[gmx-users] Message-ID:

[Kim Jessica Novacek]

Hey Mark,
I tried to set the CMAKE_LIBRARY_PATH to an actual file, because it cannot be 
found by cmake if I left it out, but it is there.
Greetings Kim
 
> > Ursprüngliche Nachricht:
> > Von: Kim Jessica Novacek 
> > An: gromacs.org_gmx-users@maillist.sys.kth.se
> > Kopie: 
> > Datum: Mon Oct 12 15:31:58 CEST 2015
> > 
> > Although I did let out the Xeon Phi Command there is still the same make 
> > error.
> > Greetings 
> > Kim
> > 
> > 
> > /usr/bin/ld: cannot find -lcudart
> > /usr/bin/ld: cannot find -lmpi
> > collect2: error: ld returned 1 exit status
> > make[2]: *** [bin/gmx_mpi] Fehler 1
> > make[1]: *** [src/programs/CMakeFiles/gmx.dir/all] Fehler 2
> > make[1]: *** Auf noch nicht beendete Prozesse wird gewartet …
> > /usr/bin/ld: cannot find -lcudart
> > /usr/bin/ld: cannot find -lmpi
> > collect2: error: ld returned 1 exit status
> > make[2]: *** [bin/template] Fehler 1
> > make[1]: *** [share/template/CMakeFiles/template.dir/all] Fehler 2
> > make: *** [all] Fehler 2
> > 
> > 
> > cmake .. -DREGRESSIONTEST_DOWNLOAD=ON -DCMAKE_C_COMPILER=/usr/bin/gcc 
> > -DGMX_MPI=ON
> > -DGMX_GPU=ON -DCUDA_TOOLKIT_ROOT_DIR=/usr/lib/nvidia-cuda-toolkit 
> > -DCMAKE_INSTALL_PREFIX=/usr
> /l
> > ocal/GROMACS -DGMX_FFT_LIBRARY=fftw3 
> > -DFFTWF_LIBRARY=/usr/local/lib/libfftw3f.a
> -DCMAKE_BUILD_T
> > YPE=DEBUG -DCMAKE_CXX_COMPILER=/usr/bin/gcc -DGMX_PREFER_STATIC_LIBS=ON 
> > -DCMAKE_C_FLAGS="-sta
> ti
> > c" -DCMAKE_CXX_FLAGS="-static" -DCMAKE_SKIP_RPATH=YES 
> > -DCMAKE_PREFIX_PATH=/usr/lib/cuda
> > -DCMAKE_LIBRARY_PATH=/usr/lib/x86_64-linux-gnu/libcudart.so 
> > -DCMAKE_PREFIX_PATH=/usr/include/
> li
> > bxml2/libxml
>
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[gmx-users] RDF com

[Deva Priya]

Hello,

I am trying to calculate the rdf using the center of mass of a sulfonate
group, SO3 with other SO3 groups in the system. The SO3 group is part of a
bigger molecule. Is it appropriate to use

gmx rdf -rdf mol_com to carry out this operation or  should I use the

gmx rdf -yescom

In each case I would specify the group that contains SO3 atoms twice for
the rdf calculation.

Thanks for your help,

Deva
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Re: [gmx-users] RDF com

[Deva Priya]

Thanks a lot, Justin.

On Sat, Oct 17, 2015 at 8:02 AM, Justin Lemkul  wrote:

>
>
> On 10/17/15 5:32 AM, Deva Priya wrote:
>
>> Hello,
>>
>> I am trying to calculate the rdf using the center of mass of a sulfonate
>> group, SO3 with other SO3 groups in the system. The SO3 group is part of a
>> bigger molecule. Is it appropriate to use
>>
>> gmx rdf -rdf mol_com to carry out this operation or  should I use the
>>
>>
> This is correct.
>
> gmx rdf -yescom
>>
>>
> Boolean options are never prefixed with "yes" so you would have gotten an
> obvious fatal error here.
>
> In each case I would specify the group that contains SO3 atoms twice for
>> the rdf calculation.
>>
>>
> Yes.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==
> --
> Gromacs Users mailing list
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> * Please search the archive at
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> posting!
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Re: [gmx-users] Energy minimization error

[faride badalkhani]

Dear gromacs users,

As I said before I faced with the minimization error, so I changed
coordinates of atoms in pdb file, but the problem is the same. the only
thing that changes in every run is atom number. I modified pdb for many
times.

Steepest Descents converged to Fmax < 1000 in 530 steps
Potential Energy  = -5.5180181e+05
Maximum force =  7.4496063e+02 on atom 501
Norm of force =  3.8248455e+01


Moreover gro structure was completely messed up when was visualized in vmd.
you can see the picture of my structure in below dropbox link:

https://www.dropbox.com/s/78v2cvii4gkd8ev/gro.bmp?dl=0
https://www.dropbox.com/s/nyzyu3zmy1vvevg/pdb.bmp?dl=0

and this is the pdb file dropbox link:

https://www.dropbox.com/s/yvxpl2igzi5ccad/120.pdb?dl=0


I used cg algorithm after steep for minimization, too. But it did not work.
is there any way to solve this problem?

any help is appreciated.

