[gmx-users] Pulling and g_wham - Two analysis problems

[Steinbrecher, Thomas (IBG)]

Dear Gromacs users,

I encountered two problems in using g_wham to calculate pmf curves from a 
pulling simulation. My system consists of a water molecule which is pulled 
through a bilayer (the reference group). I used gromacs 4.5.6 with the 
following pull code options:

pull= umbrella
pull_geometry   = cylinder
pull_r1 = 1.0
pull_r0 = 2.0
pull_group0 = DOPC
pull_start  = no
pull_init1  = -1.600
pull_dim= N N Y
pull_vec1   = 0 0 1
pull_nstxout= 1
pull_nstfout= 1
pull_group1 = PullWater
pull_rate1  = 0.004
pull_k1 = 500

(Yes the pull is very fast, as this is only a preliminary test) So only the 
z-Axis is of interest. 

My first problem is this: 

Running ten simulations yields pullx.xvg files looking like this:

> cat pullx.xvg
@title "Pull COM"
@xaxis  label "Time (ps)"
@yaxis  label "Position (nm)"
@TYPE xy
@ view 0.15, 0.15, 0.75, 0.85
@ legend on
@ legend box on
@ legend loctype view
@ legend 0.78, 0.8
@ legend length 2
@ s0 legend "1 cZ"
@ s1 legend "1 dZ"
[...]
0.0240  3.89628 -1.59424
0.0260  3.89631 -1.59401
0.0280  3.89635 -1.59387
0.0300  3.89641 -1.59381
[...]

Which contain the simulation time, reference group COM and the z-Axis distance 
between group0 and group1. The last column is obviously what I want to 
calculate my pmf from. However, when running g_wham, boundaries are 
automatically determined to be:

Determined boundaries to 3.482960 and 4.119690

So gromacs determines boundaries and builds the histogram from the second 
column in the pullx files, which of course leads to non-sensical profile 
curves. Defining boundaries by hand does not help, as the histograms contain 
only data from the second data column.


Question 1: How do I tell g_wham to use the third data column in my pullx-files?
--

The second question concerns the same system, but this time using the pullf.xvg 
files to obtain the pmf from the forces. Again, I obtain sensible looking data 
files containing e.g.

>cat pullf.xvg
@title "Pull force"
@xaxis  label "Time (ps)"
@yaxis  label "Force (kJ/mol/nm)"
@TYPE xy
0.  0.245646
0.0020  0.927539
0.0040  1.65975
[...]

Visualisation in vmd and measurement with g_dist show the pulled water molecule 
passing the bilayer, changing the delta-Z coordinate from approx. -2 to +2 nm 
in each of ten simulations. But when I feed the pullf and tpr files to g_wham, 
again false boundaries are determined:

Determined boundaries to -2.250796 and -1.270690

Apparently, calculating the position of the system along the reaction 
coordinate from the forces did not produce a correct result, g_wham 'sees' the 
system moving only along about a quarter as far along the reaction coordinate, 
than it actually moves.


Question 2: What can cause this type of behaviour, is this problem known and 
how do I avoid it?
__


I would be happy about any comments,

Kind Regards,

Thomas

Dr. Thomas Steinbrecher
Institut für Physikalische Chemie, KIT
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[gmx-users] Re: About Usage of restraint

[Justin Lemkul]

Please post all Gromacs-related questions to gmx-users.

On 2/8/13 8:46 AM, vidhya sankar wrote:

Dear Justin Thank you for your previous Mail Reply

As you
Instructed me in the Previous Mail  to insert Vertical Restraint
I Have increased  Value of  fcz to 10
While  Should I make  value of fcx and fcy to Zero  ? otherwise may  i Leave it
as such
#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
;  i funct   fcxfcyfcz
111000  1000 100
#endif


I Have Followed the Following  gromacs Hyper link to add vertical z axis 
Restraint

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

Is My way is correct or Wrong?


Wrong.  What I suggested was a restraint along z only, allowing the water 
molecules to move within the x-y plane but not descend into the hydrophobic core 
of the membrane.  The force constant in x and y should be zero, the value in z 
can be whatever you choose, but the default value of 1000 should be fine.


-Justin

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Department of Biochemistry
Virginia Tech
Blacksburg, VA
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http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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[gmx-users] About Usage of Restraint

[vidhya sankar]

Dear Justin Thank you for your previous Mail Reply

  

   As you 
Instructed me in the Previous Mail  to insert Vertical Restraint 

I Have increased  Value of  fcz to 10
While  Should I make  value of fcx and fcy to Zero  ? otherwise may  i Leave it 
as such 

#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
;  i funct   fcx    fcy    fcz
   1    1    1000  1000 100
#endif


I Have Followed the Following  gromacs Hyper link to add vertical z axis 
Restraint 


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

Is My way is correct or Wrong?
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Re: [gmx-users] g_membed deprecated?

[Mark Abraham]

On Wed, Feb 6, 2013 at 6:01 PM, Albert  wrote:

> On 02/06/2013 05:37 PM, Namita Dube wrote:
>
>> Hi,
>> There must be some kind of problem with your system.
>> have you tried using :
>> mdrun -s input.tpr -membed membed.dat -o traj.trr -c membed.pdb -e
>> ener.edr
>> -nt 1 -cpt -1 -mn index.ndx -mp merged.top -v -stepout 100
>> what it says?
>>
>> Thanks.
>>
>
>
> it stopped with errors.
>
> not eough space for XTC?
>
>
>
> However, when I run it in gromacs-4.5.6 by g_membed, it finished well.
>

g_membed was removed and re-implemented into mdrun, like the original
message said. Please file an issue at http://redmine.gromacs.org and attach
the .tpr that works with 4.5.6 and fails with 4.6, a description of what
you are doing, and anything else relevant.

