date:20161008

Re: [gmx-users] Installation of gromacs 5.1.4 in a windows system

2016-10-08 Thread Nikhil Maroli

Hi,
It's always better to use in Linux if you wanted to work in MD. Anyhow you
can have a look on this
http://www.gromacs.org/Downloads/Installation_Instructions/Windows
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Re: [gmx-users] Tabulated dihedral potential

2016-10-08 Thread Mark Abraham

Hi,

If you can't run a useful model without them, then tables are infinitely
faster. Compared to non-tabulated interactions they're slower. The scaling
of a system that uses them does not change much with system size (if
anything it's better because the steps are slower). So it depends what
question you're asking :-)

Mark

On Sat, Oct 8, 2016 at 10:13 PM Parvez Mh  wrote:

> Dear all:
>
> I would like  to use tabulated dihedral in gromacs for very a large system
> where i have some speed up concern. My question is, Does tabulated dihedral
> usages adversely affect simulation speed ?
>
> Regards
>
> Masrul
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[gmx-users] Tabulated dihedral potential

2016-10-08 Thread Parvez Mh

Dear all:

I would like  to use tabulated dihedral in gromacs for very a large system
where i have some speed up concern. My question is, Does tabulated dihedral
usages adversely affect simulation speed ?

Regards

Masrul
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[gmx-users] refinement of homology-based protein structure

2016-10-08 Thread Mahboobeh Eslami



 On Wednesday, October 5, 2016 8:11 PM, Mahboobeh Eslami 
 wrote:
 

 Hi

I hope you are very well

I designed one protein by Homology modelling approach. I want to use this 
protein as receptor in docking process. I think that, before docking process, 
initial designed protein must be refined by MD simulation. How much time should 
this simulation be done for refinement of homology-based protein structure. 
What parameters should be monitored to ensure that the time simulation is 
sufficient.

thanks for your help

best


   
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Re: [gmx-users] Catenation of trajectories

2016-10-08 Thread Mark Abraham

Sure

On Sat, Oct 8, 2016 at 8:59 PM Sun Iba  wrote:

> Hello everyonw
>
>
> I was wondering if it is possible to catenate multiple trajectories of same
> time-step and simulation length into one. Will it over write the
> information? For example I have five 50 ns trajectories of protein (time
> frames saved at 10 ps interval). The input .pdb file for second 50 ns MD
> was extracted from first trajectory and similarly other input files were
> extracted from first trajectory. Now I want to catenate these five 50 ns
> trajectories into one 250 ns trajectory. Is it possible to catenate these
> using gmx trjcat?
>
>
> Thank you
>
> Suniba
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Re: [gmx-users] gromacs build options

2016-10-08 Thread Mark Abraham

Hi,

On Sat, Oct 8, 2016 at 8:24 PM Mahmood Naderan  wrote:

> Sorry, but I got confused. I tried to follow the correct options to specify
>
> the location of libraries, bu failed...
>

Why did you change the setting that was working? FFTWF_LIBRARY wants a
library, not a path in which to search for a library. Why not do what the
install guide suggests and let GROMACS download and build FFTW for you?

mahmood@cluster:build$ cmake ..
>
> -DCMAKE_C_COMPILER=/share/apps/computer/openmpi-2.0.1/bin/mpicc
>
> -DCMAKE_CXX_COMPILER=/share/apps/computer/openmpi-2.0.1/bin/mpic++
>
>
> -DCMAKE_PREFIX_PATH=/share/apps/chemistry/gromacs-5.1:/share/apps/computer/fftw-3.3.5
>
> -DFFTWF_LIBRARY=/share/apps/computer/fftw-3.3.5/lib
>
> -DFFTWF_INCLUDE_DIR=/share/apps/computer/fftw-3.3.5/include
>
> -DBUILD_SHARED_LIBS=off -DGMX_BUILD_MDRUN_ONLY=on
>
> ...
>
> -- checking for module 'fftw3f'
>
> --   package 'fftw3f' not found
>
> -- pkg-config could not detect fftw3f, trying generic detection
>
> -- Looking for fftwf_plan_r2r_1d in /share/apps/computer/fftw-3.3.5/lib
>
> WARNING: Target "cmTryCompileExec1705831031" requests linking to directory
>
> "/share/apps/computer/fftw-3.3.5/lib".  Targets may link only to
>
> libraries.  CMake is dropping the item.
>
> -- Looking for fftwf_plan_r2r_1d in /share/apps/computer/fftw-3.3.5/lib -
>
> not found
>
> CMake Error at cmake/FindFFTW.cmake:100 (message):
>
>   Could not find fftwf_plan_r2r_1d in /share/apps/computer/fftw-3.3.5/lib,
>
>   take a look at the error message in
>
>   /share/apps/chemistry/gromacs-5.1/build/CMakeFiles/CMakeError.log



Look at this file, not some other randomly named file.