On Mon, Oct 5, 2015 at 2:08 PM, Mark Abraham 
wrote:

> Hi,
>
> Look at atom 380 and see why the forces might be high.
>
> Mark
>
> On Mon, Oct 5, 2015 at 10:15 AM faride badalkhani <
> farideh.kham...@gmail.com>
> wrote:
>
> > Thank you for your great help on specbond.dat file. I defined it and I
> > could go ahead until Energy minimization step. I have used this minim.mdp
> > file
> >
> > ; minim.mdp - used as input into grompp to generate em.tpr
> > ; Parameters describing what to do, when to stop and what to save
> > integrator= steep; Algorithm (steep = steepest descent
> > minimization)
> > emtol  = 1000.0  ; Stop minimization when the maximum force <
> > 1000.0 kJ/mol/nm
> > emstep   = 0.01  ; Energy step size
> > nsteps= 5  ; Maximum number of (minimization) steps
> to
> > perform
> >
> > ; Parameters describing how to find the neighbors of each atom and how to
> > calculate the interactions
> > nstlist  = 1; Frequency to update the neighbor list
> and
> > long range forces
> > ns_type   = grid; Method to determine neighbor list
> > (simple, grid)
> > rlist = 1.0; Cut-off for making neighbor list
> > (short range forces)
> > coulombtype= PME; Treatment of long range electrostatic
> > interactions
> > rcoulomb = 1.0; Short-range electrostatic cut-off
> > rvdw   = 1.0; Short-range Van der Waals cut-off
> > pbc = xyz ; Periodic Boundary Conditions (yes/no)
> >
> > But when I run mdrun -v -deffnm em command, I get this error:
> >
> > Energy minimization has stopped, but the forces have not converged to the
> > requested precision Fmax < 1000 (which may not be possible for your
> > system).
> > It stopped because the algorithm tried to make a new step whose size was
> > too
> > small, or there was no change in the energy since last step. Either way,
> we
> > regard the minimization as converged to within the available machine
> > precision, given your starting configuration and EM parameters.
> >
> > Double precision normally gives you higher accuracy, but this is often
> not
> > needed for preparing to run molecular dynamics.
> > You might need to increase your constraint accuracy, or turn
> > off constraints altogether (set constraints = none in mdp file)
> >
> > writing lowest energy coordinates.
> >
> > Steepest Descents converged to machine precision in 90 steps,
> > but did not reach the requested Fmax < 1000.
> > Potential Energy  = -2.3956744e+05
> > Maximum force =  1.5824519e+05 on atom 380
> > Norm of force =  1.7695243e+03
> >
> > gcq#187: "Been There, Done It" (Beavis and Butthead)
> >
> > farideh@farideh-P61A-D3:~/FARIDEH$
> >
> > I changed the emtol, emstep, and nsteps for a few times. However, I
> > couldn't resolve this problem. Could you tell me if there is something
> > wrong with the minim.mdp file?
> >
> > You can see all the files via:
> > https://www.dropbox.com/s/sq2c103yxi4mc28/Farideh.zip?dl=0
> >
> > Truly yours,
> > Farideh
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
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> > send a mail to gmx-users-requ...@gromacs.org.
> >
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Re: [gmx-users] RDF com

[Justin Lemkul]

On 10/17/15 5:32 AM, Deva Priya wrote:

Hello,

I am trying to calculate the rdf using the center of mass of a sulfonate
group, SO3 with other SO3 groups in the system. The SO3 group is part of a
bigger molecule. Is it appropriate to use

gmx rdf -rdf mol_com to carry out this operation or  should I use the



This is correct.


gmx rdf -yescom



Boolean options are never prefixed with "yes" so you would have gotten an 
obvious fatal error here.



In each case I would specify the group that contains SO3 atoms twice for
the rdf calculation.



Yes.

-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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[gmx-users] constraining charges

[gromacs query]

Hi All,

I have some amino-acid residue in which some extra side chain(s) attached
by replacing H from amino-acid. I want to simulate this with CHARMM ff.
Somehow I can choose best bonded params.

But in order to keep integral charge on this modified aminoacid I was
thinking if there is any way to derive charges of the side chain whose
formal charge (net partial charge) be equal and opposite to net charge on
amino-acid with removed Hydrogen. I saw Cgenff is available but it can not
constrain some net charge and some times it does not work because of some
non-acceptable functional groups or bonds.