Mark
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Re: [gmx-users] compiling on different architecture than the compute nodes architecture

[Mark Abraham]

On Thu, Feb 7, 2013 at 10:00 AM, Broadbent, Richard <
richard.broadben...@imperial.ac.uk> wrote:

> Dear Silard,
>
> cmake -DGMX_CPU_ACCELERATION=AVX_256 -DGMX_DEFAULT_SUFFIX=OFF
> -DGMX_BINARY_SUFFIX="_avx"  -DGMX_OPENMP=ON  -DGMX_MPI=ON -DGMX_DOUBLE=ON
> -DGMX_GPU=OFF -DGMX_PREFER_STATIC_LIBS=ON -DGMX_FFT_LIBRARY=mkl
> -DMKL_INCLUDE_DIR=$MKLROOT/include
> -DMKL_LIBRARIES="$MKLROOT/lib/intel64/libmkl_core.so;$MKLROOT/lib/intel64/l
> ibmkl_intel_lp64.so;$MKLROOT/lib/intel64/libmkl_sequential.so"
> -DCMAKE_INSTALL_PREFIX=$HOME/libs/gromacs
>
> Compiled, linked and installed without warning using intel-suite/2013,
> mpi/intel-3.1, and cmake/2.8.9 I was compiling release-4-6 out of the git
> repository ( 06935659a3125d9b44b84c57e67cb6788fda42c1 ). The job using
> that executable is still in the queue, however, another one built using
> the sse2 kernels ran a minimisation on a single core without problems.
>
> How much faster fftw3 is than mkl for gromacs, is the difference likely to
> be on the scale of 1-2% or 10%?
>

The former, I would expect. Naturally it depends on your hardware, how you
compiled FFTW, and whether/how you use PME in GROMACS. If your PME-PP load
balance has too much work for the PP nodes, then FFT performance doesn't
matter. The .log file prints lots of analysis about this, and mdrun tries
by default to do what it can to balance.

Recent versions of icc and MKL do make compiling for MKL much easier, so
we'll probably add that for 5.0

Mark


>
> Thanks,
>
> Richard
>
>
> On 07/02/2013 02:17, "Szilárd Páll"  wrote:
>
> >On Wed, Feb 6, 2013 at 6:03 PM, Richard Broadbent <
> >richard.broadben...@imperial.ac.uk> wrote:
> >
> >> Dear All,
> >>
> >> I would like to compile gromacs 4.6 to run with the correct acceleration
> >> on the compute nodes on our local cluster. Some of the nodes have intel
> >> sandy-bridge whilst others only have sse4.1 and some (including the
> >>login
> >> and single core job nodes) are still stuck on ssse3 (gmx would use sse2
> >> acceleration here).
> >>
> >> Installing several versions is not a problem however, I'm not sure how
> >>to
> >> make cmake build a version of the code that is not using the
> >>acceleration
> >> for the system on which the code is being compiled. Restrictions on job
> >> sizes makes running the compilation on the sandy-bridge nodes almost
> >> impossible. Can anyone let me know which flags cmake needs to enable
> >> avx-256 acceleration?
> >>
> >> my standard cmake line is:
> >>
> >> $ CC=mpiicc CXX=mpiicpc ; cmake -DGMX_OPENMP=ON  -DGMX_MPI=ON
> >> -DGMX_DOUBLE=ON -DGMX_GPU=OFF -DGMX_PREFER_STATIC_LIBS=ON
> >> -DGMX_FFT_LIBRARY=mkl -DMKL_INCLUDE_DIR=$MKLROOT/**include
> >> -DMKL_LIBRARIES="$MKLROOT/lib/**intel64/libmkl_core.so;$**
> >>
> >>MKLROOT/lib/intel64/libmkl_**intel_lp64.so;$MKLROOT/lib/**intel64/libmkl_
> >>sequential.so"
> >> -DCMAKE_INSTALL_PREFIX=$HOME/**libs/gromacs  ../
> >>
> >
> >Note that MKL (without the fftw wrappers) is known to not work out of the
> >box. Making it work requires a fairly simple workaround described here:
> >http://redmine.gromacs.org/issues/1110#note-3
> >
> >Additionally, note that FFTW is in most cases faster than MKL (but if you
> >find the contrary do let us know).
> >
> >--
> >Szilárd
> >
> >
> >
> >>
> >>
> >>
> >> Thanks,
> >>
> >> Richard
> >> --
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> >>
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Re: [gmx-users] Reg:1 particles communicated to PME node 0 are more than 2/3 times the cut-off

[Mark Abraham]

On Fri, Feb 8, 2013 at 7:48 AM, Subramaniam Boopathi
wrote:

> dear sir,
>how can i remove this following problem
>


>Energies (kJ/mol)
>   AngleProper Dih.  Improper Dih.  LJ-14 Coulomb-14
> 2.36059e+033.53976e+027.34586e+007.00084e+032.02621e+03
> LJ (SR)   Coulomb (SR)   Coul. recip. Position Rest.  Potential
> 7.70414e+03   -5.91044e+04   -6.76092e+031.80260e+00   -4.64104e+04
> Kinetic En.   Total Energy  Conserved En.Temperature Pressure (bar)
> 6.48550e+041.84446e+041.84446e+041.88479e+037.32453e+03
>Constr. rmsd
> 4.81184e-01
>
>
> ---
> Program mdrun_d, VERSION 4.5.5
> Source code file: pme.c, line: 538
>
> Fatal error:
> 1 particles communicated to PME node 0 are more than 2/3 times the cut-off
> out of the domain decomposition cell of their charge group in dimension y.
> This usually means that your system is not well equilibrated.
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> ---
>

Did you try following the link mdrun suggested? :-)

Mark
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Re: [gmx-users] Reg:1 particles communicated to PME node 0 are more than 2/3 times the cut-off

[Shima Arasteh]

Doesn't that mean the npt should be done for a longer time?