> to find
>
>   out what went wrong.  If you are using a static lib (.a) make sure you
>
> have
>
>   specified all dependencies of fftw3f in FFTWF_LIBRARY by hand (e.g.
>
>   -DFFTWF_LIBRARY='/path/to/libfftw3f.so;/path/to/libm.so') !
>
> Call Stack (most recent call first):
>
>   cmake/gmxManageFFTLibraries.cmake:78 (find_package)
>
>   CMakeLists.txt:666 (include)
>
>
>
>
>
> -- Configuring incomplete, errors occurred!
>
> See also
>
> "/share/apps/chemistry/gromacs-5.1/build/CMakeFiles/CMakeOutput.log".
>
> See also
>
> "/share/apps/chemistry/gromacs-5.1/build/CMakeFiles/CMakeError.log".
>
> You have changed variables that require your cache to be deleted.
>
> Configure will be re-run and you may have to reset some variables.
>
> The following variables have changed:
>
> CMAKE_CXX_COMPILER= /share/apps/computer/openmpi-2.0.1/bin/mpic++
>
>
>
> -- Generating done
>
> -- Build files have been written to:
> /share/apps/chemistry/gromacs-5.1/build
>
>
>
>
>
> mahmood@cluster:build$ ls /share/apps/computer/fftw-3.3.5/lib
>
> libfftw3.a  libfftw3.la  libfftw3_mpi.a  libfftw3_mpi.la  pkgconfig
>
>
> Unfortunately, there are no CMakeOutput.log and CMakeError.log in that
>
> folder!
>

Good! cmake didn't tell you to look there.

Can you please explain what is going wrong? Why it is saying that
>
> CMAKE_CXX_COMPILER has been changed?
>

If you tell cmake the compiler again, it's not always sure whether you mean
the same as you did last time.

Mark


>
>
>
>
> Regards,
>
> Mahmood
>
> --
>
> Gromacs Users mailing list
>
>
>
> * Please search the archive at
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> posting!
>
>
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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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[gmx-users] Catenation of trajectories

2016-10-08 Thread Sun Iba

Hello everyonw


I was wondering if it is possible to catenate multiple trajectories of same
time-step and simulation length into one. Will it over write the
information? For example I have five 50 ns trajectories of protein (time
frames saved at 10 ps interval). The input .pdb file for second 50 ns MD
was extracted from first trajectory and similarly other input files were
extracted from first trajectory. Now I want to catenate these five 50 ns
trajectories into one 250 ns trajectory. Is it possible to catenate these
using gmx trjcat?


Thank you

Suniba
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[gmx-users] PMF and lack if NPT equilibration

2016-10-08 Thread Alex

Dear gromacs user,

In a PMF simulation of a short peptide on solid surface, I am using the
"direction-periodic" as "pull-coord1-geometry" in the Z  direction, then as
you know the equilibration of the system in NPT ensemble is not doable for
the individual windows. So, for each windows of umbrella sampling, I am
going to do minimization and NVT equilibration and then MD production. I
was wondering if the lack of the NPT  equilibration would not badly affect
on the result PMF? If so, how can I compensate it somehow?

By the way, I nicely minimized. equilibrated (both NVT and NPT) and a 60 ns
of production simulation of my initial system before coming to the pulling
step.

Thanks.

Regards,
Alex
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Re: [gmx-users] gromacs build options

2016-10-08 Thread Mahmood Naderan

Sorry, but I got confused. I tried to follow the correct options to specify
the location of libraries, bu failed...


