date:20170802

When generating dihedrals, x2top sets the function to '1'. I recall 
there was a way to change that (to 3 in my case) and it worked in 
modified OPLS-AA. I am working with a different FF now and for the life 
of me cannot recall I changed that in OPLS. I could also be wrong and it 
just sets it to '3' by default in OPLS, since all dihedrals are of type 
3 in that forcefield. At any rate, i get 1 and want 3.


Any help?

Thanks,

Alex

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Re: [gmx-users] membrane-protein simulation

2017-08-02 Thread Amir Zeb

Thanks Justin

Got it, it's working.

On Wed, Aug 2, 2017 at 10:02 AM, Justin Lemkul  wrote:

>
>
> On 8/2/17 5:01 AM, Amir Zeb wrote:
>
>> Hello gmx-user
>>
>> I want to simulate a membrane protein with more than one chains like A, B,
>> C etc. I generated the strong_posre.itp  file as Justing has kindly
>> explained in his tutorial, and updated the topol.top file by inserting the
>> same lines. I also updated the minim.mdp file by inserting STRONG_POSRES.
>> Once I tried the minimization of the system before the shrinking step, I
>> got the error as below:
>>
>> Fatal error:
>> [ file strong_posre.itp, line 548 ]:
>> Atom index (544) in position_restraints out of bounds (1-543).
>> This probably means that you have inserted topology section
>> "position_restraints"
>> in a part belonging to a different molecule than you intended to.
>> In that case move the "position_restraints" section to the right molecule.
>> For more information and tips for troubleshooting, please check the
>> GROMACS
>> website at http://www.gromacs.org/Documentation/Errors
>>
>>
>> I tried so many options but could not fix the issue. Please keep in view
>> that the same procedure is working well with a single chain of the
>> protein.
>> Kindly help me how to fix this issue?
>>
>>
> You need to create restraint files for each chain separately and include
> them in each [moleculetype] separately, as explained here:
>
> http://www.gromacs.org/Documentation/Errors#Atom_index_n_in_
> position_restraints_out_of_bounds
>
> -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 http://www.gromacs.org/Support
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Re: [gmx-users] AVX related compiler error during build with P100 RHEL7

Hi,

Usually this means, like it says, that the linker isn't able to do the
required job. I don't know whether the stock RHEL 7.2 linker can, but I
imagine that's the issue. Usually using a devtoolset e.g.
https://www.softwarecollections.org/en/scls/rhscl/devtoolset-4/ is the way
to get a machine with useful tools on it rather than one with "stable" =
"old" tools, particularly when you want to use the latest hardware...

Mark

On Thu, Aug 3, 2017 at 1:28 AM Guyen Gn  wrote:

> Any update on this one??
>
> On Fri, Jul 14, 2017 at 1:30 PM, Guyen Gn  wrote:
>
> > Any ideas on this one? Thanks!
> >
> > On Mon, Jul 3, 2017 at 9:33 PM, Guyen Gn  wrote:
> >
> >> Still did not work. change xMIC to xCore and log is below (if it was
> >> other way around, then originally it must have not worked).
> >> Script file is all oneline.
> >>
> >> -- Performing Test C_xCORE_AVX512_FLAG_WORKS
> >> -- Performing Test C_xCORE_AVX512_FLAG_WORKS - Failed
> >> -- Performing Test C_mavx512f_mfma_FLAG_WORKS
> >> -- Performing Test C_mavx512f_mfma_FLAG_WORKS - Failed
> >> -- Performing Test C_mavx512f_FLAG_WORKS
> >> -- Performing Test C_mavx512f_FLAG_WORKS - Failed
> >> -- Performing Test C_arch_AVX_FLAG_WORKS
> >> -- Performing Test C_arch_AVX_FLAG_WORKS - Failed
> >> -- Performing Test C_hgnu_FLAG_WORKS
> >> -- Performing Test C_hgnu_FLAG_WORKS - Failed
> >> -- Performing Test C_FLAG_WORKS
> >> -- Performing Test C_FLAG_WORKS - Success
> >> -- Performing Test C_COMPILE_WORKS
> >> -- Performing Test C_COMPILE_WORKS - Failed
> >> -- Compiler flag was valid, but executable did not build - perhaps
> update
> >> the binutils package
> >> -- Performing Test CXX_xCORE_AVX512_FLAG_WORKS
> >> -- Performing Test CXX_xCORE_AVX512_FLAG_WORKS - Failed
> >> -- Performing Test CXX_mavx512f_mfma_FLAG_WORKS
> >> -- Performing Test CXX_mavx512f_mfma_FLAG_WORKS - Failed
> >> -- Performing Test CXX_mavx512f_FLAG_WORKS
> >> -- Performing Test CXX_mavx512f_FLAG_WORKS - Failed
> >> -- Performing Test CXX_arch_AVX_FLAG_WORKS
> >> -- Performing Test CXX_arch_AVX_FLAG_WORKS - Failed
> >> -- Performing Test CXX_hgnu_FLAG_WORKS
> >> -- Performing Test CXX_hgnu_FLAG_WORKS - Failed
> >> -- Performing Test CXX_FLAG_WORKS
> >> -- Performing Test CXX_FLAG_WORKS - Success
> >> -- Performing Test CXX_COMPILE_WORKS
> >> -- Performing Test CXX_COMPILE_WORKS - Failed
> >> -- Compiler flag was valid, but executable did not build - perhaps
> update
> >> the binutils package
> >> CMake Error at cmake/gmxManageSimd.cmake:92 (message):
> >>   Found a compiler flag for AVX 512F support, but some other problem
> >> exists.
> >>   Update your assembler and/or linker, e.g.  in the binutils package of
> >> your
> >>   distribution.
> >> Call Stack (most recent call first):
> >>   cmake/gmxManageSimd.cmake:314 (gmx_give_fatal_error_when_sim
> >> d_support_not_found)
> >>   CMakeLists.txt:666 (gmx_manage_simd)
> >>
> >>
> >> -- Configuring incomplete, errors occurred!
> >>
> >>
> >> On Mon, Jul 3, 2017 at 2:44 PM, Mark Abraham 
> >> wrote:
> >>
> >>> Hi,
> >>>
> >>> On Mon, Jul 3, 2017 at 10:50 PM Guyen Gn  wrote:
> >>>
> >>> > Sorry for long wait on response, basically i followed the instruction
> >>> at
> >>> > nvidia website:
> >>> >
> >>> > http://www.nvidia.com/object/gromacs-installation.html
> >>> >
> >>> > I instaled GPU driver versoin 369, as well as CUDA, gcc, cmake. After
> >>> that
> >>> > it tells to run following:
> >>> >
> >>> > CC=gcc CXX=g++ cmake  -DGMX_OPENMP=ON -DGMX_GPU=ON -
> >>> > DGPU_DEPLOYMENT_KIT_ROOT_DIR= -DGMX_BUILD_OWN_FFTW=ON -
> >>> > DGMX_PREFER_STATIC_LIBS=ON -DCMAKE_BUILD_TYPE=Release -
> >>> > DCMAKE_INSTALL_PREFIX=
> >>> >
> >>> > I tweaked as follows to fit my environment I setup (basically just
> >>> > installation source and run directory:
> >>> > CC=gcc CXX=g++ cmake /root/gromacs/gromacs-2016 -DGMX_OPENMP=ON
> >>> > -DGMX_GPU=ON -DGPU_DEPLOYMENT_KIT_ROOT_DIR=/usr/local/cuda
> >>> > -DGMX_BUILD_OWN_FFTW=ON -DGMX_PREFER_STATIC_LIBS=ON
> >>> > -DCMAKE_BUILD_TYPE=Release
> >>> > -DCMAKE_INSTALL_PREFIX=/root/gromacs/gromacs-2016-run inside build.sh
> >>> shell
> >>> > script.
> >>> >
> >>> > This is the full log, I highlighted toward the end section of code
> >>> where it
> >>> > started to fail. It appears something related to AVX. Thanks.,
> >>> >
> >>> > [root@localhost gromacs-2016]# ./build.sh
> >>> > CMake Error: The source directory "/root/gromacs/gromacs-2016/-" does
> >>> not
> >>> > exist.
> >>> > Specify --help for usage, or press the help button on the CMake GUI.
> >>> > ./build.sh: line 2: -DGMX_BUILD_OWN_FFTW=ON: command not found
> >>> > ./build.sh: line 3: -DCMAKE_BUILD_TYPE=Release: command not found
> >>> >
> >>>
> >>> All the above is because your script needed editing to handle newlines
> >>> from
> >>> your copy-paste.
> >>>
> >>>
> >>> > [root@localhost gromacs-2016]# nano -w build.sh
> >>> > [root@localhost

