[gmx-users] Charmm36M neutral C-terminal Proline

[Akshay]

Hello All,

I seem to be having a very particular issue with the Charmm36M force-field
available at http://mackerell.umaryland.edu/charmm_ff.shtml. The issue
occurs when using pdb2gmx's -ter flag and selecting a neutral COOH terminal
when the C-terminal residue is a Proline.

Then, when subsequent grompping, I get the two errors below where both
lines pertain to the Proline backbone CA-C bond.

ERROR 1 [file topol.top, line 493]:
  No default U-B types
ERROR 2 [file topol.top, line 649]:
  No default Proper Dih. types

Anyone else facing this issue or should I raise the issue with the 36M
developers?

Thanks,
Akshay
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[gmx-users] Gromacs to Amber

[Akshay]

Hello Everyone,

I am aware of tools like acpype and amb2gmx that allow the conversion of
Amber files for simulations using Gromacs.
But, I was wondering if anyone has written an equally simple reverse tool
that allows .itp files to be converted for use with tleap/xleap within
Amber?

Thanks,
Akshay
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[gmx-users] Replica Exchange Output control

[Akshay]

Hello Gromacs Users,

I am currently running T-REMD simulations with around 50-60 replicas.
Subsequent to simulations, I mostly use the lowest temperature trajectory
for my analysis. I need a large number of frames for dihedral PCA analysis.
But, outputting multiple xtc files takes up too much memory.

Is there a way for me to have a higher output frequency (
*nstxout-compressed*) for only the xtc file corresponding to the lowest
temperature? Will changing this option only in the low temperature .mdp
file work?

Thanks,
Akshay
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[gmx-users] REMD DLB bug

[Akshay]

Hello All,

I was running REMD simulations on Gromacs 2016.1 when my simulation crashed
with the error

Assertion failed:
Condition: comm->cycl_n[ddCyclStep] > 0
When we turned on DLB, we should have measured cycles

I saw that there was a bug #2298 reported about this recently at
https://redmine.gromacs.org/issues/2298. I wanted to know if this fix has
been implemented in the latest 2018 or 2016.4 versions?

Thanks,
Akshay
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[gmx-users] MDrun -maxh option

[Akshay]

Hello All,

The cluster of my University uses a queuing system with a maximum wall-time
of 12 hours. So, I run mdrun with the option -maxh 11.9 and subsequently
restart the simulation using the output checkpoint files iteratively.
However, the -maxh option has not been killing the jobs when I run replica
exchange jobs across nodes (4 replicas with 2 nodes for each replica (16
cores per node)). I only get an output error with the job scheduler killing
the job at the 12 hour mark.

I would love to have suggestions on how to begin my troubleshooting. Could
it be an installation issue on specific nodes? Or should I reduce the -maxh
value further to allow time for mdrun to write all the checkpoint files?

Thanks,
Akshay
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Re: [gmx-users] Density profile

[Ashutosh Akshay Shah]

Alexander,

For question 1.
-b 500 gives a time average density for 500ps or 0.5ns. If you change it to
5000, it'll show the time average density for 5ns and the graph will be
much smoother.

Regards,
Ashutosh Shah

On Friday, April 29, 2016, Alexander Alexander 
wrote:

> Dear Gromacs user,
>
> My system is a metal surface with thousands of Water molecule on it,
> normally surface(3 nm) is in the bottom of the box and the rest on top is
> water(6 nm). My target is to plot "density profile" of either WATER or OW
> or HW along to Z(Normal distance above solid surface); 5 ns NVT simulation
> applid.
>
> 1. "gmx density" has offered many options, I am not sure which I have to
> choose to do so for this system, so, what is the right command to get this
> density profile:
> Mine is below , would you please improve it? I do not know why mine is
> never like what I see in publications.
>
> gmx density -f nvt.trr -s nvt.tpr -n surf-sol.ndx -d Z -dens number -b 500
> -o HWdens.xvg
>
> 2. What is the "Relative density profile" which I see in some publications
> usually? Relative to what it is?
>
> 3. What is the difference between "radial distribution function" and
> "density profile" especially for such a goal?
>
> Thanks in advance,
> Regards,
> Alex
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Re: [gmx-users] Density as a function of time

[Ashutosh Akshay Shah]

Thanks a ton Justin :)

On Tue, Feb 16, 2016 at 12:23 PM, Justin Lemkul <jalem...@vt.edu> wrote:

>
>
> On 2/16/16 12:22 PM, Ashutosh Akshay Shah wrote:
>
>> Hello Gromacs Users,
>>
>> I want to find the number of ions in a specific part (say left half) of
>> the
>> cell as a function of time.
>>
>> gmx density gives me a time average value across the box (cell), and I
>> know
>> that I can manually find the density for small time steps(0-1,1-2 ns...)
>> and plot the values obtained for the left half of the cell as a function
>> of
>> time, but it would be much easier to do the same with a single command.
>>
>> Any suggestions?
>>
>>
> Use gmx select to find the number of ions that satisfy whatever geometric
> criteria you like.
>
> -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] Density as a function of time

[Ashutosh Akshay Shah]

Hello Gromacs Users,

I want to find the number of ions in a specific part (say left half) of the
cell as a function of time.

gmx density gives me a time average value across the box (cell), and I know
that I can manually find the density for small time steps(0-1,1-2 ns...)
and plot the values obtained for the left half of the cell as a function of
time, but it would be much easier to do the same with a single command.

Any suggestions?

Thanks in advance :)

Best,
Ashutosh Shah
Joint School of Nanoscience and Nanoengineering
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[gmx-users] Optimum slice size (-sl)

[Ashutosh Akshay Shah]

Hello GROMACS users,

What is the optimum slice size when trying to capture as much variation as
possible?

Consider a box with an electrolyte having anions and cations distributed in
it.


*Would be accurate to specify a slice size smaller than the diameter of the
ions while calculating the charge variation across the box?*
Thanks!

Ashutosh Shah
Joint School of Nanoscience and Nanoengineering
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Re: [gmx-users] Optimum slice size (-sl)

[Ashutosh Akshay Shah]

50 slices corresponds to a slice size slightly smaller than the smallest
ions' diameter.

On Sat, Feb 13, 2016 at 4:40 PM, Ashutosh Akshay Shah <as...@aggies.ncat.edu
> wrote:

> Thank you Andre and Warren!
>
> A note about PME-
> The basic principle is that a system of particles is converted into a grid
> (or "mesh") of density values. The potential is then solved for this
> density grid, and forces are applied to each particle based on what cell it
> is in, and where in the cell it lies. - from wikipedia
>
> This is a graph of potential across a box that I am simulating, using
> different number of slices. I have used the PME method in all cases. The
> minimum ion diameter is 0.25 nm. Note that my box is 12 nm in z-direction,
> but only the 3 to 9 nm portion is of significance (rest is vacuum).
>
> http://s21.postimg.org/s75ck7tdj/potentialslicescomparison.png
>
> The graph shows that more the slice size, better the resolution, even for
> PME. (no visible noise at higher slice numbers)
>
> What should I conclude out of this? Higher the number of slices, better?
> Even using PME?
>
> Ashutosh Shah
> Joint School of Nanoscience and Nanoengineering
>
>
>
>
> On Sat, Feb 13, 2016 at 1:56 PM, Warren Gallin <wgal...@ualberta.ca>
> wrote:
>
>> If you are using a slice and PME, then wouldn’t the slice have to be
>> thick enough to avoid any ion interacting with its own image in adjacent
>> slices?
>>
>> It seems to me that thickness would have to be greater than the ionic
>> radius at the very least.
>>
>> Warren Gallin
>>
>> > On Feb 13, 2016, at 8:39 AM, André Farias de Moura <mo...@ufscar.br>
>> wrote:
>> >
>> > the ions may have a radius, but they are distributed continuously along
>> the
>> > system, so you may use slice thicknesses smaller than the ionic radius
>> > you're interested in.
>> >
>> > if the simulation was made on some sort of lattice system (which was
>> very
>> > common back in the 1990's), then the shortest, physically meaningful
>> slice
>> > thickness would be the lattice width. For simulations with freely-moving
>> > species, you should only mind about precision: if thickness is too
>> small,
>> > density profiles may become too noisy, if it is too large you have loose
>> > details of the density profile (maxima, minima, etc), so it's a matter
>> or
>> > trial and error to find out what slice thickness suites you better.
>> >
>> > I hope it helps
>> >
>> > Andre
>> >
>> >
>> > On Sat, Feb 13, 2016 at 11:57 AM, Ashutosh Akshay Shah <
>> > as...@aggies.ncat.edu> wrote:
>> >
>> >> Hello GROMACS users,
>> >>
>> >> What is the optimum slice size when trying to capture as much
>> variation as
>> >> possible?
>> >>
>> >> Consider a box with an electrolyte having anions and cations
>> distributed in
>> >> it.
>> >>
>> >>
>> >> *Would be accurate to specify a slice size smaller than the diameter
>> of the
>> >> ions while calculating the charge variation across the box?*
>> >> Thanks!
>> >>
>> >> Ashutosh Shah
>> >> Joint School of Nanoscience and Nanoengineering
>> >> --
>> >> Gromacs Users mailing list
>> >>
>> >> * Please search the archive at
>> >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> >> posting!
>> >>
>> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>> >>
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>> >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> >> send a mail to gmx-users-requ...@gromacs.org.
>> >>
>> >
>> >
>> >
>> > --
>> > _
>> >
>> > Prof. Dr. André Farias de Moura
>> > Department of Chemistry
>> > Federal University of São Carlos
>> > São Carlos - Brazil
>> > phone: +55-16-3351-8090
>> > --
>> > 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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>> >
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>> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-requ...@gromacs.org.
>>
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>>
>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> posting!
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>>
>
>
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Re: [gmx-users] Optimum slice size (-sl)

[Ashutosh Akshay Shah]

Thank you Andre and Warren!

A note about PME-
The basic principle is that a system of particles is converted into a grid
(or "mesh") of density values. The potential is then solved for this
density grid, and forces are applied to each particle based on what cell it
is in, and where in the cell it lies. - from wikipedia

This is a graph of potential across a box that I am simulating, using
different number of slices. I have used the PME method in all cases. The
minimum ion diameter is 0.25 nm. Note that my box is 12 nm in z-direction,
but only the 3 to 9 nm portion is of significance (rest is vacuum).

http://s21.postimg.org/s75ck7tdj/potentialslicescomparison.png

The graph shows that more the slice size, better the resolution, even for
PME. (no visible noise at higher slice numbers)

What should I conclude out of this? Higher the number of slices, better?
Even using PME?

Ashutosh Shah
Joint School of Nanoscience and Nanoengineering




On Sat, Feb 13, 2016 at 1:56 PM, Warren Gallin <wgal...@ualberta.ca> wrote:

> If you are using a slice and PME, then wouldn’t the slice have to be thick
> enough to avoid any ion interacting with its own image in adjacent slices?
>
> It seems to me that thickness would have to be greater than the ionic
> radius at the very least.
>
> Warren Gallin
>
> > On Feb 13, 2016, at 8:39 AM, André Farias de Moura <mo...@ufscar.br>
> wrote:
> >
> > the ions may have a radius, but they are distributed continuously along
> the
> > system, so you may use slice thicknesses smaller than the ionic radius
> > you're interested in.
> >
> > if the simulation was made on some sort of lattice system (which was very
> > common back in the 1990's), then the shortest, physically meaningful
> slice
> > thickness would be the lattice width. For simulations with freely-moving
> > species, you should only mind about precision: if thickness is too small,
> > density profiles may become too noisy, if it is too large you have loose
> > details of the density profile (maxima, minima, etc), so it's a matter or
> > trial and error to find out what slice thickness suites you better.
> >
> > I hope it helps
> >
> > Andre
> >
> >
> > On Sat, Feb 13, 2016 at 11:57 AM, Ashutosh Akshay Shah <
> > as...@aggies.ncat.edu> wrote:
> >
> >> Hello GROMACS users,
> >>
> >> What is the optimum slice size when trying to capture as much variation
> as
> >> possible?
> >>
> >> Consider a box with an electrolyte having anions and cations
> distributed in
> >> it.
> >>
> >>
> >> *Would be accurate to specify a slice size smaller than the diameter of
> the
> >> ions while calculating the charge variation across the box?*
> >> Thanks!
> >>
> >> Ashutosh Shah
> >> Joint School of Nanoscience and Nanoengineering
> >> --
> >> Gromacs Users mailing list
> >>
> >> * Please search the archive at
> >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> >> posting!
> >>
> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >>
> >> * For (un)subscribe requests visit
> >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> >> send a mail to gmx-users-requ...@gromacs.org.
> >>
> >
> >
> >
> > --
> > _
> >
> > Prof. Dr. André Farias de Moura
> > Department of Chemistry
> > Federal University of São Carlos
> > São Carlos - Brazil
> > phone: +55-16-3351-8090
> > --
> > 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] Facing problem in gromacs installation

[Akshay Bhatnagar]

I have installed the cmake binary from Kitware's webpage but that did not
help, I also tried installing the ubuntu fftw-3 package using the debain
file but that also failed to help.

Earlier, I had installed the fftw, by download it from its wesite : 
http://www.fftw.org/download.html;. After this used the following steps to
install it:

1) ./configure --enable-float
2) make
3) make install
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[gmx-users] Facing problem in gromacs installation

[Akshay Bhatnagar]

I am trying to install gromacs-5.0.5 on my ubuntu based system. But wheni
try the quick installation , it is not able to find the required FFTW files
and gives a message that url is not found.

When i try the long installtion procedure, i have installed FFTW manually
from its website. Now when try to install gromacs using cmake it gives an
error :

 CMake Error at cmake/FindFFTW.cmake:167 (message):
  The FFTW library /usr/local/lib/libfftw3f.a cannot be used with shared
  libraries.  Provide a different FFTW library by setting FFTWF_LIBRARY.  If
  you don't have a different one, recompile FFTW with --enable-shared or
  --with-pic.  Or disable shared libraries for Gromacs by setting
  BUILD_SHARED_LIBS to no. 

I am not able to understand how to proceed now? Please can someone guide me
hoe to install gromacs.



With Regards
Akshay Bhatnagar
PhD Student
BITS Pilani Hyderabad Campus
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[gmx-users] Linking Gamess-US with gromacs

[Akshay Bhatnagar]

I want to perform QM/MM calculations using gromacs and Gamess-US packages.
But from the gromacs website i found that only Gromacs-UK, MOPAC and
Gaussian are in gromacs.

I just want to know, that is there a way to link gromacs with Gamess-US.

Thank you
With Regards
Akshay Bhatnagar
PhD Student
BITS Pilani Hyderabad Campus
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Re: [gmx-users] CUDA fails to allocate memory to mdrun

[Akshay Kumar Ganguly]

That seems to have addressed the problem.
Thanks and regards
Akshay
 


 On Monday, 30 March 2015 11:15 PM, Szilárd Páll pall.szil...@gmail.com 
wrote:
   

 Hi,

You can run with CPU-GPU load balancing disabled (-notunepme), that
should avoid the error. You will likely not loose much performance as
the performance difference between the first two grid settings in the
tuning output seems to be marginal.

Cheers,
--
Szilárd


On Mon, Mar 30, 2015 at 12:31 PM, Akshay Kumar Ganguly
akshaygang...@yahoo.co.in wrote:



 Hi!
 I'm running gromacs v5.0.4 on a 32-bit CentOS 6.5 OS with CUDA toolkit v4.0 
 and the latest nvidia linux driver (v340.24) for a Quadro K4200.

 My explicit solvent runs crash during pme grid optimization citing the 
 following error -

   
 - 
  

 There are: 75766 Atoms
 Initial temperature: 301.154 K

 Started mdrun on rank 0 Mon Mar 30 14:30:54 2015
            Step          Time        Lambda
              0        0.0        0.0

    Energies (kJ/mol)
          Angle    Proper Dih.  Improper Dih.          LJ-14    Coulomb-14
    6.92142e+03    9.29820e+03    3.90420e+02    3.61267e+03    4.01187e+04
        LJ (SR)  Disper. corr.  Coulomb (SR)  Coul. recip. Position Rest.
    2.14594e+05  -9.79483e+03  -1.47636e+06    6.97759e+03    2.17547e-01
      Potential    Kinetic En.  Total Energy    Temperature Pres. DC (bar)
    -1.20424e+06    1.89766e+05  -1.01448e+06    3.01035e+02  -2.11354e+02
  Pressure (bar)  Constr. rmsd
    -4.75277e+02    2.75540e-05

 step  80: timed with pme grid 60 60 60, coulomb cutoff 1.000: 3398.8 M-cycles
            Step          Time        Lambda
            100        0.2        0.0

    Energies (kJ/mol)
          Angle    Proper Dih.  Improper Dih.          LJ-14    Coulomb-14
    7.24215e+03    9.27752e+03    4.13476e+02    3.61128e+03    4.00927e+04
        LJ (SR)  Disper. corr.  Coulomb (SR)  Coul. recip. Position Rest.
    2.17175e+05  -9.83595e+03  -1.47626e+06    4.92524e+03    8.51347e+02
      Potential    Kinetic En.  Total Energy    Temperature Pres. DC (bar)
    -1.20251e+06    1.87791e+05  -1.01472e+06    2.97902e+02  -2.13130e+02
  Pressure (bar)  Constr. rmsd
    -2.43339e+02    2.65826e-05

 step  160: timed with pme grid 52 52 52, coulomb cutoff 1.102: 3359.8 M-cycles

 ---
 Program mdrun, VERSION 5.0.4
 Source code file: 
 /nmr/gromacs-5.0.4/src/gromacs/gmxlib/cuda_tools/pmalloc_cuda.cu, line: 61

 Fatal error:
 cudaMallocHost of size 2851616 bytes failed: out of memory

 For more information and tips for troubleshooting, please check the GROMACS
 website at http://www.gromacs.org/Documentation/Errors
 

 The size of the failed allocation varies from error to error but it generally 
 ranges from 2.5 to 5 mB.
 While it is likely that the newer toolkits(v5-7) have resolved this issue, I 
 am unable to use them since they lack support for 32-bit OSs.

 I would be obliged if you could suggest a way to free up some page-linked 
 memory (at least that's what google says the problem is but I'm still all at 
 sea as far as the solution goes) for mdrun and/or provide a patch for 
 pmalloc_cuda.cu.
  The problem looks to be limited to complex systems [(large proteins (150 
residues) in explicit water (~25000 molecules) cubes] as I am able to run 
smaller ones (~100 residues) with ease in explicit solvent using the GPU for 
non-bonded calculations (mdrun -v -deffnm $prot_md -nb gpu).

 I have attached herewith the corresponding log file and mdp.

 Regards,

  Akshay Kumar Ganguly

 Graduate Student,Dr. Neel S. Bhavesh lab,
 Structural and Computational Biology Group,
 International Centre for Genetic Engineering and Biotechnology,
 New Delhi - 67



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Re: [gmx-users] CUDA fails to allocate memory to mdrun

[Akshay Kumar Ganguly]

 

Hi!
I'm running gromacs v5.0.4 on a 32-bit CentOS 6.5 OS with CUDA toolkit v4.0 and 
the latest nvidia linux driver (v340.24) for a Quadro K4200.

My explicit solvent runs crash during pme grid optimization citing the 
following error - 

  
- 
 

There are: 75766 Atoms
Initial temperature: 301.154 K

Started mdrun on rank 0 Mon Mar 30 14:30:54 2015
   Step   Time Lambda
  0    0.0    0.0

   Energies (kJ/mol)
  Angle    Proper Dih.  Improper Dih.  LJ-14 Coulomb-14
    6.92142e+03    9.29820e+03    3.90420e+02    3.61267e+03    4.01187e+04
    LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip. Position Rest.
    2.14594e+05   -9.79483e+03   -1.47636e+06    6.97759e+03    2.17547e-01
  Potential    Kinetic En.   Total Energy    Temperature Pres. DC (bar)
   -1.20424e+06    1.89766e+05   -1.01448e+06    3.01035e+02   -2.11354e+02
 Pressure (bar)   Constr. rmsd
   -4.75277e+02    2.75540e-05

step   80: timed with pme grid 60 60 60, coulomb cutoff 1.000: 3398.8 M-cycles
   Step   Time Lambda
    100    0.2    0.0

   Energies (kJ/mol)
  Angle    Proper Dih.  Improper Dih.  LJ-14 Coulomb-14
    7.24215e+03    9.27752e+03    4.13476e+02    3.61128e+03    4.00927e+04
    LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip. Position Rest.
    2.17175e+05   -9.83595e+03   -1.47626e+06    4.92524e+03    8.51347e+02
  Potential    Kinetic En.   Total Energy    Temperature Pres. DC (bar)
   -1.20251e+06    1.87791e+05   -1.01472e+06    2.97902e+02   -2.13130e+02
 Pressure (bar)   Constr. rmsd
   -2.43339e+02    2.65826e-05

step  160: timed with pme grid 52 52 52, coulomb cutoff 1.102: 3359.8 M-cycles

---
Program mdrun, VERSION 5.0.4
Source code file: 
/nmr/gromacs-5.0.4/src/gromacs/gmxlib/cuda_tools/pmalloc_cuda.cu, line: 61

Fatal error:
cudaMallocHost of size 2851616 bytes failed: out of memory

For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors


The size of the failed allocation varies from error to error but it generally 
ranges from 2.5 to 5 mB.
While it is likely that the newer toolkits(v5-7) have resolved this issue, I am 
unable to use them since they lack support for 32-bit OSs. 

I would be obliged if you could suggest a way to free up some page-linked 
memory (at least that's what google says the problem is but I'm still all at 
sea as far as the solution goes) for mdrun and/or provide a patch for 
pmalloc_cuda.cu. 
 The problem looks to be limited to complex systems [(large proteins (150 
residues) in explicit water (~25000 molecules) cubes] as I am able to run 
smaller ones (~100 residues) with ease in explicit solvent using the GPU for 
non-bonded calculations (mdrun -v -deffnm $prot_md -nb gpu).

I have attached herewith the corresponding log file and mdp.

Regards,
 
 Akshay Kumar Ganguly

Graduate Student,Dr. Neel S. Bhavesh lab,
Structural and Computational Biology Group,
International Centre for Genetic Engineering and Biotechnology,
New Delhi - 67


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mail to gmx-users-requ...@gromacs.org.

[gmx-users] Reg: topology and parameter files for dichlormethane

[Akshay Bhatnagar]

Hello

I want to simulate an amino acid in dichloromethane as solvent. can anyone
provide me with the topology and parameter files for dichloromethane.

With Regards
Akshay Bhatnagar
PhD Student
BITS Pilani Hyderabad Campus
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