mahmood@cluster:build$ cmake ..
-DCMAKE_C_COMPILER=/share/apps/computer/openmpi-2.0.1/bin/mpicc
-DCMAKE_CXX_COMPILER=/share/apps/computer/openmpi-2.0.1/bin/mpic++
-DCMAKE_PREFIX_PATH=/share/apps/chemistry/gromacs-5.1:/share/apps/computer/fftw-3.3.5
-DFFTWF_LIBRARY=/share/apps/computer/fftw-3.3.5/lib
-DFFTWF_INCLUDE_DIR=/share/apps/computer/fftw-3.3.5/include
-DBUILD_SHARED_LIBS=off -DGMX_BUILD_MDRUN_ONLY=on
...
-- checking for module 'fftw3f'
--   package 'fftw3f' not found
-- pkg-config could not detect fftw3f, trying generic detection
-- Looking for fftwf_plan_r2r_1d in /share/apps/computer/fftw-3.3.5/lib
WARNING: Target "cmTryCompileExec1705831031" requests linking to directory
"/share/apps/computer/fftw-3.3.5/lib".  Targets may link only to
libraries.  CMake is dropping the item.
-- Looking for fftwf_plan_r2r_1d in /share/apps/computer/fftw-3.3.5/lib -
not found
CMake Error at cmake/FindFFTW.cmake:100 (message):
  Could not find fftwf_plan_r2r_1d in /share/apps/computer/fftw-3.3.5/lib,
  take a look at the error message in
  /share/apps/chemistry/gromacs-5.1/build/CMakeFiles/CMakeError.log to find
  out what went wrong.  If you are using a static lib (.a) make sure you
have
  specified all dependencies of fftw3f in FFTWF_LIBRARY by hand (e.g.
  -DFFTWF_LIBRARY='/path/to/libfftw3f.so;/path/to/libm.so') !
Call Stack (most recent call first):
  cmake/gmxManageFFTLibraries.cmake:78 (find_package)
  CMakeLists.txt:666 (include)


-- Configuring incomplete, errors occurred!
See also
"/share/apps/chemistry/gromacs-5.1/build/CMakeFiles/CMakeOutput.log".
See also
"/share/apps/chemistry/gromacs-5.1/build/CMakeFiles/CMakeError.log".
You have changed variables that require your cache to be deleted.
Configure will be re-run and you may have to reset some variables.
The following variables have changed:
CMAKE_CXX_COMPILER= /share/apps/computer/openmpi-2.0.1/bin/mpic++

-- Generating done
-- Build files have been written to: /share/apps/chemistry/gromacs-5.1/build





mahmood@cluster:build$ ls /share/apps/computer/fftw-3.3.5/lib
libfftw3.a  libfftw3.la  libfftw3_mpi.a  libfftw3_mpi.la  pkgconfig






Unfortunately, there are no CMakeOutput.log and CMakeError.log in that
folder!
Can you please explain what is going wrong? Why it is saying that
CMAKE_CXX_COMPILER has been changed?


Regards,
Mahmood
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Re: [gmx-users] Errors during energy minimization of POPC membrane

2016-10-08 Thread Justin Lemkul


On 10/8/16 1:10 PM, Roshan Shrestha wrote:

Justin,
 I have attached here with both my POPC membrane that I have created
using charmm gui builder and the topology file. Still in dilemma, what caused so
many errors during its energy minimization.



The topology defines angles for the water molecules, which it should not. 
Remove the waters from the [atoms] and all bonded directives.  The #include 
statement for TIP3P takes care of all the waters.


-Justin


--
Roshan Shrestha
Graduate Student
Central Department of Physics,Tribhuvan University
Kathmandu,Nepal




--
==

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] gromacs build options

2016-10-08 Thread Mark Abraham

Hi,

On Sat, Oct 8, 2016 at 5:31 PM Mahmood Naderan  wrote:

> I got an error regarding fftw3. Maybe not related to GMX itself, but I
>
> appreciate any comment for that.
>
>
>
>
>
> root@cluster:build#

Do not configure software as root, unless your preferred hobby is
reinstalling operating systems. Particularly do not do so when you're using
unfamiliar configuration systems to configure unfamiliar software, so
you're not sure what the consequences of any action might be...

Only "make install" to a destination that needs root privileges needs root
privileges.

> /share/apps/computer/cmake-3.2.3-Linux-x86_64/bin/cmake
>
> .. -DCMAKE_C_COMPILER=/share/ap
>
> ps/computer/openmpi-2.0.1/bin/mpicc
>
> -DCMAKE_CXX_COMPILER=/share/apps/computer/openmpi-2.0.1/bin/mpic++
>
> -DCMAKE_PREFIX_PATH=/share/apps/chemistry/gromacs-5.1
>
> -DBUILD_SHARED_LIBS=off
>
> -DFFTWF_LIBRARY=/share/apps/computer/fftw-3.3.5/lib/libfftw3_mpi.a
>
> -DFFTWF_INCLUDE_DIR=/share/apps/computer/fftw-3.3.5/include
>

If you would like to manage this manually, then you're going to have to
read the .log file that cmake mentioned and work out what the problem is.