Re: [gmx-users] AVX related compiler error during build with P100 RHEL7

2017-08-02 Thread Guyen Gn

Any update on this one??

On Fri, Jul 14, 2017 at 1:30 PM, Guyen Gn  wrote:

> Any ideas on this one? Thanks!
>
> On Mon, Jul 3, 2017 at 9:33 PM, Guyen Gn  wrote:
>
>> Still did not work. change xMIC to xCore and log is below (if it was
>> other way around, then originally it must have not worked).
>> Script file is all oneline.
>>
>> -- Performing Test C_xCORE_AVX512_FLAG_WORKS
>> -- Performing Test C_xCORE_AVX512_FLAG_WORKS - Failed
>> -- Performing Test C_mavx512f_mfma_FLAG_WORKS
>> -- Performing Test C_mavx512f_mfma_FLAG_WORKS - Failed
>> -- Performing Test C_mavx512f_FLAG_WORKS
>> -- Performing Test C_mavx512f_FLAG_WORKS - Failed
>> -- Performing Test C_arch_AVX_FLAG_WORKS
>> -- Performing Test C_arch_AVX_FLAG_WORKS - Failed
>> -- Performing Test C_hgnu_FLAG_WORKS
>> -- Performing Test C_hgnu_FLAG_WORKS - Failed
>> -- Performing Test C_FLAG_WORKS
>> -- Performing Test C_FLAG_WORKS - Success
>> -- Performing Test C_COMPILE_WORKS
>> -- Performing Test C_COMPILE_WORKS - Failed
>> -- Compiler flag was valid, but executable did not build - perhaps update
>> the binutils package
>> -- Performing Test CXX_xCORE_AVX512_FLAG_WORKS
>> -- Performing Test CXX_xCORE_AVX512_FLAG_WORKS - Failed
>> -- Performing Test CXX_mavx512f_mfma_FLAG_WORKS
>> -- Performing Test CXX_mavx512f_mfma_FLAG_WORKS - Failed
>> -- Performing Test CXX_mavx512f_FLAG_WORKS
>> -- Performing Test CXX_mavx512f_FLAG_WORKS - Failed
>> -- Performing Test CXX_arch_AVX_FLAG_WORKS
>> -- Performing Test CXX_arch_AVX_FLAG_WORKS - Failed
>> -- Performing Test CXX_hgnu_FLAG_WORKS
>> -- Performing Test CXX_hgnu_FLAG_WORKS - Failed
>> -- Performing Test CXX_FLAG_WORKS
>> -- Performing Test CXX_FLAG_WORKS - Success
>> -- Performing Test CXX_COMPILE_WORKS
>> -- Performing Test CXX_COMPILE_WORKS - Failed
>> -- Compiler flag was valid, but executable did not build - perhaps update
>> the binutils package
>> CMake Error at cmake/gmxManageSimd.cmake:92 (message):
>>   Found a compiler flag for AVX 512F support, but some other problem
>> exists.
>>   Update your assembler and/or linker, e.g.  in the binutils package of
>> your
>>   distribution.
>> Call Stack (most recent call first):
>>   cmake/gmxManageSimd.cmake:314 (gmx_give_fatal_error_when_sim
>> d_support_not_found)
>>   CMakeLists.txt:666 (gmx_manage_simd)
>>
>>
>> -- Configuring incomplete, errors occurred!
>>
>>
>> On Mon, Jul 3, 2017 at 2:44 PM, Mark Abraham 
>> wrote:
>>
>>> Hi,
>>>
>>> On Mon, Jul 3, 2017 at 10:50 PM Guyen Gn  wrote:
>>>
>>> > Sorry for long wait on response, basically i followed the instruction
>>> at
>>> > nvidia website:
>>> >
>>> > http://www.nvidia.com/object/gromacs-installation.html
>>> >
>>> > I instaled GPU driver versoin 369, as well as CUDA, gcc, cmake. After
>>> that
>>> > it tells to run following:
>>> >
>>> > CC=gcc CXX=g++ cmake  -DGMX_OPENMP=ON -DGMX_GPU=ON -
>>> > DGPU_DEPLOYMENT_KIT_ROOT_DIR= -DGMX_BUILD_OWN_FFTW=ON -
>>> > DGMX_PREFER_STATIC_LIBS=ON -DCMAKE_BUILD_TYPE=Release -
>>> > DCMAKE_INSTALL_PREFIX=
>>> >
>>> > I tweaked as follows to fit my environment I setup (basically just
>>> > installation source and run directory:
>>> > CC=gcc CXX=g++ cmake /root/gromacs/gromacs-2016 -DGMX_OPENMP=ON
>>> > -DGMX_GPU=ON -DGPU_DEPLOYMENT_KIT_ROOT_DIR=/usr/local/cuda
>>> > -DGMX_BUILD_OWN_FFTW=ON -DGMX_PREFER_STATIC_LIBS=ON
>>> > -DCMAKE_BUILD_TYPE=Release
>>> > -DCMAKE_INSTALL_PREFIX=/root/gromacs/gromacs-2016-run inside build.sh
>>> shell
>>> > script.
>>> >
>>> > This is the full log, I highlighted toward the end section of code
>>> where it
>>> > started to fail. It appears something related to AVX. Thanks.,
>>> >
>>> > [root@localhost gromacs-2016]# ./build.sh
>>> > CMake Error: The source directory "/root/gromacs/gromacs-2016/-" does
>>> not
>>> > exist.
>>> > Specify --help for usage, or press the help button on the CMake GUI.
>>> > ./build.sh: line 2: -DGMX_BUILD_OWN_FFTW=ON: command not found
>>> > ./build.sh: line 3: -DCMAKE_BUILD_TYPE=Release: command not found
>>> >
>>>
>>> All the above is because your script needed editing to handle newlines
>>> from
>>> your copy-paste.
>>>
>>>
>>> > [root@localhost gromacs-2016]# nano -w build.sh
>>> > [root@localhost gromacs-2016]# pwd
>>> > /root/gromacs/gromacs-2016
>>> > [root@localhost gromacs-2016]# mkdir ~/gromacs/gromacs-run
>>> > [root@localhost gromacs-2016]# ./build.sh
>>> > -- The C compiler identification is GNU 4.8.5
>>> > -- The CXX compiler identification is GNU 4.8.5
>>> > -- Check for working C compiler: /usr/bin/gcc
>>> > -- Check for working C compiler: /usr/bin/gcc -- works
>>> > -- Detecting C compiler ABI info
>>> > -- Detecting C compiler ABI info - done
>>> > -- Check for working CXX compiler: /usr/bin/g++
>>> > -- Check for working CXX compiler: /usr/bin/g++ -- works
>>> > -- Detecting CXX compiler ABI info
>>> > -- Detecting CXX compiler ABI info - done
>>> > -- Performing Test CXXFLAG_STD_CXX0X
>>> > --

Re: [gmx-users] CHARMM36 for GMX

That's true, a lot of redundant stuff there and once again these are very
basic forcefield facts for what biochem folks do. In my case, I have a
bunch of very simple situations in crystal structures, but now I gotta use
CHARMM or AMBER (lipids!) and charge assignment (half the time perfectly
applicable to organic chemistry, yet entirely untouched in this field) in
those simple situations becomes a challenge, especially when they control
critical physics in the system. All in all, I hate reading detailed FF
documentation. However, so as not to post questions like a good 90% of what
we see on this board, I'm pretty sure I'll have to with CHARMM. I will do
my best not to contribute to the whole "please do my job for me" effort
here. :) As I told Mark, it is the developers' fault -- people use the
incorrect tool just because it is a great piece of software. Take it as a
compliment.

As always, thanks.

Alex

On Wed, Aug 2, 2017 at 12:59 PM, Justin Lemkul  wrote:

>
>
> On 8/2/17 2:52 PM, Alex wrote:
>
>> Yeah, those are indeed there for the particular molecules, thanks. I
>> understand that this is the only way to go, it's just that my use of GMX
>> is
>> somewhat different in that I rarely use molecules in the normal sense, and
>> OPLS-AA, being a LEGO for simple groups, has been very convenient with
>> that
>> catalog you mentioned. Like, place a carboxyl termination somewhere, or
>> have a hole in a bulk sheet of graphene, etc.
>>
>>
> All additive force fields are constructed in the same way, from building
> blocks.  It's just that OPLS-AA uses a huge amount of (redundant in many
> cases) atom types and can be mapped to different charges based on different
> situations. It's also why OPLS-AA has separate bonded and nonbonded atom
> types.  There is greater diversity among nonbonded types but fewer bonded
> types, reducing the dimensionality of the internal parameters rather than
> having huge amounts of duplicated bonded parameters for types that really
> aren't different.
>
>
> -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
>
> * 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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[gmx-users] segmentation fault for unknown reason

2017-08-02 Thread gangotri dey

Hello!

I am trying to minimize a periodic MnO2 surface using UFF force fields. I
have previously computed many structures using MnO2 clusters. I did not
face much problem.

However, when I am trying to compute the minimization using the following
minim.mdp there is segmentation error as follows.

; minim.mdp - used as input into grompp to generate em.tpr
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 = 50; Frequency to update the
neighbor list and long range forces
cutoff-scheme   = Verlet
ns_type = grid  ; Method to determine neighbor list
(simple, grid)
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)


Error:

Steepest Descents:
   Tolerance (Fmax)   =  1.0e+03
   Number of steps=5
Step=0, Dmax= 1.0e-02 nm, Epot=  3.46301e+34 Fmax= 2.91045e+06, atom=
289
[fen2.hpcc.rutgers.edu:mpi_rank_0][error_sighandler] Caught error:
Segmentation fault (signal 11)
./script: line 5: 54036 Segmentation fault  (core dumped) gmx_mpi mdrun
-ntomp 1 -v -deffnm em

I do not understand this problem. Is there anything wrong with my structure
or the minim.mdp?



*Thank you*

*Gangotri Dey*
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Re: [gmx-users] CHARMM36 for GMX




On 8/2/17 2:52 PM, Alex wrote:

Yeah, those are indeed there for the particular molecules, thanks. I
understand that this is the only way to go, it's just that my use of GMX is
somewhat different in that I rarely use molecules in the normal sense, and
OPLS-AA, being a LEGO for simple groups, has been very convenient with that
catalog you mentioned. Like, place a carboxyl termination somewhere, or
have a hole in a bulk sheet of graphene, etc.



All additive force fields are constructed in the same way, from building blocks. 
 It's just that OPLS-AA uses a huge amount of (redundant in many cases) atom 
types and can be mapped to different charges based on different situations. 
It's also why OPLS-AA has separate bonded and nonbonded atom types.  There is 
greater diversity among nonbonded types but fewer bonded types, reducing the 
dimensionality of the internal parameters rather than having huge amounts of 
duplicated bonded parameters for types that really aren't different.


-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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Re: [gmx-users] CHARMM36 for GMX

Yeah, those are indeed there for the particular molecules, thanks. I
understand that this is the only way to go, it's just that my use of GMX is
somewhat different in that I rarely use molecules in the normal sense, and
OPLS-AA, being a LEGO for simple groups, has been very convenient with that
catalog you mentioned. Like, place a carboxyl termination somewhere, or
have a hole in a bulk sheet of graphene, etc.

In any case, thank you.

Alex

On Wed, Aug 2, 2017 at 12:41 PM, Justin Lemkul  wrote:

>
>
> On 8/2/17 2:38 PM, Alex wrote:
>
>> Huh. Most of my work has been with OPLS-AA, so I took that for granted.
>> Where would the actual charges be, then?
>>
>>
> In the .rtp file, where residues are defined.  Charges are not (and should
> not) necessarily be linked to atom types; they are a function of
> parametrized groups or molecules.
>
>
> -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
>
> * 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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> send a mail to gmx-users-requ...@gromacs.org.
>
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Re: [gmx-users] CHARMM36 for GMX




On 8/2/17 2:38 PM, Alex wrote:

Huh. Most of my work has been with OPLS-AA, so I took that for granted.
Where would the actual charges be, then?



In the .rtp file, where residues are defined.  Charges are not (and should not) 
necessarily be linked to atom types; they are a function of parametrized groups 
or molecules.


-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] CHARMM36 for GMX

Hi all,

I am not entirely sure it's a question for the Gromacs community, as this
is regarding CHARMM36, but it appears that the original forcefield is fine,
while I am confused by its Gromacs version.

Namely this: the MacKerell website distributes a Gromacs version of
CHARMM36 where ffnonbonded.itp has pretty much all default charges set to
zero. Is this called for??

I apologize in advance if this is a dumb or misdirected question, as I've
never worked with CHARMM before.

Thank you,

Alex
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Re: [gmx-users] G_MMPBSA

2017-08-02 Thread Suhaib Shekfeh

Did you try the pre-compiled version from here:

http://rashmikumari.github.io/g_mmpbsa/Download-and-Installation.html

it worked just fine with me on debian and CentOS. Offcourse you need to
have APBS installed.



On Thu, Jul 27, 2017 at 7:04 PM, Mark Abraham 
wrote:

> Hi,
>
> You should start by reading and following the installation guide of this
> non-GROMACS tool. If you have questions, asking on its forum is probably
> best ;-) And please do provide some detail and what you did and where it
> went wrong.
>
> Mark
>
> On Thu, 27 Jul 2017 18:14 S M Bargeen Turzo 
> wrote:
>
> > Hi all,
> >
> > I am trying to install g_mmpbsa gromacs package(
> > http://rashmikumari.github.io/g_mmpbsa/) but it's not working. Can
> anyone
> > please guide me through the installation process of this package?
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Re: [gmx-users] QM/MM in Gromacs-5.1.4?

2017-08-02 Thread Clinton King

Follow the instructions at http://wwwuser.gwdg.de/~ggroenh/qmmm.html

Also, you need to set the following variable at compile time
-DGMX_QMMM_ORCA=ON

--
Clinton King
Graduate Student
Chemistry Department
Brigham Young University


> Message: 3
> Date: Wed, 2 Aug 2017 15:01:29 +0200
> From: Albert 
> To: gmx-us...@gromacs.org
> Subject: [gmx-users] QM/MM in Gromacs-5.1.4?
> Message-ID: <798bdbd3-6055-79fa-46aa-361cbe067...@gmail.com>
> Content-Type: text/plain; charset=utf-8; format=flowed
>
> Hello,
>
> I would like to use ORCA as a QM engine for Gromacs QM/MM simulation. I
> am just wondering shall we add additional options to cmake when we
> compile Gromacs?
>
> Thanks a lot
>
> Albert
>
>
>
>
>
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Re: [gmx-users] -multidir option in REMD (GROMACS v2016.1) -resolved

2017-08-02 Thread ABEL Stephane

THank you Mark and Johannes, 

I finally resolved my problem by using your solutions and can launch my REMD 
simulations 

Best

Stéphane

--

Message: 1
Date: Wed, 02 Aug 2017 10:59:10 +
From: Mark Abraham 
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] -multidir option in REMD (GROMACS v2016.1)
Message-ID:

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

Hi,

On Wed, Aug 2, 2017 at 11:22 AM ABEL Stephane  wrote:

> Dear all,
>
> I would like to do a REMD of a system with 75 replicas (with 75
> directories named md_0,..., md_75) and I have two questions.
>
> 1) To launch the md calculation we should use the followng command :
>
> mpirun -np 4 mdrun_mpi -v -multidir sim[0123] -replex XXX
>
> My question is since I have 75 replicas (directories). How I should set
> the argument of -multidir ? Like this : -multidir md_[01234...75] or only
> "md_".
>

The -multidir option needs a list of all your directories. The best way to
do that is with shell (e.g. wildcard) expansion. Just using "md_" doesn't
get expanded by anything. I recently observed someone suggest that
"md_{0..75}" might do what you want, but I've never tried it. Anyway, md_*
will expand them all, and IIRC mdrun will sort out the ordering from the
values of the REMD control parameter.

> I have used the following command : mdrun_mpi -v -multidir
> ./"$Stage1_FileName"/md_ -replex 500, but the program stops with the
> following error : Need at least two replicas for replica exchange (option
> -multi)
>

Since there's only one directory named, because the shell couldn't expand
anything for you, mdrun doesn't know how to proceed. Pro tip - get it
working for a small number of replicas (e.g. 2) before worrying about using
all 75.

> 2) Second question It is not clear to me how I should set the number of
> step in the mdp file of each replica use in the production runs.  For
> instance I want to do a simulation of 50 ns, should I set nsteps =
> 500/75
>

Each simulation is independent and every e.g. mdp parameter is particular
to it. So choose your number of steps in each mdp file to be the length of
a single replica. Obviously nsteps * dt = time in the usual way, but since
we don't know dt, you'll have to compute your nsteps ;-)

Mark

Could you help me ?
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Re: [gmx-users] Clayff forcefield




On 8/2/17 5:20 AM, G R wrote:

  I try to implement CLYFF in gromacs. I created ffbonded.itp,
 ffnonbonded.itp, atomtype.atp, forcefield.doc, forcefield.itp and
 molecule.rtp. I want  to simulate Kaolinite, and I try to use pdb2gmx to
 create a topology. My first question is that should I create any other
 files? second, In molecule.rtp, I just write the atom type, atom name
and
 charges. should I add bonds for each atom? Also, in rtp file, I don't
know
 what should I write as a residue?


For a system like you're dealing with, pdb2gmx is not the correct approach.  Try 
x2top with a suitable .n2t file (which you'll have to create).


-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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Re: [gmx-users] LINCS warning during energy minimization of nitrogen with virtual site




On 8/2/17 9:12 AM, Ali Ahmed wrote:

Dear all,
Thank you for helping me. All I get from grompp is this
--

gmx grompp -f grompp.mdp -c N2_box.gro -po mdout.mdp -p topol.top -o
topol.tpr

Ignoring obsolete mdp entry 'title'
Ignoring obsolete mdp entry 'cpp'

Back Off! I just backed up mdout.mdp to ./#mdout.mdp.2#

NOTE 1 [file grompp.mdp]:
   The group cutoff scheme is deprecated since GROMACS 5.0 and will be
   removed in a future release when all interaction forms are supported for
   the verlet scheme. The verlet scheme already scales better, and it is
   compatible with GPUs and other accelerators.

Setting the LD random seed to 1000542586
Generated 120 of the 120 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 120 of the 120 1-4 parameter combinations
Excluding 2 bonded neighbours molecule type 'N_2'
Cleaning up constraints and constant bonded interactions with virtual sites
Analysing residue names:
There are:  2493  Other residues


Simplify your system - work with one molecule and print out the forces at each 
step to see if there is something haywire going on.


-Justin


Analysing residues not classified as Protein/DNA/RNA/Water and splitting
into groups...
Number of degrees of freedom in T-Coupling group System is 12462.00

NOTE 2 [file grompp.mdp]:
   You are using a plain Coulomb cut-off, which might produce artifacts.
   You might want to consider using PME electrostatics.


Largest charge group radii for Van der Waals: 0.056, 0.056 nm
Largest charge group radii for Coulomb:   0.056, 0.056 nm
This run will generate roughly 90 Mb of data

There were 2 notes

Back Off! I just backed up topol.tpr to ./#topol.tpr.1#

gcq#454: "I never see what has been done; I only see what remains to be
done." (Marie Curie)


On Tue, Aug 1, 2017 at 5:08 PM, Justin Lemkul  wrote:




On 8/1/17 6:07 PM, Ali Ahmed wrote:


Dear Dr. Dallas,
Thank you for your reply. Actually, I'm new to GROMACS and
I appreciate your support.


--
Here is what I get before crashing. Too many warning then crush.



This is not diagnostic of anything useful.  You've been asked several
times to provide the output of grompp, not mdrun.  The grompp output can be
suggestive of issues you may not have considered.

-Justin


Step 37, time 0.037 (ps)  LINCS WARNING


relative constraint deviation after LINCS:

rms 0.002768, max 0.195102 (between atoms 34930 and 34931)

bonds that rotated more than 30 degrees:

   atom 1 atom 2  angle  previous, current, constraint length

  193194   51.70.1100   0.1100  0.1100

54409  54410   32.30.1100   0.1100  0.1100

On Tue, Aug 1, 2017 at 4:49 PM, Dallas Warren 
wrote:

Copy the output from both of those commands, most importantly (as Mark

has asked) that from the first one gmx grompp

You need to show people exactly what you are seeing, not what you say
you are seeing.  The latter you are filtering it, and most likely not
providing all the important information.  The former allows those
trying to help to see all the information that they need to see.
Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.war...@monash.edu
-
When the only tool you own is a hammer, every problem begins to resemble
a
nail.


On 2 August 2017 at 04:05, Ali Ahmed  wrote:


Hi,
Thank you for your help.

well I used this command

gmx grompp -f em.mdp -c box.gro -p topol.top -o em.tpr
gmx mdrun -v -deffnm em

and I got all the warnings. Here is my em.mdp



-



integrator = steep

emtol   = 10.0

emstep  = 0.001

nsteps  = 5

energygrps   = system

; Parameters describing how to find the neighbors of each atom and how
to
calculate the interactions

nstlist   = 1

cutoff-scheme   = group

ns_type= grid

coulombtype= PME

rcoulomb = 1.0

rvdw= 1.0

pbc  = xyz

On Tue, Aug 1, 2017 at 11:07 AM, Mark Abraham  wrote:

Dear Mark

Yes, all the warnings are from grompp.
I have no idea where is the problem in the structure or the topology
Thank you

On Mon, Jul 31, 2017 at 2:34 PM, Mark

Re: [gmx-users] Error in itp file




On 8/2/17 12:35 PM, Souvik Dey wrote:

Hi,

I just generated an itp file from ACPYPE. However, if I try to add ions it
shows the following error:

Fatal error:
Syntax error - File FAD.itp, line 3
Last line read:
'[ atomtypes ]'
Invalid order for directive atomtypes


Can somebody say how do I fix this?



This exact situation is described here:

http://www.gromacs.org/Documentation/Errors#Invalid_order_for_directive_xxx

-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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Re: [gmx-users] membrane-protein simulation

On 8/2/17 5:01 AM, Amir Zeb wrote:

Hello gmx-user

I want to simulate a membrane protein with more than one chains like A, B,
C etc. I generated the strong_posre.itp file as Justing has kindly
explained in his tutorial, and updated the topol.top file by inserting the
same lines. I also updated the minim.mdp file by inserting STRONG_POSRES.
Once I tried the minimization of the system before the shrinking step, I
got the error as below:

Fatal error:
[ file strong_posre.itp, line 548 ]:
Atom index (544) in position_restraints out of bounds (1-543).
This probably means that you have inserted topology section
"position_restraints"
in a part belonging to a different molecule than you intended to.
In that case move the "position_restraints" section to the right molecule.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors

I tried so many options but could not fix the issue. Please keep in view
that the same procedure is working well with a single chain of the protein.
Kindly help me how to fix this issue?

You need to create restraint files for each chain separately and include them in
each [moleculetype] separately, as explained here:

http://www.gromacs.org/Documentation/Errors#Atom_index_n_in_position_restraints_out_of_bounds

-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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Re: [gmx-users] Creating Custom .rtp files




On 8/2/17 5:07 AM, Momin Ahmad wrote:
I think the reason for the weird log is the "|" command that lets you write 
the output of another command into a file. In the case of the error i could 
choose the forcefield before the error occurred. The methane was called "CH4" 
before, i just changed the names for troubleshooting. This time i did copy 
manually. Files are attached. There are two comments that show the differences 
in the versions. Again: the two .rtp files for both versions are identical and 
the same .pdb file is used.




Works fine for me using the files you provided on Redmine.  I suspect you're 
just not managing your files correctly.  Make sure your methane.rtp is in the 
force field subdirectory, not the working directory or anywhere else.


-Justin



Am 01.08.2017 um 20:42 schrieb Justin Lemkul:



On 8/1/17 10:32 AM, Momin Ahmad wrote:
please finde the files attached to this email: log-files for the 5.1.2 
version and the 2016.3 version, also again the .rtp file and the .pdb file




The screen output seems garbled to me, with the fatal error coming before the 
force field selection, and multiple locations being used. I can't figure out 
what's going on.  Your .rtp needs to be in the force field directory that you 
choose, either locally (within the working directory) or system-wide (wherever 
that is installed).  Note also that "CH4" and "CH41" are different, because 
one error indicates that pdb2gmx finds CH4 when your .rtp is clearly CH41.


-Justin



Am 01.08.2017 um 00:48 schrieb Justin Lemkul:



On 7/31/17 7:47 AM, Momin Ahmad wrote:

Hello,

the .rtp file is located in the same directory as the force-field. When i 
type gmx gmx2pdb . then the log shows that the right path is considered 
and loads the needed .rtp fiels that already exist in the forc-field file. 
But my custom one is ignored.




Please post the full screen output of pdb2gmx, including the force field 
selection.  If your .rtp file is not being read, it is likely misformatted, 
in which case you should either write your new residue entries in an 
existing file or upload it to a file-sharing service so we can provide 
feedback.


-Justin


Greets
Momin Ahmad

Am 25.07.2017 um 16:34 schrieb RAHUL SURESH:

On Tue, 25 Jul 2017 at 5:58 PM, Momin Ahmad  wrote:


Hi,

I created a custom .pdb file and the associated .rtp file for the
force-field (amber99sb-ildn.ff). The command pdb2gmx works fine for the
5.1.2 version of gromacs but not for the 2016.3 version. The 2016.3
version is a local installation in my /home/user folder. The log shows
the correct paths but does not consider my custom .rtp file.

I would recommend to check whether the rtp file location and source where
gmx  you have installed match. Apart from that I do not think any error
with version of Gromacs.


Am i doing
something wrong with the newer version? I added two simple files of my
problem. Thanks in advance.

Cheers
Momin Ahmad
Karlsruher Institut of Technology
Germany
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--
==

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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Re: [gmx-users] Error in itp file

2017-08-02 Thread Mohammad Zahidul Hossain Khan

Hi

Can you tell me, how have you used ACPYPE for itp.

On Aug 2, 2017 9:36 AM, "Souvik Dey"  wrote:

> Hi,
>
> I just generated an itp file from ACPYPE. However, if I try to add ions it
> shows the following error:
>
> Fatal error:
> Syntax error - File FAD.itp, line 3
> Last line read:
> '[ atomtypes ]'
> Invalid order for directive atomtypes
>
>
> Can somebody say how do I fix this?
>
> Regards,
> Souvik Dey
>
> --
> Souvik Dey
> Integrated Science Education & Research Centre
> Visva Bharati University
> Santiniketan-731235
> West Bengal
> 8981736643
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[gmx-users] Error in itp file

2017-08-02 Thread Souvik Dey

Hi,

I just generated an itp file from ACPYPE. However, if I try to add ions it
shows the following error:

Fatal error:
Syntax error - File FAD.itp, line 3
Last line read:
'[ atomtypes ]'
Invalid order for directive atomtypes


Can somebody say how do I fix this?

Regards,
Souvik Dey

-- 
Souvik Dey
Integrated Science Education & Research Centre
Visva Bharati University
Santiniketan-731235
West Bengal
8981736643
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[gmx-users] Fwd: meaning of -sigfac option in gmx sigeps

2017-08-02 Thread Tamisra Pal

Hi Everyone,
Can anyone help me regarding the -sigfac option in gmx sigeps?
What does this -sigfac imply?
The LJ potential form is
U(r) = (27/4)*epsilon [ (sigma/r)^9 - (sigma/r)^6 ]

-- 
Tamisra Pal

Post Doctoral Research Fellow
Technische Universität Darmstadt
Institut für Festkörperphysik
Hochschulstraße 6
64289 Darmstadt , Germany
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Re: [gmx-users] LINCS warning during energy minimization of nitrogen with virtual site

2017-08-02 Thread Ali Ahmed

Dear all,
Thank you for helping me. All I get from grompp is this
--

gmx grompp -f grompp.mdp -c N2_box.gro -po mdout.mdp -p topol.top -o
topol.tpr

Ignoring obsolete mdp entry 'title'
Ignoring obsolete mdp entry 'cpp'

Back Off! I just backed up mdout.mdp to ./#mdout.mdp.2#

NOTE 1 [file grompp.mdp]:
  The group cutoff scheme is deprecated since GROMACS 5.0 and will be
  removed in a future release when all interaction forms are supported for
  the verlet scheme. The verlet scheme already scales better, and it is
  compatible with GPUs and other accelerators.

Setting the LD random seed to 1000542586
Generated 120 of the 120 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 120 of the 120 1-4 parameter combinations
Excluding 2 bonded neighbours molecule type 'N_2'
Cleaning up constraints and constant bonded interactions with virtual sites
Analysing residue names:
There are:  2493  Other residues
Analysing residues not classified as Protein/DNA/RNA/Water and splitting
into groups...
Number of degrees of freedom in T-Coupling group System is 12462.00

NOTE 2 [file grompp.mdp]:
  You are using a plain Coulomb cut-off, which might produce artifacts.
  You might want to consider using PME electrostatics.


Largest charge group radii for Van der Waals: 0.056, 0.056 nm
Largest charge group radii for Coulomb:   0.056, 0.056 nm
This run will generate roughly 90 Mb of data

There were 2 notes

Back Off! I just backed up topol.tpr to ./#topol.tpr.1#

gcq#454: "I never see what has been done; I only see what remains to be
done." (Marie Curie)


On Tue, Aug 1, 2017 at 5:08 PM, Justin Lemkul  wrote:

>
>
> On 8/1/17 6:07 PM, Ali Ahmed wrote:
>
>> Dear Dr. Dallas,
>> Thank you for your reply. Actually, I'm new to GROMACS and
>> I appreciate your support.
>> 
>> 
>> --
>> Here is what I get before crashing. Too many warning then crush.
>>
>>
> This is not diagnostic of anything useful.  You've been asked several
> times to provide the output of grompp, not mdrun.  The grompp output can be
> suggestive of issues you may not have considered.
>
> -Justin
>
>
> Step 37, time 0.037 (ps)  LINCS WARNING
>>
>> relative constraint deviation after LINCS:
>>
>> rms 0.002768, max 0.195102 (between atoms 34930 and 34931)
>>
>> bonds that rotated more than 30 degrees:
>>
>>   atom 1 atom 2  angle  previous, current, constraint length
>>
>>  193194   51.70.1100   0.1100  0.1100
>>
>>54409  54410   32.30.1100   0.1100  0.1100
>>
>> On Tue, Aug 1, 2017 at 4:49 PM, Dallas Warren 
>> wrote:
>>
>> Copy the output from both of those commands, most importantly (as Mark
>>> has asked) that from the first one gmx grompp
>>>
>>> You need to show people exactly what you are seeing, not what you say
>>> you are seeing.  The latter you are filtering it, and most likely not
>>> providing all the important information.  The former allows those
>>> trying to help to see all the information that they need to see.
>>> Catch ya,
>>>
>>> Dr. Dallas Warren
>>> Drug Delivery, Disposition and Dynamics
>>> Monash Institute of Pharmaceutical Sciences, Monash University
>>> 381 Royal Parade, Parkville VIC 3052
>>> dallas.war...@monash.edu
>>> -
>>> When the only tool you own is a hammer, every problem begins to resemble
>>> a
>>> nail.
>>>
>>>
>>> On 2 August 2017 at 04:05, Ali Ahmed  wrote:
>>>
 Hi,
 Thank you for your help.

 well I used this command

 gmx grompp -f em.mdp -c box.gro -p topol.top -o em.tpr
 gmx mdrun -v -deffnm em

 and I got all the warnings. Here is my em.mdp
 

>>> -
>>>

 integrator = steep

 emtol   = 10.0

 emstep  = 0.001

 nsteps  = 5

 energygrps   = system

 ; Parameters describing how to find the neighbors of each atom and how
 to
 calculate the interactions

 nstlist   = 1

 cutoff-scheme   = group

 ns_type= grid

 coulombtype= PME

 rcoulomb = 1.0

 rvdw= 1.0

 pbc  = xyz

 On Tue, Aug 1, 2017 at 11:07 AM, Mark Abraham 
 wrote:

 Hi,
>
> No, only mdrun issues LINCS warnings. grompp issues different warnings,
>
 and
>>>
 I would like you to check whether you had any from grompp that you may
>
 not
>>>
 have considered. :-)
>
> Mark
>
> On

[gmx-users] Dynamics only for cavity in molecule.

2017-08-02 Thread nikolaev

Hello!

I want to run dynamics only for a relatively small cavity of my molecule,
with all other atoms frozen. For this reason, I also don't use solvent,
because it won't move anyway. I run the simulation on GPU (gromacs 5.1.2),
i.e. I use the Verlet scheme, pbc = xyz. However, when I start running
simulations, I get violent behavior: the molecule immediately falls
apart!! I am sure that I just made a silly thing in the parameters, but
what is it? Here I attach my dynamics .mdp parameters:


define = -DPOSRES
integrator = md
dt = 0.001
nsteps = 120

nstxout = 1000
nstvout = 1000
nstxtcout = 1000
nstlog = 100
nstenergy = 1000

continuation   = no
constraints= none

tcoupl = V-rescale
tc_grps = System
tau_t = 0.1
ref_t = 0

cutoff-scheme = Verlet
ns_type   = grid
nstlist   = 10
rcoulomb  = 0.9
rvdw  = 0.9

coulombtype   = PME
pme_order = 4
fourierspacing = 0.16

pbc  = xyz
gen_vel  = no

DispCorr = EnerPres

;
; Freezing atoms # this is all the atoms except for the cavity inside
;
freezegrps = GroupDyna
freezedim = Y Y Y
;
; Heating
;
annealing = single
annealing_npoints = 2
annealing_time = 0 50
annealing_temp = 0 298


Thank you in advance,
Dmitrii.

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[gmx-users] QM/MM in Gromacs-5.1.4?

2017-08-02 Thread Albert


Hello,

I would like to use ORCA as a QM engine for Gromacs QM/MM simulation. I 
am just wondering shall we add additional options to cmake when we 
compile Gromacs?


Thanks a lot

Albert

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Re: [gmx-users] hole in the simulation box

2017-08-02 Thread edesantis


thank you for your suggestion,

I've tuned the gmx solvate -radius parameter until I achieved the 
stability of the box dimensions in the NPT ensemble, now it seem the 
everything is working...


thanks again,

regards,
Emiliano



On 2017-08-01 00:10, Dallas Warren wrote:

There are insufficient waters in the box to fill it up completely.

Two solutions that come to mind, add more water so it reaches the
appropriate simulated density under those conditions, or run under NPT
until reaches appropriate simulated density then swap back to NVT.
Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.war...@monash.edu
-
When the only tool you own is a hammer, every problem begins to 
resemble a nail.



On 31 July 2017 at 18:14, edesantis  wrote:

Hi gromacs users,

I am trying to simulate a crystal supershell (5x5x5 unit cells) with 
martini

ff in gromacs 5.

I build the system in aa representation, then I converted it in CG 
using the

martinize.py script,

following the tutorial, I've done a brief equilibration in water, the 
after

the solvatation of the system with non-polarizable water, I've perform
another energy minimization followed by the equilibration.

then I've performed md simulation in the NVT ensemble.

It happened that during the first steps of md, an empty (no protein no
water) hole was created in my simulation box. during the md simulation 
the
hole size became bigger (this hole doesn't appear if I do the 
simulation in
NPT, but I'd prefer to avoid this ensemble since a dynamic volume of 
the box

could alter the reticolar parameters of my crystal),

I've tried to calculate forces using different algorithms but the hole 
is

formed every time.

the density of my system is 1.1 times the experimental one.

Do you have an idea of the reason why I found this hole? do you have 
any

suggestion to avoid its formation??


thank you in advance,
regards
Emiliano De Santis

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Re: [gmx-users] Error in the replica order in REMD (GMX v2016.1)

2017-08-02 Thread Hermann, Johannes

I solved it rather the brute force way: In the shell script which I 
execute to run all my simulations I defined a variable for my Multidir 
and filled it with all the directories (which were then in order).

somewhere in the shell script:

[...]

MULTIDIR=""
LAMBDALIST=(0 1 2 3 4 5)
$MDRUN=Your_Individua_MDrun_command
$FREE_ENERGY=YOUR_INDIVIDUAL_DIRECTORY

for i in ${LAMBDALIST[@]}; do
  LAMBDA=$i
  cd $FREE_ENERGY
  mkdir Lambda_$LAMBDA
  cd $FREE_ENERGY/Lambda_$LAMBDA
  mkdir Production_MD
  cd Production_MD
  MULTIDIR="$MULTIDIR $FREE_ENERGY/Lambda_$LAMBDA/Production_MD"
done

$MDRUN -v -deffnm fec -multidir $MULTIDIR -replex 1000

You can adapt this for your needs.

On 02.08.2017 13:11, Mark Abraham wrote:

Hi,

The shell expansion is sorted alphabetically, rather than numerically, so
the order is md_0, md_1, md_10, md_11, etc. Either make your directories
like md_000, md_001, md_002, so the sortings are the same, or use a more
complex wildcard like -multidir md_[0-9] md_[1-9][0-9]

Mark

On Wed, Aug 2, 2017 at 1:06 PM ABEL Stephane  wrote:


Hello again

Thanks to J. Hermann  I can start my simulations, however few seconds
after the beginning of the run I have the following error

"Replicas with indices 2 < 12 have temperatures 271.9 > 254.27, please
order your replicas on increasing temperature"

I do not understand this error, since my replicas seem well ordered (i
think) : ref_t in replicas 2 is 254.27 K  and ref_t in replicas 12 is
271.9) I check this with the ref_t in the mdp. For this calculation I used
the cpt file to generate the tpr.

Could you help me again ?

Stéphane




Stéphane Abel, Ph.D.

CEA Saclay DSV/ISVFJ/SB2SM
Institut de Biologie Intégrative de la Cellule (I2BC)
Bat 528, Office 138C
Gif-sur-Yvette, F-91191 FRANCE
Phone (portable) : +33 6 49 37 70 60 <+33%206%2049%2037%2070%2060>
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--
__
*Technische Universität München*
*Johannes Hermann, M.Sc.*
Lehrstuhl für Bioverfahrenstechnik
Boltzmannstr. 15
D-85748 Garching
Tel: +49 8928915730
Fax: +49 8928915714

Email: j.herm...@lrz.tum.de
http://www.biovt.mw.tum.de/

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Re: [gmx-users] Error in the replica order in REMD (GMX v2016.1)

Hi,

The shell expansion is sorted alphabetically, rather than numerically, so
the order is md_0, md_1, md_10, md_11, etc. Either make your directories
like md_000, md_001, md_002, so the sortings are the same, or use a more
complex wildcard like -multidir md_[0-9] md_[1-9][0-9]

Mark

On Wed, Aug 2, 2017 at 1:06 PM ABEL Stephane  wrote:

> Hello again
>
> Thanks to J. Hermann  I can start my simulations, however few seconds
> after the beginning of the run I have the following error
>
> "Replicas with indices 2 < 12 have temperatures 271.9 > 254.27, please
> order your replicas on increasing temperature"
>
> I do not understand this error, since my replicas seem well ordered (i
> think) : ref_t in replicas 2 is 254.27 K  and ref_t in replicas 12 is
> 271.9) I check this with the ref_t in the mdp. For this calculation I used
> the cpt file to generate the tpr.
>
> Could you help me again ?
>
> Stéphane
>
>
>
> 
> Stéphane Abel, Ph.D.
>
> CEA Saclay DSV/ISVFJ/SB2SM
> Institut de Biologie Intégrative de la Cellule (I2BC)
> Bat 528, Office 138C
> Gif-sur-Yvette, F-91191 FRANCE
> Phone (portable) : +33 6 49 37 70 60 <+33%206%2049%2037%2070%2060>
> --
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> posting!
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>
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[gmx-users] Error in the replica order in REMD (GMX v2016.1)

2017-08-02 Thread ABEL Stephane

Hello again

Thanks to J. Hermann  I can start my simulations, however few seconds after the 
beginning of the run I have the following error

"Replicas with indices 2 < 12 have temperatures 271.9 > 254.27, please order 
your replicas on increasing temperature"

I do not understand this error, since my replicas seem well ordered (i think) : 
ref_t in replicas 2 is 254.27 K  and ref_t in replicas 12 is 271.9) I check 
this with the ref_t in the mdp. For this calculation I used the cpt file to 
generate the tpr.

Could you help me again ?

Stéphane



   
Stéphane Abel, Ph.D.

CEA Saclay DSV/ISVFJ/SB2SM
Institut de Biologie Intégrative de la Cellule (I2BC)
Bat 528, Office 138C 
Gif-sur-Yvette, F-91191 FRANCE
Phone (portable) : +33 6 49 37 70 60
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Re: [gmx-users] GPU job failed

Hi,

My first guess is that the implementation of PLUMED doesn't support this.
Does a normal non-PLUMED simulation run correctly when called in this
manner?

Mark

On Wed, Aug 2, 2017 at 9:55 AM Albert  wrote:

> Hello,
>
> I am trying to run Gromacs with the following command line:
>
>
>   mpirun -np 4 gmx_mpi mdrun -v -g 7.log -s 7.tpr -x 7.xtc -c 7.gro -e
> 7.edr -plumed plumed.dat -ntomp 2 -gpu_id 0123
>
> but it always failed with the following messages:
>
> Running on 1 node with total 24 cores, 48 logical cores, 4 compatible GPUs
> Hardware detected on host cudaC.europe.actelion.com (the node of MPI
> rank 0):
>CPU info:
>  Vendor: GenuineIntel
>  Brand:  Intel(R) Xeon(R) CPU E5-2680 v3 @ 2.50GHz
>  SIMD instructions most likely to fit this hardware: AVX2_256
>  SIMD instructions selected at GROMACS compile time: AVX2_256
>GPU info:
>  Number of GPUs detected: 4
>  #0: NVIDIA GeForce GTX TITAN X, compute cap.: 5.2, ECC:  no, stat:
> compatible
>  #1: NVIDIA GeForce GTX TITAN X, compute cap.: 5.2, ECC:  no, stat:
> compatible
>  #2: NVIDIA GeForce GTX TITAN X, compute cap.: 5.2, ECC:  no, stat:
> compatible
>  #3: NVIDIA GeForce GTX TITAN X, compute cap.: 5.2, ECC:  no, stat:
> compatible
>
> Reading file 7.tpr, VERSION 5.1.3 (single precision)
> Changing nstlist from 20 to 40, rlist from 1.02 to 1.08
>
> Using 4 MPI processes
> Using 2 OpenMP threads per MPI process
>
> On host cudaC.europe.actelion.com 4 compatible GPUs are present, with
> IDs 0,1,2,3
> On host cudaC.europe.actelion.com 4 GPUs auto-selected for this run.
> Mapping of GPU IDs to the 4 PP ranks in this node: 0,1,2,3
>
>
> ---
> Program gmx mdrun, VERSION 5.1.3
> Source code file:
> /home/albert/Downloads/gromacs/gromacs-5.1.3/src/gromacs/mdlib/nbnxn_cuda/
> nbnxn_cuda_data_mgmt.cu,
> line: 403
>
> Fatal error:
> cudaCreateTextureObject on nbfp_texobj failed: invalid argument
>
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> ---
>
> Does anybody have any idea what's happening?
>
> THX a lot.
>
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Re: [gmx-users] -multidir option in REMD (GROMACS v2016.1)