Sincerely,
Shima



From: Mark Abraham 
To: Discussion list for GROMACS users  
Sent: Friday, February 8, 2013 5:37 PM
Subject: Re: [gmx-users] Reg:1 particles communicated to PME node 0 are more 
than 2/3 times the cut-off

On Fri, Feb 8, 2013 at 7:48 AM, Subramaniam Boopathi
wrote:

> dear sir,
>            how can i remove this following problem
>


>    Energies (kJ/mol)
>           Angle    Proper Dih.  Improper Dih.          LJ-14     Coulomb-14
>     2.36059e+03    3.53976e+02    7.34586e+00    7.00084e+03    2.02621e+03
>         LJ (SR)   Coulomb (SR)   Coul. recip. Position Rest.      Potential
>     7.70414e+03   -5.91044e+04   -6.76092e+03    1.80260e+00   -4.64104e+04
>     Kinetic En.   Total Energy  Conserved En.    Temperature Pressure (bar)
>     6.48550e+04    1.84446e+04    1.84446e+04    1.88479e+03    7.32453e+03
>    Constr. rmsd
>     4.81184e-01
>
>
> ---
> Program mdrun_d, VERSION 4.5.5
> Source code file: pme.c, line: 538
>
> Fatal error:
> 1 particles communicated to PME node 0 are more than 2/3 times the cut-off
> out of the domain decomposition cell of their charge group in dimension y.
> This usually means that your system is not well equilibrated.
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> ---
>

Did you try following the link mdrun suggested? :-)

Mark
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[gmx-users] Re: Membrane simulation - error during EM after inflation step

[John K]

Hello Justin,

I fixed the problem by placing my protein in its right position within the
unit cell.
Thank you so much for your timely help.

John K



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Re: [gmx-users] problems for GPU simulations

[Albert]

Hi:

 thanks for kind comments.
 It works fine now after I recompiled Gromacs carefully.

best
Albert

On 02/08/2013 03:43 AM, Szilárd Páll wrote:

Hi,

If you have two GTX 590-s four devices should show up in nvidia-smi and
mdrun should also show four devices detected. As nvidia-smi shows only two
GPUs means that one of your cards is not functioning properly.

You can try to check what GPU devices does you operating system "see"
independently form the driver using the lspci command, e.g:
lspci | grep -i ".*VGA.*NVIDIA.*"

If you see two PCI devices in this output that means that both cards are
detected by the operating system. If nvidia-smi does not show all four
GPUs, there must be something wrong with your driver.

Cheers,

--
Szilárd


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[gmx-users] npt equilbration + density

[Bahar Mehrpuyan]

Dear gmx users


My system is a single amino acid in water. I use two stage equilibration :  NVT 
(300 k) and NPT (300k , 1 barr) with position restrain.

NPT simulation were done for 2.4 ns and 1.14 barr was obtained for pressure.

but density is 974.031 . is this reasonable?

should i change the NPT simulation time?

thanks in advance.
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Re: [gmx-users] Reg:1 particles communicated to PME node 0 are more than 2/3 times the cut-off

[Justin Lemkul]

On 2/8/13 9:12 AM, Shima Arasteh wrote:



Doesn't that mean the npt should be done for a longer time?



No.  Look at the snippet of the .log file - the temperature at step zero is > 
1800K!  That indicates that the system is wildly unstable from the very start. 
Solutions to the problem are suggested in the link Mark provided, which have 
also been posted thousands of times to this list ;)


-Justin


From: Mark Abraham 
To: Discussion list for GROMACS users 
Sent: Friday, February 8, 2013 5:37 PM
Subject: Re: [gmx-users] Reg:1 particles communicated to PME node 0 are more 
than 2/3 times the cut-off

On Fri, Feb 8, 2013 at 7:48 AM, Subramaniam Boopathi
wrote:


dear sir,
 how can i remove this following problem





 Energies (kJ/mol)
AngleProper Dih.  Improper Dih.  LJ-14 Coulomb-14
  2.36059e+033.53976e+027.34586e+007.00084e+032.02621e+03
  LJ (SR)   Coulomb (SR)   Coul. recip. Position Rest.  Potential
  7.70414e+03   -5.91044e+04   -6.76092e+031.80260e+00   -4.64104e+04
  Kinetic En.   Total Energy  Conserved En.Temperature Pressure (bar)
  6.48550e+041.84446e+041.84446e+041.88479e+037.32453e+03
 Constr. rmsd
  4.81184e-01


---
Program mdrun_d, VERSION 4.5.5
Source code file: pme.c, line: 538

Fatal error:
1 particles communicated to PME node 0 are more than 2/3 times the cut-off
out of the domain decomposition cell of their charge group in dimension y.
This usually means that your system is not well equilibrated.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---



Did you try following the link mdrun suggested? :-)

Mark



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


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[gmx-users] Re: Adsorption layer of water molecules

[ypca]

The increase of the box volume occur in the beginning of the npt
equilibration. The analysis of pressure was like that:

Pressure nvt = fluctuates between 500 bar
Pressure npt = fluctuates 1 bar
Pressure in production stage = fluctuates 1 bar

Actually, the problem is that water molecules go very far away from the
protein.
These are links to the images of the protein in water, one view close and
another with a smaller zoom. It's like the box has exploded and water has
became free, like no interactions occur between the protein and water.

http://www.dta.ufv.br/arquivos/proteinaway.png
http://www.dta.ufv.br/arquivos/proteinclose.png

Thanks for looking into it!





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Re: [gmx-users] npt equilbration + density

[Justin Lemkul]

On 2/8/13 10:49 AM, Bahar Mehrpuyan wrote:

Dear gmx users


My system is a single amino acid in water. I use two stage equilibration :  NVT 
(300 k) and NPT (300k , 1 barr) with position restrain.

NPT simulation were done for 2.4 ns and 1.14 barr was obtained for pressure.

but density is 974.031 . is this reasonable?



That depends on the water model you use and what its expected density is.

-Justin

--


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


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Re: [gmx-users] Re: Adsorption layer of water molecules

[Justin Lemkul]

On 2/8/13 11:25 AM, ypca wrote:

The increase of the box volume occur in the beginning of the npt
equilibration. The analysis of pressure was like that:

Pressure nvt = fluctuates between 500 bar
Pressure npt = fluctuates 1 bar
Pressure in production stage = fluctuates 1 bar

Actually, the problem is that water molecules go very far away from the
protein.
These are links to the images of the protein in water, one view close and
another with a smaller zoom. It's like the box has exploded and water has
became free, like no interactions occur between the protein and water.

http://www.dta.ufv.br/arquivos/proteinaway.png
http://www.dta.ufv.br/arquivos/proteinclose.png



Please post a complete .mdp file and the box vectors of your starting and ending 
configurations.  In reality, the system probably should have exploded and failed 
to run.  You did not do any post-processing with trjconv, correct?  The output 
you have shown is the actual mdrun output, yes?


-Justin

--


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


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Re: [gmx-users] Restarting simulation

[Justin Lemkul]

On 2/8/13 12:31 AM, James Starlight wrote:

Dear Gromacs Users!

I try to restart canceled (by cnttl+z) simulation using cpt file

  mdrun -v -deffnm md_b2ar_APO -cpi md_b2ar_APO_prev


after this I obtain error like

Checksum wrong for 'md_b2ar_APO.log'. The file has been replaced or
its contents have been modified. Cannot do appending because of this
condition.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors


My log file end with the common gromac's stats

Force evaluation time GPU/CPU: 9.129 ms/9.997 ms = 0.913
For optimal performance this ratio should be close to 1!

Core t (s)   Wall t (s)(%)
Time:  128.610   36.400  353.3
  (ns/day)(hour/ns)
Performance:   10.3542.318
Finished mdrun on node 0 Fri Feb  8 09:16:12 2013


How should I fix it?



In theory, that shouldn't happen, otherwise just use -noappend and concatenate 
relevant output later.


-Justin

--


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


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Re: [gmx-users] Re: Re: Error- Simulation box resizes during mdrun

[Justin Lemkul]

On 2/8/13 2:51 AM, Bharath K. Srikanth wrote:

Justin,

You're right, the density of the box does increase during the simulation.


How large is the increase in density?


But I don't believe the water is particularly sparse, since I've never
encountered this issue in previous simulations, when I used these
parameters for genbox while inserting water. The system density also
appears to have an acceptable value in the beginning.

Is there any other way I can approach this, for example, is there a
command/md.mdp option that would fix the size of my simulation box to the
initial values?



A fixed box is achieved by running in the NVT ensemble, but that may or may not 
be appropriate for membranes.


-Justin


3) I then re-inserted the peptide by editing the coordinate file, and ran
an energy minimization. Then I added water using genbox, and ran another
EM.

4) Then I ran the simulation for 3,000,000 steps (90 ns). While this was
happening, I observed that the size of the box was beginning to change, in
the z direction (not in the y direction as I said yesterday, but still,
parallel to the plane of the bilayer).

I've included some pictures here (in the .tga format), from before and
after the simulation. When I ran it in vmd using the initial coordinates
and the trajectory file, I could actually see the box resizing during the
run.

https://www.dropbox.com/l/UJuFbDTPaISIpkSf

I'm sure there's a very simple explanation, but I can't seem to figure it
out.



It's hard to tell from the way things are rendered, but it seems to me
that your
water is very diffuse, and over the course of the simulation, the density
of the
system is increasing to try to fill a lot of void space.  A simple
analysis of
density should show this rather clearly.







--


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


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Re: [gmx-users] MARTINI force-field in pulling simulations

[Davide Mercadante]

Thanks Justin.

The help has been much appreciated.

Cheers,
Davide

On 7/02/13 8:46 PM, "Justin Lemkul"  wrote:

>
>
>On 2/7/13 2:29 PM, Davide Mercadante wrote:
>> Thank you Justin,
>>
>> I guess this means that this kind of simulations is not possible
>>without a
>> modification of the forcefield (which would ultimately mean using a
>> different forcefield I believe)?
>>
>
>If you're looking to unfold secondary structure elements, yes.
>
>-Justin
>
>> Thanks.
>>
>> Cheers,
>> Davide
>>
>> On 7/02/13 8:09 PM, "Justin Lemkul"  wrote:
>>
>>>
>>>
>>> On 2/7/13 1:44 PM, Davide Mercadante wrote:
 Dear Justin,

 Thank you for your reply. I decreased the time step from 0.02 to 0.005
 and
 run the simulation again. The simulation still crashes giving LINCS
 warning on the same atoms but does it later.
 Do you advice to keep reducing the time step in order to reach a
 simulated
 time where the pull of the whole molecule occurs and I see the force
 peaking? I am still not sure why this happens...

>>>
>>> No, I think the issue is probably more fundamental.  MARTINI uses fixed
>>> secondary structure (bonds in the topology to preserve geometry).
>>>You're
>>> probably just pulling against those and the algorithms that work on
>>> bonded
>>> interactions are failing.
>>>
>>> -Justin
>>>
 Thanks.

 Davide

 On 7/02/13 1:05 PM, "Justin Lemkul"  wrote:

>
>
> On 2/7/13 5:20 AM, Davide Mercadante wrote:
>> Dear All,
>>
>> I am trying to run a pulling simulation on a small protein (18 aa)
>> using
>> the GC forcefield MARTINI (v2.2). I have energy minimized and
>> equilibrated (NPT) my system and everything seems fine. My system
>> consists of the protein + water + ions NA+ and CL-.
>>
>> After the equilibration I start a constant velocity pulling along
>>the
>> z-direction of the last atom of the chain while the first atom is
>> positionally restrained in xyz (basically I am stretching the
>> protein).
>> At some point from the start of the pulling simulation and before
>> reaching the full extension of the chain (force profile is still
>> steadily increasing without peaking) the simulation crashes giving
>>me
>> these LINCS warnings:
>>
>> Step 293252, time 5865.04 (ps)  LINCS WARNING
>> relative constraint deviation after LINCS:
>> rms 0.157274, max 0.291135 (between atoms 10 and 11)
>> bonds that rotated more than 30 degrees:
>> atom 1 atom 2  angle  previous, current, constraint length
>>
>> Step 293252, time 5865.04 (ps)  LINCS WARNING
>> relative constraint deviation after LINCS:
>> rms 0.128562, max 0.230219 (between atoms 7 and 8)
>> bonds that rotated more than 30 degrees:
>> atom 1 atom 2  angle  previous, current, constraint length
>>
>> Step 293253, time 5865.06 (ps)  LINCS WARNING
>> relative constraint deviation after LINCS:
>> rms 0.413291, max 0.828515 (between atoms 7 and 8)
>>
>> Step 293253, time 5865.06 (ps)  LINCS WARNING
>> relative constraint deviation after LINCS:
>> rms 0.587032, max 0.986890 (between atoms 11 and 13)
>> bonds that rotated more than 30 degrees:
>> atom 1 atom 2  angle  previous, current, constraint length
>>  7  8   46.60.2686   0.0579  0.3500
>> 10 11  121.30.2481   0.0550  0.3500
>> 13 15  168.50.2851   0.0278  0.3500
>>
>> Step 293253, time 5865.06 (ps)  LINCS WARNING
>> relative constraint deviation after LINCS:
>> rms 0.108373, max 0.322423 (between atoms 19 and 21)
>> bonds that rotated more than 30 degrees:
>> atom 1 atom 2  angle  previous, current, constraint length
>> bonds that rotated more than 30 degrees:
>> atom 1 atom 2  angle  previous, current, constraint length
>>  7  8   45.00.2686   0.0600  0.3500
>> 10 11   88.10.2481   0.0497  0.3500
>> Wrote pdb files with previous and current coordinates
>> Wrote pdb files with previous and current coordinates
>>
>> Step 293254, time 5865.08 (ps)  LINCS WARNING
>> relative constraint deviation after LINCS:
>> rms 0.330732, max 0.654588 (between atoms 23 and 25)
>> bonds that rotated more than 30 degrees:
>> atom 1 atom 2  angle  previous, current, constraint length
>> 21 23   42.00.2905   0.1426  0.3500
>> 17 18   92.90.3146   0.1560  0.3000
>> 15 17   35.30.5839   0.4003  0.3500
>> 13 15  141.60.0278   0.2742  0.3500
>>
>> Step 293254, time 5865.08 (ps)  LINCS WARNING
>> relative constraint deviation after LINCS:
>> rms 0.312540, max 0.87 (between atoms 19 and 21)
>> bonds that rotated more than 30 degrees:
>> atom 1 atom 2  angle  previous, current, const

Re: [gmx-users] npt equilbration + density

[Bahar Mehrpuyan]

Thanks Justin for the reply.

 i use SPC water model (12000 molecules). in literature there are 
different values for density which depend simulation time, number of 
water molecules , etc. (for example this paper : 
jcp.aip.org/resource/1/jcpsa6/v108/i24/p10220_s1)



 From: Justin Lemkul 
To: Bahar Mehrpuyan ; Discussion list for GROMACS 
users  
Sent: Friday, February 8, 2013 7:56 PM
Subject: Re: [gmx-users] npt equilbration + density
 


On 2/8/13 10:49 AM, Bahar Mehrpuyan wrote:
> Dear gmx users
>
>
> My system is a single amino acid in water. I use two stage equilibration :  
> NVT (300 k) and NPT (300k , 1 barr) with position restrain.
>
> NPT simulation were done for 2.4 ns and 1.14 barr was obtained for pressure.
>
> but density is 974.031 . is this reasonable?
>

That depends on the water model you use and what its expected density is.

-Justin

-- 


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


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Re: [gmx-users] npt equilbration + density

[Justin Lemkul]

On 2/8/13 11:54 AM, Bahar Mehrpuyan wrote:

Thanks Justin for the reply.
  i use SPC water model (12000 molecules). in literature there are different
values for density which depend simulation time, number of water molecules ,
etc. (for example this paper : jcp.aip.org/resource/1/jcpsa6/v108/i24/p10220_s1)



The results will also depend to a much larger extent on the proper use of 
cutoffs, long-range electrostatics algorithms, etc.  People get different 
results when making changes.  Somewhere in the ballpark of 980 kg m^-3 seems 
about right for SPC, but a proper assessment would require comparison with work 
that uses the same run parameters that you did.


-Justin



*From:* Justin Lemkul 
*To:* Bahar Mehrpuyan ; Discussion list for GROMACS
users 
*Sent:* Friday, February 8, 2013 7:56 PM
*Subject:* Re: [gmx-users] npt equilbration + density



On 2/8/13 10:49 AM, Bahar Mehrpuyan wrote:
 > Dear gmx users
 >
 >
 > My system is a single amino acid in water. I use two stage equilibration :
NVT (300 k) and NPT (300k , 1 barr) with position restrain.
 >
 > NPT simulation were done for 2.4 ns and 1.14 barr was obtained for pressure.
 >
 > but density is 974.031 . is this reasonable?
 >

That depends on the water model you use and what its expected density is.

-Justin

--


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






--


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


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[gmx-users] Re: Adsorption layer of water molecules

[ypca]

Actually, I used trjconv (nojump) and these are the images of the run after
the post-processing. 
I didn't understand very well what you mean with the box vectors of the
starting and ending.
When I used editconf, it has shown:

box vectors :  7.205 10.465 11.742 (nm) 
new box vectors :  7.589  7.589  7.589 (nm) 

The .mdp files I have used:

NVT

title= 1ns_pr_fixo
cpp  = /lib/cpp
define   = -DPOSRES
integrator   = md
tinit= 0
dt   = 0.002
nsteps   = 50 ; total 1000 ps
comm-mode= Linear
nstcomm  = 1
nstxout  = 100
nstvout  = 100
nstfout  = 100
nstlog   = 100
nstenergy= 100
nstxtcout= 100
xtc-precision= 1000
constraint_algorithm = lincs
lincs_iter   = 1
lincs_order  = 4
energygrps   = Protein Non-Protein  
nstlist  = 5
ns_type  = grid
pbc  = xyz
rlist= 1.0
domain-decomposition = no
coulombtype  = PME
pme_order= 4
fourierspacing   = 0.16
rcoulomb = 1.0
vdw-type = Cut-off
rvdw = 1.0
DispCorr = EnerPres
optimize_fft = yes
Tcoupl   = V-rescale
tc-grps  = Protein Non-Protein 
tau-t= 0.10.1
ref-t= 348348
gen_vel  = yes
gen_temp = 348
gen_seed = -1
Pcoupl   = no
compressibility  = 4.56e-5
constraints  = all-bonds
unconstrained-start  = no
morse= no

NPT

title= 1000ps_pr_fixo
cpp  = /lib/cpp
define   = -DPOSRES
integrator   = md
tinit= 0
dt   = 0.002
nsteps   = 50 ; total 1000 ps
comm_mode= Linear
nstcomm  = 1
nstxout  = 100
nstvout  = 100
nstfout  = 100
nstlog   = 100
nstenergy= 100
nstxtcout= 100
xtc-precision= 1000
energygrps   = Protein Non-Protein  
constraint_algorithm = lincs
lincs_iter   = 1
lincs_order  = 4
nstlist  = 5
ns_type  = grid
pbc  = xyz
rlist= 1.0
domain-decomposition = no
coulombtype  = PME
pme_order= 4
fourierspacing   = 0.16
rcoulomb = 1.0
vdw-type = Cut-off
rvdw = 1.0
DispCorr = EnerPres
optimize_fft = yes
Tcoupl   = V-rescale
tc-grps  = Protein Non-Protein 
tau-t= 0.10.1
ref-t= 348348
gen_vel  = no
gen_temp = 348
gen_seed = -1
Pcoupl   = Parrinello-Rahman
Pcoupltype   = Isotropic
tau_p= 1.0
compressibility  = 4.56e-5
ref_p= 1.0
refcoord_scaling = com
constraints  = all-bonds
unconstrained-start  = no
morse= no

PRODUCTION

title= 100 ns
cpp  = /lib/cpp
include  = 
define   = 
integrator   = md
tinit= 0 
dt   = 0.002
nsteps   = 5000 ;100ns 
comm-mode= Linear
nstcomm  = 1
nstxout  = 5 ; trr
nstvout  = 5 ; velocidades
nstfout  = 5 ; forcas
nstlog   = 1000
nstenergy= 1000
nstxtcout= 1 ; xtc
xtc-precision= 1000
constraint_algorithm = lincs
lincs_iter   = 1
lincs_order  = 4
energygrps   = Protein Non-Protein   
nstlist  = 5
ns_type  = grid
pbc  = xyz
rlist= 1.0
domain-decomposition = no
coulombtype  = PME
pme_order= 4
fourierspacing   = 0.16 
rcoulomb = 1.0
epsilon-r= 1
vdw-type = Cut-off
rvdw = 1.0
DispCorr = EnerPres
optimize_fft = yes
Tcoupl   = V-rescale
tc-grps  = Protein Non-Protein 
tau-t= 0.10.1   
ref-t= 348348 
gen_vel  = no
gen_temp

Re: [gmx-users] Re: Adsorption layer of water molecules

[Justin Lemkul]

On 2/8/13 12:11 PM, ypca wrote:

Actually, I used trjconv (nojump) and these are the images of the run after
the post-processing.


Then the output is exactly what you should be seeing.  If you remove jumps, then 
molecules simply diffuse outward.  There is nothing wrong at all with the 
trajectory.



I didn't understand very well what you mean with the box vectors of the
starting and ending.
When I used editconf, it has shown:

box vectors :  7.205 10.465 11.742 (nm)
new box vectors :  7.589  7.589  7.589 (nm)



I wanted to see this to make sure the box wasn't doing anything funny.  As you 
can see, there are indeed some changes in the box, but it got smaller over time, 
not vastly larger if the water molecules were actually diffusing out into the void.


Conclusion: nothing wrong.  For proper visualization, trjconv -pbc mol -ur 
compact with or without -center if you want to center the protein.


-Justin


The .mdp files I have used:

NVT

title= 1ns_pr_fixo
cpp  = /lib/cpp
define   = -DPOSRES
integrator   = md
tinit= 0
dt   = 0.002
nsteps   = 50 ; total 1000 ps
comm-mode= Linear
nstcomm  = 1
nstxout  = 100
nstvout  = 100
nstfout  = 100
nstlog   = 100
nstenergy= 100
nstxtcout= 100
xtc-precision= 1000
constraint_algorithm = lincs
lincs_iter   = 1
lincs_order  = 4
energygrps   = Protein Non-Protein  
nstlist  = 5
ns_type  = grid
pbc  = xyz
rlist= 1.0
domain-decomposition = no
coulombtype  = PME
pme_order= 4
fourierspacing   = 0.16
rcoulomb = 1.0
vdw-type = Cut-off
rvdw = 1.0
DispCorr = EnerPres
optimize_fft = yes
Tcoupl   = V-rescale
tc-grps  = Protein Non-Protein
tau-t= 0.10.1
ref-t= 348348
gen_vel  = yes
gen_temp = 348
gen_seed = -1
Pcoupl   = no
compressibility  = 4.56e-5
constraints  = all-bonds
unconstrained-start  = no
morse= no

NPT

title= 1000ps_pr_fixo
cpp  = /lib/cpp
define   = -DPOSRES
integrator   = md
tinit= 0
dt   = 0.002
nsteps   = 50 ; total 1000 ps
comm_mode= Linear
nstcomm  = 1
nstxout  = 100
nstvout  = 100
nstfout  = 100
nstlog   = 100
nstenergy= 100
nstxtcout= 100
xtc-precision= 1000
energygrps   = Protein Non-Protein  
constraint_algorithm = lincs
lincs_iter   = 1
lincs_order  = 4
nstlist  = 5
ns_type  = grid
pbc  = xyz
rlist= 1.0
domain-decomposition = no
coulombtype  = PME
pme_order= 4
fourierspacing   = 0.16
rcoulomb = 1.0
vdw-type = Cut-off
rvdw = 1.0
DispCorr = EnerPres
optimize_fft = yes
Tcoupl   = V-rescale
tc-grps  = Protein Non-Protein
tau-t= 0.10.1
ref-t= 348348
gen_vel  = no
gen_temp = 348
gen_seed = -1
Pcoupl   = Parrinello-Rahman
Pcoupltype   = Isotropic
tau_p= 1.0
compressibility  = 4.56e-5
ref_p= 1.0
refcoord_scaling = com
constraints  = all-bonds
unconstrained-start  = no
morse= no

PRODUCTION

title= 100 ns
cpp  = /lib/cpp
include  =
define   =
integrator   = md
tinit= 0
dt   = 0.002
nsteps   = 5000 ;100ns
comm-mode= Linear
nstcomm  = 1
nstxout  = 5 ; trr
nstvout  = 5 ; velocidades
nstfout  = 5 ; forcas
nstlog   = 1000
nstenergy= 1000
nstxtcout= 1 ; xtc
xtc-precision= 1000
constraint_algorithm = lincs
lincs_iter   = 1
lincs_order  = 4
energygrps   = Protein Non-Protein
nstlist  = 5
ns_type  = grid
pbc   

[gmx-users] Re: Adsorption layer of water molecules

[ypca]

Thank you very much!

But when I use trjconv how you said, the water molecules are still in the
cubic form, like in the beginning. Isn't there any problem?



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Re: [gmx-users] Re: Adsorption layer of water molecules

[Justin Lemkul]

On 2/8/13 12:49 PM, ypca wrote:

Thank you very much!

But when I use trjconv how you said, the water molecules are still in the
cubic form, like in the beginning. Isn't there any problem?




Why is that a problem?

-Justin

--


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


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[gmx-users] Re: Adsorption layer of water molecules

[ypca]

But are these modifies just a question about the visualization of the
trajectory? 

Thank you very mych!



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Re: [gmx-users] Re: Adsorption layer of water molecules

[Justin Lemkul]

On 2/8/13 1:10 PM, ypca wrote:

But are these modifies just a question about the visualization of the
trajectory?



Yes.  Please do some background reading on periodic boundary conditions if any 
of this is unfamiliar to you.


-Justin

--


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


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[gmx-users] genion error - No line with moleculetype 'SOL' found the [ molecules ] section of file ‘topol.top’

[Ashima]

Dear All,
 
I need to add 6 CL ions to make the system neutral but when I type the
command line
 
genion -s ions.tpr -o solv_ions.gro -p topol.top -pname NA -nname CL -nn 6
 
and choose group 15 (SOL), the error is
 
Fatal error:
No line with moleculetype 'SOL' found the [ molecules ] section of file
‘topol.top’

when I check the ‘topol.top’ file I found there are 24504 SOL molecules
present.
 
My topology file looks like this
 
; Include water topology
#include "amber99sb.ff/tip3p.itp"
 
#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
;  i funct   fcxfcyfcz
   11   1000   1000   1000
#endif
 
; Include topology for ions
#include "amber99sb.ff/ions.itp"
 
[ system ]
; Name
Protein
 
[ molecules ]
; Compound#mols
Protein_chain_A  1
Ligand   1
SOL  24504

Please let me know how to rectify the problem
 
regards,
Ashima




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Re: [gmx-users] GROMACS Error

[Mark Abraham]

Not sure - perhaps if you've edited this file by hand (or in an
inappropriate editor) there's a tab-vs-space issue, or missing line ending
on the final line.

Mark

On Fri, Feb 8, 2013 at 7:40 PM, Asma Mushtaq  wrote:

> Dear All,
>
>
>
> I need to add 6 CL ions to make the system neutral but when I type the
> command line
>
>
>
> genion -s ions.tpr -o solv_ions.gro -p topol.top -pname NA -nname CL -nn 6
>
>
>
> and choose group 15 (SOL), the error is
>
>
>
> Fatal error:
>
> No line with moleculetype 'SOL' found the [ molecules ] section of file
> ‘topol.top’
>
>
>
> but when I check the ‘topol.top’ file I found there are 24504 SOL molecules
> present.
>
>
>
> My topology file looks like this
>
>
>
> ; Include water topology
>
> #include "amber99sb.ff/tip3p.itp"
>
>
>
> #ifdef POSRES_WATER
>
> ; Position restraint for each water oxygen
>
> [ position_restraints ]
>
> ;  i funct   fcxfcyfcz
>
>11   1000   1000   1000
>
> #endif
>
>
>
> ; Include topology for ions
>
> #include "amber99sb.ff/ions.itp"
>
>
>
> [ system ]
>
> ; Name
>
> Protein
>
>
>
> [ molecules ]
>
> ; Compound#mols
>
> Protein_chain_A  1
>
> ATQwild  1
>
> SOL  24504
>
>
>
>
>
> Please let me know how to rectify the problem
>
>
>
>
>
> regards,
>
>
>
> Ashima
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Re: [gmx-users] Pulling and g_wham - Two analysis problems

[Justin Lemkul]

On 2/8/13 6:00 AM, Steinbrecher, Thomas (IBG) wrote:

Dear Gromacs users,

I encountered two problems in using g_wham to calculate pmf curves from a 
pulling simulation. My system consists of a water molecule which is pulled 
through a bilayer (the reference group). I used gromacs 4.5.6 with the 
following pull code options:

pull= umbrella
pull_geometry   = cylinder
pull_r1 = 1.0
pull_r0 = 2.0
pull_group0 = DOPC
pull_start  = no
pull_init1  = -1.600
pull_dim= N N Y
pull_vec1   = 0 0 1
pull_nstxout= 1
pull_nstfout= 1
pull_group1 = PullWater
pull_rate1  = 0.004
pull_k1 = 500

(Yes the pull is very fast, as this is only a preliminary test) So only the 
z-Axis is of interest.

My first problem is this:

Running ten simulations yields pullx.xvg files looking like this:


cat pullx.xvg

@title "Pull COM"
@xaxis  label "Time (ps)"
@yaxis  label "Position (nm)"
@TYPE xy
@ view 0.15, 0.15, 0.75, 0.85
@ legend on
@ legend box on
@ legend loctype view
@ legend 0.78, 0.8
@ legend length 2
@ s0 legend "1 cZ"
@ s1 legend "1 dZ"
[...]
0.0240  3.89628 -1.59424
0.0260  3.89631 -1.59401
0.0280  3.89635 -1.59387
0.0300  3.89641 -1.59381
[...]

Which contain the simulation time, reference group COM and the z-Axis distance 
between group0 and group1. The last column is obviously what I want to 
calculate my pmf from. However, when running g_wham, boundaries are 
automatically determined to be:

Determined boundaries to 3.482960 and 4.119690

So gromacs determines boundaries and builds the histogram from the second 
column in the pullx files, which of course leads to non-sensical profile 
curves. Defining boundaries by hand does not help, as the histograms contain 
only data from the second data column.


Question 1: How do I tell g_wham to use the third data column in my pullx-files?
--

The second question concerns the same system, but this time using the pullf.xvg 
files to obtain the pmf from the forces. Again, I obtain sensible looking data 
files containing e.g.


cat pullf.xvg

@title "Pull force"
@xaxis  label "Time (ps)"
@yaxis  label "Force (kJ/mol/nm)"
@TYPE xy
0.  0.245646
0.0020  0.927539
0.0040  1.65975
[...]

Visualisation in vmd and measurement with g_dist show the pulled water molecule 
passing the bilayer, changing the delta-Z coordinate from approx. -2 to +2 nm 
in each of ten simulations. But when I feed the pullf and tpr files to g_wham, 
again false boundaries are determined:

Determined boundaries to -2.250796 and -1.270690

Apparently, calculating the position of the system along the reaction 
coordinate from the forces did not produce a correct result, g_wham 'sees' the 
system moving only along about a quarter as far along the reaction coordinate, 
than it actually moves.


Question 2: What can cause this type of behaviour, is this problem known and 
how do I avoid it?
__


I would be happy about any comments,


Both of the issues sound like bugs.  Please file a report on redmine.gromacs.org 
with all files necessary to reproduce the problem.


-Justin

--


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


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[gmx-users] Diffusion beyond periodic boundary

[Kenji Mochizuki]

Dear All

I have performed MD run with periodic boundary condition, 
which system is consist of water and LJ particles.

I would like to know the time dependence of the dislocated distance (diffusion) 
from the starting time (t=0).
Firstly, I made pdb file of the trajectory, then calculated the distance from 
pdb file. 

However, when the particle goes beyond periodic boundary,
the x-y-z coordination is rewind into the box size.
So, the dislocated distance is wrong.

Could you please tell me how to calculate the dislocated distance accurately ? 

Best regards

Kenji


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[gmx-users] genion error - No line with moleculetype 'SOL' found the [ molecules ] section of file ‘topol.top’ [only with PROTEIN-LIGAND complex]

[Ashima]

Dear All, 
  
I need to add 6 CL ions to make the system neutral but when I type the
command line 
  
genion -s ions.tpr -o solv_ions.gro -p topol.top -pname NA -nname CL -nn 6 

I am able to add the ion easily to a protein or protein-peptide complex by
using the above command line where I replace the 6 SOL with 6 CL ions.

But when I use the above command line for Protein-Ligand complex
  
and choose group 15 (SOL), the error is 
  
Fatal error: 
No line with moleculetype 'SOL' found the [ molecules ] section of file
‘topol.top’ 

when I check the ‘topol.top’ file I found there are 24504 SOL molecules
present. 
  
My topology file looks like this 
  
; Include water topology 
#include "amber99sb.ff/tip3p.itp" 
  
#ifdef POSRES_WATER 
; Position restraint for each water oxygen 
[ position_restraints ] 
;  i funct   fcxfcyfcz 
   11   1000   1000   1000 
#endif 
  
; Include topology for ions 
#include "amber99sb.ff/ions.itp" 
  
[ system ] 
; Name 
Protein 
  
[ molecules ] 
; Compound#mols 
Protein_chain_A  1 
Ligand   1 
SOL  24504 

Please let me know how to rectify the problem 
  
regards, 
Ashima 



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[gmx-users] genion error { problem only with PROTEIN-LIGAND complex} - No line with moleculetype 'SOL' found the [ molecules ] section of file ‘topol.top’

[Ashima]

Dear All, 
  
I need to add 6 CL ions to make the system neutral but when I type the
command line 
  
genion -s ions.tpr -o solv_ions.gro -p topol.top -pname NA -nname CL -nn 6 

I am able to add the ion easily to a protein or protein-peptide complex by
using the above command line where I replace the 6 SOL with 6 CL ions. 

But when I use the above command line for Protein-Ligand complex 
  
and choose group 15 (SOL), the error is 
  
Fatal error: 
No line with moleculetype 'SOL' found the [ molecules ] section of file
‘topol.top’ 

when I check the ‘topol.top’ file I found there are 24504 SOL molecules
present. 
  
My topology file looks like this 
  
; Include water topology 
#include "amber99sb.ff/tip3p.itp" 
  
#ifdef POSRES_WATER 
; Position restraint for each water oxygen 
[ position_restraints ] 
;  i funct   fcxfcyfcz 
   11   1000   1000   1000 
#endif 
  
; Include topology for ions 
#include "amber99sb.ff/ions.itp" 
  
[ system ] 
; Name 
Protein 
  
[ molecules ] 
; Compound#mols 
Protein_chain_A  1 
Ligand   1 
SOL  24504 

Please let me know how to rectify the problem 
  
regards, 
Ashima



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