Please suggest, Thanks


 Jiom
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Re: [gmx-users] Energy minimization error

[Mark Abraham]

Hi,

What some visualization program shows about bonds doesn't mean anything -
it has not parsed your topology. You have no option but to look at the .top
produced and reason about what it shows, but yours is very complex. I
strongly recommend starting with something simpler than a multiply branched
dendrimer. Join two units with a specbond, inspect the .top so that you
know it has what you think it has, and get that to EM and simulation
stably. Then you can get more complex.

Mark

On Sat, Oct 17, 2015 at 3:58 PM faride badalkhani 
wrote:

> Dear gromacs users,
>
> As I said before I faced with the minimization error, so I changed
> coordinates of atoms in pdb file, but the problem is the same. the only
> thing that changes in every run is atom number. I modified pdb for many
> times.
>
> Steepest Descents converged to Fmax < 1000 in 530 steps
> Potential Energy  = -5.5180181e+05
> Maximum force =  7.4496063e+02 on atom 501
> Norm of force =  3.8248455e+01
>
>
> Moreover gro structure was completely messed up when was visualized in vmd.
> you can see the picture of my structure in below dropbox link:
>
> https://www.dropbox.com/s/78v2cvii4gkd8ev/gro.bmp?dl=0
> https://www.dropbox.com/s/nyzyu3zmy1vvevg/pdb.bmp?dl=0
>
> and this is the pdb file dropbox link:
>
> https://www.dropbox.com/s/yvxpl2igzi5ccad/120.pdb?dl=0
>
>
> I used cg algorithm after steep for minimization, too. But it did not work.
> is there any way to solve this problem?
>
> any help is appreciated.
>
> On Mon, Oct 5, 2015 at 2:08 PM, Mark Abraham 
> wrote:
>
> > Hi,
> >
> > Look at atom 380 and see why the forces might be high.
> >
> > Mark
> >
> > On Mon, Oct 5, 2015 at 10:15 AM faride badalkhani <
> > farideh.kham...@gmail.com>
> > wrote:
> >
> > > Thank you for your great help on specbond.dat file. I defined it and I
> > > could go ahead until Energy minimization step. I have used this
> minim.mdp
> > > file
> > >
> > > ; minim.mdp - used as input into grompp to generate em.tpr
> > > ; Parameters describing what to do, when to stop and what to save
> > > integrator= steep; Algorithm (steep = steepest descent
> > > minimization)
> > > emtol  = 1000.0  ; Stop minimization when the maximum
> force <
> > > 1000.0 kJ/mol/nm
> > > emstep   = 0.01  ; Energy step size
> > > nsteps= 5  ; Maximum number of (minimization) steps
> > to
> > > perform
> > >
> > > ; Parameters describing how to find the neighbors of each atom and how
> to
> > > calculate the interactions
> > > nstlist  = 1; Frequency to update the neighbor list
> > and
> > > long range forces
> > > ns_type   = grid; Method to determine neighbor list
> > > (simple, grid)
> > > rlist = 1.0; Cut-off for making neighbor list
> > > (short range forces)
> > > coulombtype= PME; Treatment of long range electrostatic
> > > interactions
> > > rcoulomb = 1.0; Short-range electrostatic cut-off
> > > rvdw   = 1.0; Short-range Van der Waals cut-off
> > > pbc = xyz ; Periodic Boundary Conditions
> (yes/no)
> > >
> > > But when I run mdrun -v -deffnm em command, I get this error:
> > >
> > > Energy minimization has stopped, but the forces have not converged to
> the
> > > requested precision Fmax < 1000 (which may not be possible for your
> > > system).
> > > It stopped because the algorithm tried to make a new step whose size
> was
> > > too
> > > small, or there was no change in the energy since last step. Either
> way,
> > we
> > > regard the minimization as converged to within the available machine
> > > precision, given your starting configuration and EM parameters.
> > >
> > > Double precision normally gives you higher accuracy, but this is often
> > not
> > > needed for preparing to run molecular dynamics.
> > > You might need to increase your constraint accuracy, or turn
> > > off constraints altogether (set constraints = none in mdp file)
> > >
> > > writing lowest energy coordinates.
> > >
> > > Steepest Descents converged to machine precision in 90 steps,
> > > but did not reach the requested Fmax < 1000.
> > > Potential Energy  = -2.3956744e+05
> > > Maximum force =  1.5824519e+05 on atom 380
> > > Norm of force =  1.7695243e+03
> > >
> > > gcq#187: "Been There, Done It" (Beavis and Butthead)
> > >
> > > farideh@farideh-P61A-D3:~/FARIDEH$
> > >
> > > I changed the emtol, emstep, and nsteps for a few times. However, I
> > > couldn't resolve this problem. Could you tell me if there is something
> > > wrong with the minim.mdp file?
> > >
> > > You can see all the files via:
> > > https://www.dropbox.com/s/sq2c103yxi4mc28/Farideh.zip?dl=0
> > >
> > > Truly yours,
> > > Farideh
> > > --
> > > Gromacs Users mailing list
> > >
> > > * Please search the archive at
> > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > >