling with Berendsen thermostats).
How can I judge the quality of results ?

The temperature quickly evolved from 300K to the prescribed 270 K and
then fluctuated by 2-3 K. (One would think that velocities are generated
according to the reference temperature, 270K?)

The pressure fluctuated a lot and is -179 at the end of the run; what is
the significance of this result?

The volume and density evolved rather smoothly to reasonable values. I
have two values for the density; according to the .log file, it is
0.9937E03 and according to g_energy, it is 1.015E03; which should I
believe?

Can I consider my system to be fully equilibrated? Since the run lasted
50 mn on a signle node, I cans easily extend the equilibration. A last
point is not clear; which file should I start from to extend the
computation: .cpt, .trr, or .xtc?

Thank you again for taking pains with an ignorant user
JP Grivet

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Re: [gmx-users] Using lennard jones and buckingham terms simultaneously

[Gareth Tribello]

Hello again

Still trying to get this carbonate forcefield to work with gromacs.  I now
know that the tables and so on are being read in correctly as I can get
gromacs to reproduce the energies that I get for the various terms when I
calculate them by hand/with a separate program.  There is stilla a problem
with the charge groups however.  As when I attempt to split up the atoms in
the water molecule the simulation fails.  Again checking that I am doing
this correctly I would replace:

;   at type   res nr  res name  at name   cg nr charge
mass
1   amber99_61  1   SOL  OW1   0
16.0
2   amber99_60  1   SOL HW21   0.52422
1.00800
3   amber99_60  1   SOL HW31   0.52422
1.00800
4   MW  1   SOL MW4   1  -1.04844
0.0

with

;   at type   res nr  res name  at name   cg nr charge
mass
1   amber99_61  1   SOL  OW1   0
16.0
2   amber99_60  1   SOL HW22   0.52422
1.00800
3   amber99_60  1   SOL HW33   0.52422
1.00800
4   MW  1   SOL MW4   4  -1.04844
0.0

The problem I get (even if I just run water without any carbonate/tabulated
potentials) if I do the above is that the settles algorithm fails.

I'm obviously missing something fundamental - I'm not even sure that cg nr
stands for the charge group.  Any help would be greatly appreciated.

Gareth

On Thu, Mar 25, 2010 at 11:07 PM, Mark Abraham wrote:

> On 26/03/2010 7:03 AM, Gareth Tribello wrote:
>
>> Hello again
>>
>> I have tried to do as you suggest and use tables but I have a new
>> problem.  First let me describe my process and then you can let me know
>> if there is anything wrong in the stages:
>>
>> OK so first you include the following directives into the mdp file:
>>
>> coulombtype = pme   (or whatever sort of coulomb interaction you are
>> using)
>> vdw-type = user
>>
>> energygrps  = Ca CCA OCA OW HW
>> energygrp_table   = Ca OCA Ca CCA OCA OCA OCA OW OCA HW
>>
>> Gromacs is then (at some stage) going to look for a series of files called
>>
>> table.xvg  -   which is the default 6-12 Lennard Jones that will be used
>> for most of the atoms
>> table_Ca_OCA.xvg  - which are the Buckingham interactions between your
>> various atom types.
>> table_Ca_CCA.xvg
>> table_OCA_OCA.xvg
>> table_OCA_OW.xvg
>> table_OCA_HW.xvg
>>
>> These files have the format (and contents) described in section 6.7 of
>> the manual.  Finally, you define the various energy groups Ca, OCA and
>> so on in your index.ndx file.
>>
>> The problem is that grompp gives me the following error:
>>
>> "atoms 1 and 2 in charge group 1 of molecule type 'SOL' are in different
>> energy groups"
>>
>> (incidentally these atoms 1 and 2 are OW and HW)
>>
>> Does this mean that I cannot use different tabulated potentials for
>> different atoms in a molecules?  By which I mean that I can't use
>> different tabulated potentials for the OW Ca and HW Ca interactions for
>> example?
>>
>
> Charge groups are the fundamental unit GROMACS uses in constructing a
> simulation. Energy groups are the next "higher" layer in the data
> structures, and these must be sets of whole charge groups. With some
> electrostatics models, looping over charge groups whose charge is preferably
> an integer is essential for modelling correct behaviour. GROMACS does a
> complex sorting of all the interactions between charge groups into lists
> that allow it to iterate over charge groups and energy groups. A user table
> then gets applied to a whole intra- or inter- energy-group loop. Thus your
> attempt violates this precondition.
>
> However, PME does not require the use of charge groups for accurate
> results, since all inter-atomic electrostatic interactions get treated,
> regardless of distance. So you could decompose your water molecules into two
> charge groups, O and Hs. (Caveat, a near-brokenly bad PME approximation
> might get a little worse with arbitrary charge groups)
>
>
>  Final question, as its not clear to me from the manual, if you use a
>> tabulated potential for Lennard Jones and you use mix type 2 (so are you
>> are providing epsilon and sigma in the input rather than A and B) does
>> gromacs still know that it has to manipulate the input parameters in
>> order to get the coefficients of the (tabulated) g(r) and h(r)
>> dispersion and repulsion functions (I mean the g(r) and h(r) defined in
>> section 6.7 of the manual here)?  At the same time does it also know not
>> to do anything to the parameters you input for the (tabulated)
>> buckingham potentials (as for a buckingham you are providing A and C)?
>>
>
> I expect the point of the tables is that GROMACS just uses them per
> equation 6.23. Thus I'd expect C6 and C12 in that equation to be constructed
> according to whatever combination

RE: [gmx-users] problem with the energy minimization of a system composed of two NA+ ions and explicit water

[Berk Hess]

> Date: Tue, 30 Mar 2010 08:13:11 -0400
> From: jalem...@vt.edu
> To: gmx-users@gromacs.org
> Subject: Re: [gmx-users] problem with the energy minimization of a system 
> composed of two NA+ ions and explicit water
> 
> 
> 
> Ozge Engin wrote:
> > Hi all,
> > 
> > First of all, thank you for your quick reply Justin. Here, I want to 
> > state the problem in a clearer way.
> > 
> > I have been trying to calculate the PMF between two NA+ ions in explicit 
> > water. In order to do that I first pulled one of the NA+ ions 
> > continuously with respect to the other until the farthest point on the 
> > PMF curve was reached. After that I split the continuous pulling 
> > trajectory from the points that are in correspondence with the 
> > constraint points of the PMF curve. These were done via *genera_start_4* 
> > script.
> > 
> 
> You don't have a PMF curve.  I expect you're referring either to the 
> pullf.xvg 
> or pullx.xvg files generated from the COM pulling output.  PMF is calculated 
> later, through umbrella sampling.
> 
> > I took each starting conformation, that was obtained from continuous 
> > pulling, solvated with water, and then energy minimized. Then, I 
> > prepared the systems for constraint pulling MD production runs. These 
> 
> Weren't these systems already solvated in the above pulling?  If you add 
> water 
> differently to each system, you may get unreliable results.  Use 
> water-containing configurations from the original SMD trajectory (above) as 
> your 
> input configurations.
> 
> > were done via *input* script. Interestingly, systems (ion+water) at some 
> > of the constraint points could not been energy minimized, it reached to 
> > the machine epsilon, but not to the desired criteria. The force per atom 
> > was too high, around the order of ^4. Moreover, this issue was not 
> > distance-dependent, which means that the energy minimization worked for 
> > smaller constraint points, but not for some of the larger constraint 
> > points. When I looked at the problematic trajectories, I saw that bonds 
> > of a water molecule near the box boundary was longer. I thought that 
> > this may be due to genbox command. Because of the small radius of NA+ 
> 
> Perhaps.  See the above comment.  It's better to not re-solvate after the 
> fact. 
>   Was the initial pull actually conducted in vacuo?
> 
> > ion it may not check the overlaps among the atoms. In order to test 
> > whether it is the case I increased the LJ parameters of the ion. This 
> > worked for some of the points, but not for others. (Note that the 
> > diameter is still smaller than the constraint distance between the two 
> > ions.) 
> > 
> > I use ffG45a3 force field, and the scripts given above. I tried this 
> > with different versions of Gromacs: 4.0.7, 4.0.5, and faced with similar 
> > problems.
> > 
> 
> Is the total pull distance less than half the box vector along which you are 
> pulling?  If not, you will be getting bizarre behavior from the pull code 
> related to PBC.
> 
> Also realize that when you say you are doing constraint pulling, it will 
> require 
> some trickery to calculate the PMF after your simulations are done.  What you 
> want is umbrella sampling.  You can get the PMF from constraint forces, but 
> there is no automated tool to do this in Gromacs (see the list archive for a 
> few 
> posts on how you could approach that).  I'd say make your life easy and use 
> umbrella sampling for the actual data collection :)

I don't agree with that.
Constraining is simpler, since you can simply integrate the mean force
(you have to take care with the entropy effect, but that old holds for
umbrella sampling).
Anyhow, I assume Ozge is using a script I provided her.
I can clean that up and post it if it is of general use.

Berk

> 
> -Justin
> 
> > Kind Regards
> > 
> > -- 
> > Ozge Engin
> > ★☆
> > 
> 
> -- 
> 
> 
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
> 
> -- 
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Re: [gmx-users] Signal 11 crash

[Justin A. Lemkul]

程迪 wrote:

Hi, Sander Pronk

I checked the md.log file. nothing is logged when the program crash.

I just used the single precision version of Gromacs. It output some atom 
cannot be settled when crash happend.





Then you can't claim that "nothing is logged" - this is the kind of error that 
Gromacs will report.  Your system is unstable, probably due to insufficient 
energy minimization or equilibration.  See here:


http://www.gromacs.org/Documentation/Errors#LINCS.2fSETTLE.2fSHAKE_warnings
http://www.gromacs.org/Documentation/Terminology/Blowing_Up

-Justin



--

Message: 3
Date: Tue, 30 Mar 2010 12:43:50 +0200
From: Sander Pronk mailto:pr...@cbr.su.se>>
Subject: Re: [gmx-users] Signal 11 crash
To: Discussion list for GROMACS users >
Message-ID: <23481805-5219-49d9-a697-75775b803...@cbr.su.se 
>

Content-Type: text/plain; charset="utf-8"

Signal 11 on Linux is a segmentation fault: either you've hit a bug in 
mdrun, or there was some faulty input causing it to crash.

You'll need to look at your md.log to see what happened.

Sander

On Mar 30, 2010, at 12:11 , 程迪 wrote:

 > Hi, gmx-users
 >
 > I just encountered a singal 11 problem. I ran gromacs 4.0.7 on 64bit 
ubuntu. 4 core Xeon

 >
 > imb F  2% step 22400, will finish Wed Mar 31 00:41:41 2010
 > imb F  3% step 22500, will finish Wed Mar 31 00:41:49 2010
 > imb F  2% step 22600, will finish Wed Mar 31 00:41:57 2010
 > imb F  3% step 22700, will finish Wed Mar 31 00:41:42 2010
 > imb F  2% step 22800, will finish Wed Mar 31 00:41:50 2010
 > imb F  2% step 22900, will finish Wed Mar 31 00:41:58 2010
 > imb F  3% step 23000, will finish Wed Mar 31 00:41:43 2010
 > imb F  3% step 23100, will finish Wed Mar 31 00:41:51 2010
 > imb F  3% step 23200, will finish Wed Mar 31 00:41:59 2010
 > rank 3 in job 1  chengdi-desktop_38817   caused collective abort of 
all ranks

 >   exit status of rank 3: killed by signal 11
 > rank 2 in job 1  chengdi-desktop_38817   caused collective abort of 
all ranks

 >   exit status of rank 2: killed by signal 11
 > rank 1 in job 1  chengdi-desktop_38817   caused collective abort of 
all ranks

 >   exit status of rank 1: killed by signal 11
 >
 > What's wrong?
 >
 > My .mdp file is as follows:
 > title   =  fws
 > cpp =  /usr/bin/cpp
 > ;constraints =  all-bonds
 > constraint_algorithm=  LINCS
 > integrator  =  md
 > dt  =  0.001; ps !
 > nsteps  =  50; total 500 ps.
 > nstcomm =  1
 > nstxout =  500
 > nstvout =  0
 > nstfout =  0
 > nstlist =  10
 > ns_type =  grid
 > rlist   =  1.0
 > coulombtype=  PME
 > rcoulomb=  1.0
 > vdwtype =  cut-off
 > rvdw=  1.4
 > fourierspacing=  0.12
 > fourier_nx=  0
 > fourier_ny=  0
 > fourier_nz=  0
 > pme_order=  6
 > ewald_rtol=  1e-5
 > optimize_fft=  yes
 > ; Berendsen temperature coupling is on in three groups
 > Tcoupl  =  berendsen
 > tc_grps= System
 > tau_t   =  0.1
 > ref_t   =  300
 > ; Pressure coupling is on
 > Pcoupl  =  parrinello-rahman
 > pcoupltype  =  isotropic
 > tau_p   =  1.0
 > compressibility =  4.5e-5
 > ref_p   =  1.0
 > ; Generate velocites is on at 300 K.
 > gen_vel =  yes
 > gen_temp=  300.0
 > gen_seed=  173529
 > ; pbc
 > pbc= xyz
 > ;pull code
 > pull = constraint
 > pull_geometry = direction
 > pull_dim= N N Y
 > pull_start= yes
 > pull_nstxout= 500
 > pull_nstfout= 100
 > pull_ngroups = 1
 > pull_group0= DPPC
 > pull_group1= MOL
 > pull_vec1= 0.0 0.0 -1.0
 > pull_rate1= 0.01
 >
 > Any comments is appreciable.
 >
 > Di Cheng
 >
 > University of Science and Technology of China
 > Hefei, Anhui Province 230026
 > P. R. China
 > E-mail: chen...@mail.ustc.edu.cn 
 > Tel.: +86-15321055911
 >
 > --



--


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


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Re: [gmx-users] Parallel pulling with Gromacs 4.0.7: COMM mode problem

[Aykut Erbas]

Hi

Actually you might be right about the domain decomposition


G3 pull.pdo output file on single machine

focus on the 2nd and 3rd columns which are x and y positions of the 
surface: almost *unchanged* as expected for COMM_grps=surface option

*
2.003.1495211.5768115.770928
7.1495211.8748201.676811
2.2011723.1495211.5768125.761463
7.1495411.8807461.676812
2.4003913.1495201.5768135.771702
7.1495601.8676921.676813
2.6015623.1495191.5768135.797871
7.1495791.8796501.676813
2.8007813.1495181.5768125.794115
7.1495981.8877281.676812
20001.003.1495171.5768135.778761
7.1496171.8708231.676813
20001.2011723.1495181.5768155.783334
7.1496381.8492831.676815
20001.4003913.1495171.5768155.780031
7.1496581.8771581.676815

.
.
3.4023443.1497991.5769112.249830
9.1497391.6045631.676911
3.6015623.1497971.5769112.209385
9.1497571.6223801.676911
3.8007813.1497921.5769112.215503
9.1497731.6532461.676911
4.003.1497911.5769122.221903
9.1497911.6597811.676912




G4 pull.xvg output (in parellel), 2nd and 3rd columns which are x and y 
positions of the surface: *changing*, contradiction to COMM_grps=surface 
option


*
0.4000 3.1498  2.997  -0.391131  -0.331925
0.8000 3.14903 2.99499 -0.391976   -0.346309
1.2000 3.14753 2.99846 -0.372158   -0.407621
1.6000 3.14635 3.00695 -0.337084   -0.422437
2. 3.14465 3.00585 -0.306999   -0.474991
2.4000 3.14365 3.00408 -0.30164-0.48047
2.8000 3.14338 3.00447 -0.285076   -0.483861
3.2000 3.14361 3.00119 -0.226717   -0.460955

..
2838.   3.20024 0.6623251.7185  0.986139
2838.4000   3.19435 0.6619131.74023 1.0404
2838.8000   3.18835 0.6661711.8073  1.02766
2839.2000   3.18264 0.6582611.81687 0.999429
2839.6000   3.17766 0.6684391.82782 1.05693


here is the log file for G4 (pulling) run in parallel


Initializing Domain Decomposition on 32 nodes
Dynamic load balancing: auto
Will sort the charge groups at every domain (re)decomposition
Initial maximum inter charge-group distances:
   two-body bonded interactions: 0.507 nm, LJ-14, atoms 5186 5197
 multi-body bonded interactions: 0.507 nm, Proper Dih., atoms 5186 5197
Minimum cell size due to bonded interactions: 0.557 nm
Maximum distance for 5 constraints, at 120 deg. angles, all-trans: 0.200 nm
Estimated maximum distance required for P-LINCS: 0.200 nm
Guess for relative PME load: 0.20
Will use 24 particle-particle and 8 PME only nodes
This is a guess, check the performance at the end of the log file
Using 8 separate PME nodes
Scaling the initial minimum size with 1/0.8 (option -dds) = 1.25
Optimizing the DD grid for 24 cells with a minimum initial size of 0.697 nm
The maximum allowed number of cells is: X 9 Y 4 Z 9
Domain decomposition grid 4 x 2 x 3, separate PME nodes 8

comm-mode angular will give incorrect results when the comm group 
partially crosses a periodic boundary

Interleaving PP and PME nodes
This is a particle-particle only node

Domain decomposition nodeid 0, coordinates 0 0 0

Table routines are used for coulomb: TRUE
Table routines are used for vdw: FALSE
Will do PME sum in reciprocal space.

  --- Thank You ---  
Using a Gaussian width (1/beta) of 0.25613 nm for Ewald
Cut-off's:   NS: 0.8   Coulomb: 0.8   LJ: 0.8
System total charge: -0.000
Generated table with 3600 data points for Ewald.
Tabscale = 2000 points/nm
Generated table with 3600 data points for LJ6.
Tabscale = 2000 points/nm
Generated table with 3600 data points for LJ12.
Tabscale = 2000 points/nm
Generated table with 3600 data points for 1-4 COUL.
Tabscale = 2000 points/nm
Generated table with 3600 data points for 1-4 LJ6.
Tabscale = 2000 points/nm
Generated table with 3600 data points for 1-4 LJ12.
Tabscale = 2000 points/nm

Enabling SPC water optimization for 3021 molecules.

Configuring nonbonded kernels...


Removing pbc first time

Will apply umbrella COM pulling in geometry 'position'
between a reference group and 1 group
Pull group 0:  5181 atoms, mass 56947.551
Pull group 1:13 atoms, mass   116.120

Initializing Parallel LINear Constraint Solver



Linking all bonded interactions to atoms
There are 85833 inter charge-group exclusions,
will use an extra communication step for exclusion forces for PME

The initial number of communication pu

Re: Re: [gmx-users] Signal 11 crash

[程迪]

Hi, Sander Pronk

I checked the md.log file. nothing is logged when the program crash.

I just used the single precision version of Gromacs. It output some atom
cannot be settled when crash happend.



--

Message: 3
Date: Tue, 30 Mar 2010 12:43:50 +0200
From: Sander Pronk 
Subject: Re: [gmx-users] Signal 11 crash
To: Discussion list for GROMACS users 
Message-ID: <23481805-5219-49d9-a697-75775b803...@cbr.su.se>
Content-Type: text/plain; charset="utf-8"

Signal 11 on Linux is a segmentation fault: either you've hit a bug in
mdrun, or there was some faulty input causing it to crash.
You'll need to look at your md.log to see what happened.

Sander

On Mar 30, 2010, at 12:11 , 程迪 wrote:

> Hi, gmx-users
>
> I just encountered a singal 11 problem. I ran gromacs 4.0.7 on 64bit
ubuntu. 4 core Xeon
>
> imb F  2% step 22400, will finish Wed Mar 31 00:41:41 2010
> imb F  3% step 22500, will finish Wed Mar 31 00:41:49 2010
> imb F  2% step 22600, will finish Wed Mar 31 00:41:57 2010
> imb F  3% step 22700, will finish Wed Mar 31 00:41:42 2010
> imb F  2% step 22800, will finish Wed Mar 31 00:41:50 2010
> imb F  2% step 22900, will finish Wed Mar 31 00:41:58 2010
> imb F  3% step 23000, will finish Wed Mar 31 00:41:43 2010
> imb F  3% step 23100, will finish Wed Mar 31 00:41:51 2010
> imb F  3% step 23200, will finish Wed Mar 31 00:41:59 2010
> rank 3 in job 1  chengdi-desktop_38817   caused collective abort of all
ranks
>   exit status of rank 3: killed by signal 11
> rank 2 in job 1  chengdi-desktop_38817   caused collective abort of all
ranks
>   exit status of rank 2: killed by signal 11
> rank 1 in job 1  chengdi-desktop_38817   caused collective abort of all
ranks
>   exit status of rank 1: killed by signal 11
>
> What's wrong?
>
> My .mdp file is as follows:
> title   =  fws
> cpp =  /usr/bin/cpp
> ;constraints =  all-bonds
> constraint_algorithm=  LINCS
> integrator  =  md
> dt  =  0.001; ps !
> nsteps  =  50; total 500 ps.
> nstcomm =  1
> nstxout =  500
> nstvout =  0
> nstfout =  0
> nstlist =  10
> ns_type =  grid
> rlist   =  1.0
> coulombtype=  PME
> rcoulomb=  1.0
> vdwtype =  cut-off
> rvdw=  1.4
> fourierspacing=  0.12
> fourier_nx=  0
> fourier_ny=  0
> fourier_nz=  0
> pme_order=  6
> ewald_rtol=  1e-5
> optimize_fft=  yes
> ; Berendsen temperature coupling is on in three groups
> Tcoupl  =  berendsen
> tc_grps= System
> tau_t   =  0.1
> ref_t   =  300
> ; Pressure coupling is on
> Pcoupl  =  parrinello-rahman
> pcoupltype  =  isotropic
> tau_p   =  1.0
> compressibility =  4.5e-5
> ref_p   =  1.0
> ; Generate velocites is on at 300 K.
> gen_vel =  yes
> gen_temp=  300.0
> gen_seed=  173529
> ; pbc
> pbc= xyz
> ;pull code
> pull = constraint
> pull_geometry = direction
> pull_dim= N N Y
> pull_start= yes
> pull_nstxout= 500
> pull_nstfout= 100
> pull_ngroups = 1
> pull_group0= DPPC
> pull_group1= MOL
> pull_vec1= 0.0 0.0 -1.0
> pull_rate1= 0.01
>
> Any comments is appreciable.
>
> Di Cheng
>
> University of Science and Technology of China
> Hefei, Anhui Province 230026
> P. R. China
> E-mail: chen...@mail.ustc.edu.cn
> Tel.: +86-15321055911
>
> --
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[gmx-users] Parallel pulling with Gromacs 4.0.7: COMM mode problem

[chris . neale]

If you pull in G3 with AFM option, with your reference groups is the  
surface, in the output pull.pdo file what you will get is  solute  
(pulled group) coordinates /wrt the surface...


Yes. Can we see the data that you get as output in each case and tell  
us what the major difference is?


the coordinates of your reference groups as a function of time does  
not change, right...


Not normally true. A pulling force will be applied to your surface in  
addition to your solute. The only thing that might keep it static is:



Note that I have angular COMM mode for such simulation.
comm_mode= angular
nstcomm  = 1
comm_grps= DIAM


But who knows how and if this works in gromacs 4 with domain  
decomposition. Please try gromacs 4 in serial and see if you get the  
same unexpected results.


that the output coordinates for my pulled groups should be /wrt the  
surface (DIAM) However, the situation is completely, how can I say,  
smtg else...


Can you show some data for this?


however, it treats like iit_grps is 0 0 0 all the time but it is not


Can you show some data for this?


In the log file, I can see that COMM grp is the surface and the pulling
is /wrt the surface again but the output gives smtg as COMM grp is  
the whole box


Can you show some data for this?

Also, please use entire words. smtg and /wrt, while quicker to type,  
are actually harder and more annoying to read.



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Re: [gmx-users] Parallel pulling with Gromacs 4.0.7: COMM mode problem

[Aykut Erbas]

Hi Chris

Thanks for your replay

I will go through step by step

chris.ne...@utoronto.ca wrote:
Correction: what you are actually doing is pulling your solute to the 
(X,Y) center of mass of your surface + (2.0 * 0.001/ps) nm in X + the 
initial center of mass distance in X and Y.



That is actually what I expected but it does smtg else


-- original message --

Dear Aykut,

Please give a more complete description of 1) the .mdp options and
expected behaviour that you get with gmx 3.3.3 on a single core and 2)
the .mdp options and difference that you get with gmx 4.0.7 in parallel.



If you pull in G3 with AFM option, with your reference groups is the 
surface, in the output pull.pdo file what you will get is  solute 
(pulled group) coordinates /wrt the surface...
the coordinates of your reference groups as a function of time does not 
change, right...

Note that I have angular COMM mode for such simulation.


G3 pull.ppa I used

runtype = afm
Skip steps  = 100
ngroups = 1
group1  = AA1
reference_group = DIAM
pulldim = Y Y N
afm_k1  = 15.0
afm_rate1   = 0.0001
afm_dir1= 1.0 0.0 0.0
afm_init1   = 2.0 0.1 1.1


G4 mdp file, which is unsuccessful to reproduce above simulations under G3

comm_mode= angular
nstcomm  = 1
comm_grps= DIAM
;PULLING
pull = umbrella
pull_start   = yes
pull_geometry= position
pull_dim = Y Y N
pull_nstxout = 200
pull_nstfout = 200
pull_ngroups = 1
pull_group0  = DIAM
pull_group1  = AA1
pull_vec1= 1.0 0.0 0.0
pull_init1   = 2.0 0.1 1.0
pull_rate1   = 0.0001
pull_k1  = 15


For example, the following text is difficult to understand and doesn't
match with the .mdp options that you provide below: "the surface moves
in the opposite direction of motion and you have the pulling
coordinates in absolute coord"


That means that if you set
init_groups0=surface
COMM_grps=surface
COMM_mode=surface

that the output coordinates for my pulled groups should be /wrt the 
surface (DIAM)

However, the situation is completely, how can I say, smtg else...

1) the surface is moving although it should not (in principle, above G4 
mdp file eliminates any DIAM motion)

2) output pulled groups coordinates are /wrt  absolute coordinates.
3) the init_grps, which is the surface, moves in the opposite direction 
of the pulling to conserve momentum of the whole system. This cannot be 
because my COMM group is the surface, not the entire system


as you said

init_grps + (2.0 * 0.001/ps) + the initial center of mass distance in X 
and Y



however, it treats like iit_grps is 0 0 0 all the time
but it is not


In the log file, I can see that COMM grp is the surface and the pulling 
is /wrt the surface again

but the output gives smtg as COMM grp is the whole box

That said, I'll take a guess that your problem is related to your X*Y
only (no Z) pull group:

pull_dim = Y Y N

That you seem to think will include some Z component:

pull_init1   = 2.0 0.0 1.0

But what you are actually doing is pulling your solute to the (X,Y)
center of mass of your surface + (2.0 * 0.001/ps) nm in X.

Which seems strange given that you are using semi-isotropic pressure
coupling ... a method intended to treat the Z dimension in a special
way, and not the X dimension.



There is no problem about the system parameters I have bunch of 
simulations running well under G3
the pressure is anisotropic since compressibility of the surface is 
different than the water.

Finally, you could easily test for yourself what happens when you run
gmx 4.0.7 in serial so that you could compare to gmx 3.3.3 in serial
and thus simplify the issue here.

G3 pulling code unfortunately is not so efficient (especially in the 
cluster I use: hostfile problems),

actually this why I switched to G4


Chris.



Thanks again
I hope I've described the problem
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[gmx-users] Parallel pulling with Gromacs 4.0.7: COMM mode problem

[chris . neale]

Correction: what you are actually doing is pulling your solute to the  
(X,Y) center of mass of your surface + (2.0 * 0.001/ps) nm in X + the  
initial center of mass distance in X and Y.


-- original message --

Dear Aykut,

Please give a more complete description of 1) the .mdp options and
expected behaviour that you get with gmx 3.3.3 on a single core and 2)
the .mdp options and difference that you get with gmx 4.0.7 in parallel.

For example, the following text is difficult to understand and doesn't
match with the .mdp options that you provide below: "the surface moves
in the opposite direction of motion and you have the pulling
coordinates in absolute coord"

That said, I'll take a guess that your problem is related to your X*Y
only (no Z) pull group:

pull_dim = Y Y N

That you seem to think will include some Z component:

pull_init1   = 2.0 0.0 1.0

But what you are actually doing is pulling your solute to the (X,Y)
center of mass of your surface + (2.0 * 0.001/ps) nm in X.

Which seems strange given that you are using semi-isotropic pressure
coupling ... a method intended to treat the Z dimension in a special
way, and not the X dimension.

Finally, you could easily test for yourself what happens when you run
gmx 4.0.7 in serial so that you could compare to gmx 3.3.3 in serial
and thus simplify the issue here.

Chris.


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Re: [gmx-users] problem with the energy minimization of a system composed of two NA+ ions and explicit water

[Justin A. Lemkul]

Ozge Engin wrote:

Hi all,

First of all, thank you for your quick reply Justin. Here, I want to 
state the problem in a clearer way.


I have been trying to calculate the PMF between two NA+ ions in explicit 
water. In order to do that I first pulled one of the NA+ ions 
continuously with respect to the other until the farthest point on the 
PMF curve was reached. After that I split the continuous pulling 
trajectory from the points that are in correspondence with the 
constraint points of the PMF curve. These were done via *genera_start_4* 
script.




You don't have a PMF curve.  I expect you're referring either to the pullf.xvg 
or pullx.xvg files generated from the COM pulling output.  PMF is calculated 
later, through umbrella sampling.


I took each starting conformation, that was obtained from continuous 
pulling, solvated with water, and then energy minimized. Then, I 
prepared the systems for constraint pulling MD production runs. These 


Weren't these systems already solvated in the above pulling?  If you add water 
differently to each system, you may get unreliable results.  Use 
water-containing configurations from the original SMD trajectory (above) as your 
input configurations.


were done via *input* script. Interestingly, systems (ion+water) at some 
of the constraint points could not been energy minimized, it reached to 
the machine epsilon, but not to the desired criteria. The force per atom 
was too high, around the order of ^4. Moreover, this issue was not 
distance-dependent, which means that the energy minimization worked for 
smaller constraint points, but not for some of the larger constraint 
points. When I looked at the problematic trajectories, I saw that bonds 
of a water molecule near the box boundary was longer. I thought that 
this may be due to genbox command. Because of the small radius of NA+ 


Perhaps.  See the above comment.  It's better to not re-solvate after the fact. 
 Was the initial pull actually conducted in vacuo?


ion it may not check the overlaps among the atoms. In order to test 
whether it is the case I increased the LJ parameters of the ion. This 
worked for some of the points, but not for others. (Note that the 
diameter is still smaller than the constraint distance between the two 
ions.) 

I use ffG45a3 force field, and the scripts given above. I tried this 
with different versions of Gromacs: 4.0.7, 4.0.5, and faced with similar 
problems.




Is the total pull distance less than half the box vector along which you are 
pulling?  If not, you will be getting bizarre behavior from the pull code 
related to PBC.


Also realize that when you say you are doing constraint pulling, it will require 
some trickery to calculate the PMF after your simulations are done.  What you 
want is umbrella sampling.  You can get the PMF from constraint forces, but 
there is no automated tool to do this in Gromacs (see the list archive for a few 
posts on how you could approach that).  I'd say make your life easy and use 
umbrella sampling for the actual data collection :)


-Justin


Kind Regards

--
Ozge Engin
★☆



--


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


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[gmx-users] Parallel pulling with Gromacs 4.0.7: COMM mode problem

[chris . neale]

Dear Aykut,

Please give a more complete description of 1) the .mdp options and  
expected behaviour that you get with gmx 3.3.3 on a single core and 2)  
the .mdp options and difference that you get with gmx 4.0.7 in parallel.


For example, the following text is difficult to understand and doesn't  
match with the .mdp options that you provide below: "the surface moves  
in the opposite direction of motion and you have the pulling  
coordinates in absolute coord"


That said, I'll take a guess that your problem is related to your X*Y  
only (no Z) pull group:


pull_dim = Y Y N

That you seem to think will include some Z component:

pull_init1   = 2.0 0.0 1.0

But what you are actually doing is pulling your solute to the (X,Y)  
center of mass of your surface + (2.0 * 0.001/ps) nm in X.


Which seems strange given that you are using semi-isotropic pressure  
coupling ... a method intended to treat the Z dimension in a special  
way, and not the X dimension.


Finally, you could easily test for yourself what happens when you run  
gmx 4.0.7 in serial so that you could compare to gmx 3.3.3 in serial  
and thus simplify the issue here.


Chris.

-- original message --

Hi everyone

I have a pulling code running in parallel (32 processors) with Gromacs 4.0.7
The systems composes of a surface and a protein

with Gromacs 3.3.3 (on single processors ) when I set the COMM mode for
the surface, the surface stands still,
and of course for the pulling code (reference groups is also surface) ,
the position of the protein is given /wrt the surface.
However for G4, no matter which group you set for COMM mode, the surface
moves in the opposite direction of motion and you have the pulling
coordinates in absolute coord. which is not what I want.

I want a pilling output /wrt the surface as in G3

Has anyone experienced smtg like this?
suggestions will be appreciated

Thanks
Aykut


*.mdp file
DIAM=surface
//

integrator   = md
nsteps= 3000
dt   = 0.002
nstlist = 50
nstxout  = 2
nstvout  = 2
nstfout   = 2
nstxtcout   = 4000
nstlog= 2
nstenergy  = 2
constraints = hbonds
ns_type = grid
coulombtype = pme
pme_order = 4
fourierspacing   = 0.12
rlist= 0.8
rvdw = 0.8
rcoulomb   = 0.8
energygrps= DIAM Protein SOL
tcoupl   = berendsen
tc_grps  = DIAM Protein SOL
tau_t= 0.1 0.1 0.1
ref_t= 300 300 300
gen_vel  = yes
Pcoupl   = berendsen
Pcoupltype   = semiisotropic
compressibility  = 2.5E-8 4.5E-5
tau_p= 1.0 1.0
ref_p= 1.0 1.0
comm_mode= angular
nstcomm  = 1
comm_grps= DIAM

;PULLING
pull = umbrella
pull_start   = yes
pull_geometry= position
pull_dim = Y Y N
pull_nstxout = 200
pull_nstfout = 200
pull_ngroups = 1
pull_group0  = DIAM
pull_group1  = AA1
pull_vec1= 1.0 0.0 0.0
pull_init1   = 2.0 0.0 1.0
pull_rate1   = 0.001
pull_k1  = 50
///

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[gmx-users] problem with the energy minimization of a system composed of two NA+ ions and explicit water

[Ozge Engin]

Hi all,

First of all, thank you for your quick reply Justin. Here, I want to state
the problem in a clearer way.

I have been trying to calculate the PMF between two NA+ ions in explicit
water. In order to do that I first pulled one of the NA+ ions continuously
with respect to the other until the farthest point on the PMF curve was
reached. After that I split the continuous pulling trajectory from the
points that are in correspondence with the constraint points of the PMF
curve. These were done via *genera_start_4* script.

I took each starting conformation, that was obtained from continuous
pulling, solvated with water, and then energy minimized. Then, I prepared
the systems for constraint pulling MD production runs. These were done via *
input* script. Interestingly, systems (ion+water) at some of the constraint
points could not been energy minimized, it reached to the machine epsilon,
but not to the desired criteria. The force per atom was too high, around the
order of ^4. Moreover, this issue was not distance-dependent, which means
that the energy minimization worked for smaller constraint points, but not
for some of the larger constraint points. When I looked at the problematic
trajectories, I saw that bonds of a water molecule near the box boundary was
longer. I thought that this may be due to genbox command. Because of the
small radius of NA+ ion it may not check the overlaps among the atoms. In
order to test whether it is the case I increased the LJ parameters of the
ion. This worked for some of the points, but not for others. (Note that the
diameter is still smaller than the constraint distance between the two
ions.)

I use ffG45a3 force field, and the scripts given above. I tried this with
different versions of Gromacs: 4.0.7, 4.0.5, and faced with similar
problems.

Kind Regards
-- 
Ozge Engin
★☆


genera_start_4
Description: Binary data


input
Description: Binary data
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Re: [gmx-users] git installation error

[Sander Pronk]

It looks like you're you're using gcc; is that right? If so, you're probably 
using an old (pre-2005) version. Try a newer one: it's free!

Sander


On Mar 30, 2010, at 13:00 , babu gokul wrote:

>  I tried to install git version of Gromacs but when i make the file its shows 
> the following error
>  
> "cc -DHAVE_CONFIG_H -I. -I../../../../src -I/usr/include/libxml2 
> -I../../../../include -DGMXLIBDIR=\"/usr/local/gromacs/share/top\" -O3 
> -fomit-frame-pointer -finline-functions -Wall -Wno-unused -msse2 
> -funroll-all-loops -std=gnu99 -I./include -MT nb_kernel400_ia32_sse.lo -MD 
> -MP -MF .deps/nb_kernel400_ia32_sse.Tpo -c nb_kernel400_ia32_sse.c -o 
> nb_kernel400_ia32_sse.o
> nb_kernel400_ia32_sse.c: In function `nb_kernel400_ia32_sse':
> nb_kernel400_ia32_sse.c:93: warning: implicit declaration of function 
> `_mm_castsi128_ps'
> nb_kernel400_ia32_sse.c:93: error: invalid initializer
> nb_kernel400_ia32_sse.c:94: error: invalid initializer
> nb_kernel400_ia32_sse.c:95: error: invalid initializer
> make[5]: *** [nb_kernel400_ia32_sse.lo] Error 1
> make[5]: Leaving directory 
> `/git_gromacs/gromacs/src/gmxlib/nonbonded/nb_kernel_ia32_sse'
> make[4]: *** [all-recursive] Error 1
> make[4]: Leaving directory `/git_gromacs/gromacs/src/gmxlib/nonbonded'
> make[3]: *** [all-recursive] Error 1
> make[3]: Leaving directory `/git_gromacs/gromacs/src/gmxlib'
> make[2]: *** [all-recursive] Error 1
> make[2]: Leaving directory `/git_gromacs/gromacs/src'
> make[1]: *** [all] Error 2
> make[1]: Leaving directory `/git_gromacs/gromacs/src'
> make: *** [all-recursive] Error 1"
>  
> could anyone help me in this regard
>  
> E R Azhaigya singam
> 
> The INTERNET now has a personality. YOURS! See your Yahoo! Homepage.-- 
> gmx-users mailing listgmx-users@gromacs.org
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[gmx-users] git installation error

[babu gokul]

 I tried to install git version of Gromacs but when i make the file its shows 
the following error 

"cc -DHAVE_CONFIG_H -I. -I../../../../src -I/usr/include/libxml2 
-I../../../../include -DGMXLIBDIR=\"/usr/local/gromacs/share/top\" -O3 
-fomit-frame-pointer -finline-functions -Wall -Wno-unused -msse2 
-funroll-all-loops -std=gnu99 -I./include -MT nb_kernel400_ia32_sse.lo -MD -MP 
-MF .deps/nb_kernel400_ia32_sse.Tpo -c nb_kernel400_ia32_sse.c -o 
nb_kernel400_ia32_sse.o
nb_kernel400_ia32_sse.c: In function `nb_kernel400_ia32_sse':
nb_kernel400_ia32_sse.c:93: warning: implicit declaration of function 
`_mm_castsi128_ps'
nb_kernel400_ia32_sse.c:93: error: invalid initializer
nb_kernel400_ia32_sse.c:94: error: invalid initializer
nb_kernel400_ia32_sse.c:95: error: invalid initializer
make[5]: *** [nb_kernel400_ia32_sse.lo] Error 1
make[5]: Leaving directory 
`/git_gromacs/gromacs/src/gmxlib/nonbonded/nb_kernel_ia32_sse'
make[4]: *** [all-recursive] Error 1
make[4]: Leaving directory `/git_gromacs/gromacs/src/gmxlib/nonbonded'
make[3]: *** [all-recursive] Error 1
make[3]: Leaving directory `/git_gromacs/gromacs/src/gmxlib'
make[2]: *** [all-recursive] Error 1
make[2]: Leaving directory `/git_gromacs/gromacs/src'
make[1]: *** [all] Error 2
make[1]: Leaving directory `/git_gromacs/gromacs/src'
make: *** [all-recursive] Error 1"
 
could anyone help me in this regard
 
E R Azhaigya singam


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Re: [gmx-users] Signal 11 crash

[Sander Pronk]

Signal 11 on Linux is a segmentation fault: either you've hit a bug in mdrun, 
or there was some faulty input causing it to crash. 
You'll need to look at your md.log to see what happened.

Sander

On Mar 30, 2010, at 12:11 , 程迪 wrote:

> Hi, gmx-users
> 
> I just encountered a singal 11 problem. I ran gromacs 4.0.7 on 64bit ubuntu. 
> 4 core Xeon
> 
> imb F  2% step 22400, will finish Wed Mar 31 00:41:41 2010
> imb F  3% step 22500, will finish Wed Mar 31 00:41:49 2010
> imb F  2% step 22600, will finish Wed Mar 31 00:41:57 2010
> imb F  3% step 22700, will finish Wed Mar 31 00:41:42 2010
> imb F  2% step 22800, will finish Wed Mar 31 00:41:50 2010
> imb F  2% step 22900, will finish Wed Mar 31 00:41:58 2010
> imb F  3% step 23000, will finish Wed Mar 31 00:41:43 2010
> imb F  3% step 23100, will finish Wed Mar 31 00:41:51 2010
> imb F  3% step 23200, will finish Wed Mar 31 00:41:59 2010
> rank 3 in job 1  chengdi-desktop_38817   caused collective abort of all ranks
>   exit status of rank 3: killed by signal 11 
> rank 2 in job 1  chengdi-desktop_38817   caused collective abort of all ranks
>   exit status of rank 2: killed by signal 11 
> rank 1 in job 1  chengdi-desktop_38817   caused collective abort of all ranks
>   exit status of rank 1: killed by signal 11 
> 
> What's wrong? 
> 
> My .mdp file is as follows:
> title   =  fws 
> cpp =  /usr/bin/cpp 
> ;constraints =  all-bonds
> constraint_algorithm=  LINCS
> integrator  =  md
> dt  =  0.001; ps !
> nsteps  =  50; total 500 ps.
> nstcomm =  1
> nstxout =  500
> nstvout =  0
> nstfout =  0
> nstlist =  10 
> ns_type =  grid
> rlist   =  1.0
> coulombtype=  PME
> rcoulomb=  1.0
> vdwtype =  cut-off
> rvdw=  1.4
> fourierspacing=  0.12
> fourier_nx=  0
> fourier_ny=  0
> fourier_nz=  0
> pme_order=  6
> ewald_rtol=  1e-5
> optimize_fft=  yes
> ; Berendsen temperature coupling is on in three groups
> Tcoupl  =  berendsen
> tc_grps= System
> tau_t   =  0.1
> ref_t   =  300
> ; Pressure coupling is on
> Pcoupl  =  parrinello-rahman 
> pcoupltype  =  isotropic
> tau_p   =  1.0
> compressibility =  4.5e-5
> ref_p   =  1.0
> ; Generate velocites is on at 300 K.
> gen_vel =  yes
> gen_temp=  300.0
> gen_seed=  173529
> ; pbc
> pbc= xyz
> ;pull code
> pull = constraint
> pull_geometry = direction
> pull_dim= N N Y
> pull_start= yes
> pull_nstxout= 500
> pull_nstfout= 100
> pull_ngroups = 1
> pull_group0= DPPC
> pull_group1= MOL
> pull_vec1= 0.0 0.0 -1.0
> pull_rate1= 0.01
> 
> Any comments is appreciable.
> 
> Di Cheng
> 
> University of Science and Technology of China
> Hefei, Anhui Province 230026
> P. R. China
> E-mail: chen...@mail.ustc.edu.cn
> Tel.: +86-15321055911
> 
> -- 
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[gmx-users] Parallel pulling with Gromacs 4.0.7: COMM mode problem

[Aykut Erbas]

Hi everyone

I have a pulling code running in parallel (32 processors) with Gromacs 4.0.7
The systems composes of a surface and a protein

with Gromacs 3.3.3 (on single processors ) when I set the COMM mode for 
the surface, the surface stands still,
and of course for the pulling code (reference groups is also surface) , 
the position of the protein is given /wrt the surface.
However for G4, no matter which group you set for COMM mode, the surface 
moves in the opposite direction of motion and you have the pulling 
coordinates in absolute coord. which is not what I want.


I want a pilling output /wrt the surface as in G3

Has anyone experienced smtg like this?
suggestions will be appreciated

Thanks
Aykut


*.mdp file
DIAM=surface
//

integrator   = md
nsteps= 3000
dt   = 0.002
nstlist = 50
nstxout  = 2
nstvout  = 2
nstfout   = 2
nstxtcout   = 4000
nstlog= 2
nstenergy  = 2
constraints = hbonds
ns_type = grid
coulombtype = pme
pme_order = 4
fourierspacing   = 0.12
rlist= 0.8
rvdw = 0.8
rcoulomb   = 0.8
energygrps= DIAM Protein SOL
tcoupl   = berendsen
tc_grps  = DIAM Protein SOL
tau_t= 0.1 0.1 0.1
ref_t= 300 300 300
gen_vel  = yes
Pcoupl   = berendsen
Pcoupltype   = semiisotropic
compressibility  = 2.5E-8 4.5E-5
tau_p= 1.0 1.0
ref_p= 1.0 1.0
comm_mode= angular
nstcomm  = 1
comm_grps= DIAM

;PULLING
pull = umbrella
pull_start   = yes
pull_geometry= position
pull_dim = Y Y N
pull_nstxout = 200
pull_nstfout = 200
pull_ngroups = 1
pull_group0  = DIAM
pull_group1  = AA1
pull_vec1= 1.0 0.0 0.0
pull_init1   = 2.0 0.0 1.0
pull_rate1   = 0.001
pull_k1  = 50
///
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[gmx-users] Signal 11 crash

[程迪]

Hi, gmx-users

I just encountered a singal 11 problem. I ran gromacs 4.0.7 on 64bit ubuntu.
4 core Xeon

imb F  2% step 22400, will finish Wed Mar 31 00:41:41 2010
imb F  3% step 22500, will finish Wed Mar 31 00:41:49 2010
imb F  2% step 22600, will finish Wed Mar 31 00:41:57 2010
imb F  3% step 22700, will finish Wed Mar 31 00:41:42 2010
imb F  2% step 22800, will finish Wed Mar 31 00:41:50 2010
imb F  2% step 22900, will finish Wed Mar 31 00:41:58 2010
imb F  3% step 23000, will finish Wed Mar 31 00:41:43 2010
imb F  3% step 23100, will finish Wed Mar 31 00:41:51 2010
imb F  3% step 23200, will finish Wed Mar 31 00:41:59 2010
rank 3 in job 1  chengdi-desktop_38817   caused collective abort of all
ranks
  exit status of rank 3: killed by signal 11
rank 2 in job 1  chengdi-desktop_38817   caused collective abort of all
ranks
  exit status of rank 2: killed by signal 11
rank 1 in job 1  chengdi-desktop_38817   caused collective abort of all
ranks
  exit status of rank 1: killed by signal 11

What's wrong?

My .mdp file is as follows:
title   =  fws
cpp =  /usr/bin/cpp
;constraints =  all-bonds
constraint_algorithm=  LINCS
integrator  =  md
dt  =  0.001; ps !
nsteps  =  50; total 500 ps.
nstcomm =  1
nstxout =  500
nstvout =  0
nstfout =  0
nstlist =  10
ns_type =  grid
rlist   =  1.0
coulombtype=  PME
rcoulomb=  1.0
vdwtype =  cut-off
rvdw=  1.4
fourierspacing=  0.12
fourier_nx=  0
fourier_ny=  0
fourier_nz=  0
pme_order=  6
ewald_rtol=  1e-5
optimize_fft=  yes
; Berendsen temperature coupling is on in three groups
Tcoupl  =  berendsen
tc_grps= System
tau_t   =  0.1
ref_t   =  300
; Pressure coupling is on
Pcoupl  =  parrinello-rahman
pcoupltype  =  isotropic
tau_p   =  1.0
compressibility =  4.5e-5
ref_p   =  1.0
; Generate velocites is on at 300 K.
gen_vel =  yes
gen_temp=  300.0
gen_seed=  173529
; pbc
pbc= xyz
;pull code
pull = constraint
pull_geometry = direction
pull_dim= N N Y
pull_start= yes
pull_nstxout= 500
pull_nstfout= 100
pull_ngroups = 1
pull_group0= DPPC
pull_group1= MOL
pull_vec1= 0.0 0.0 -1.0
pull_rate1= 0.01

Any comments is appreciable.

Di Cheng

University of Science and Technology of China
Hefei, Anhui Province 230026
P. R. China
E-mail: chen...@mail.ustc.edu.cn
Tel.: +86-15321055911
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