Or just follow
http://manual.gromacs.org/documentation/2016/install-guide/index.html#helping-cmake-find-the-right-libraries-headers-or-programs
and
let cmake do its job of working out what your toolchain can do, if it's
possible.

Mark

> -- No compatible CUDA toolkit found (v4.0+), disabling native GPU
>
> acceleration
>
> -- Looking for fftwf_plan_r2r_1d in
>
> /share/apps/computer/fftw-3.3.5/lib/libfftw3_mpi.a
>
> -- Looking for fftwf_plan_r2r_1d in
>
> /share/apps/computer/fftw-3.3.5/lib/libfftw3_mpi.a - not found
>
> CMake Error at cmake/FindFFTW.cmake:100 (message):
>
>   Could not find fftwf_plan_r2r_1d in
>
>   /share/apps/computer/fftw-3.3.5/lib/libfftw3_mpi.a, take a look at the
>
>   error message in
>
>   /share/apps/chemistry/gromacs-5.1/build/CMakeFiles/CMakeError.log to find
>
>   out what went wrong.  If you are using a static lib (.a) make sure you
>
> have
>
>   specified all dependencies of fftw3f in FFTWF_LIBRARY by hand (e.g.
>
>   -DFFTWF_LIBRARY='/path/to/libfftw3f.so;/path/to/libm.so') !
>
> Call Stack (most recent call first):
>
>
>
>
>
>
>
>
>
>
>
> I don't understand the last message. Should I use shared libs only?
>
>
>
>
>
>
>
> Regards,
>
> Mahmood
>
> --
>
> 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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Re: [gmx-users] gromacs build options

2016-10-08 Thread Mahmood Naderan

I got an error regarding fftw3. Maybe not related to GMX itself, but I
appreciate any comment for that.


root@cluster:build# /share/apps/computer/cmake-3.2.3-Linux-x86_64/bin/cmake
.. -DCMAKE_C_COMPILER=/share/ap
ps/computer/openmpi-2.0.1/bin/mpicc
-DCMAKE_CXX_COMPILER=/share/apps/computer/openmpi-2.0.1/bin/mpic++
-DCMAKE_PREFIX_PATH=/share/apps/chemistry/gromacs-5.1
-DBUILD_SHARED_LIBS=off
-DFFTWF_LIBRARY=/share/apps/computer/fftw-3.3.5/lib/libfftw3_mpi.a
-DFFTWF_INCLUDE_DIR=/share/apps/computer/fftw-3.3.5/include
-- No compatible CUDA toolkit found (v4.0+), disabling native GPU
acceleration
-- Looking for fftwf_plan_r2r_1d in
/share/apps/computer/fftw-3.3.5/lib/libfftw3_mpi.a
-- Looking for fftwf_plan_r2r_1d in
/share/apps/computer/fftw-3.3.5/lib/libfftw3_mpi.a - not found
CMake Error at cmake/FindFFTW.cmake:100 (message):
  Could not find fftwf_plan_r2r_1d in
  /share/apps/computer/fftw-3.3.5/lib/libfftw3_mpi.a, take a look at the
  error message in
  /share/apps/chemistry/gromacs-5.1/build/CMakeFiles/CMakeError.log to find
  out what went wrong.  If you are using a static lib (.a) make sure you
have
  specified all dependencies of fftw3f in FFTWF_LIBRARY by hand (e.g.
  -DFFTWF_LIBRARY='/path/to/libfftw3f.so;/path/to/libm.so') !
Call Stack (most recent call first):





I don't understand the last message. Should I use shared libs only?



Regards,
Mahmood
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Re: [gmx-users] gromacs build options

2016-10-08 Thread Mark Abraham

Yep. The build system notices that MPI is available, and you will see that
it builds gmx_mpi, rather than gmx. gmx_mpi -version will confirm that the
MPI library is not the built-in thread MPI.

Mark

On Sat, Oct 8, 2016 at 4:59 PM Mahmood Naderan  wrote:

> OK. I ran
>
> /share/apps/computer/cmake-3.2.3-Linux-x86_64/bin/cmake ..
> -DCMAKE_C_COMPILER=/share/apps/computer/openmpi-2.0.1/bin/mpicc
> -DCMAKE_CXX_COMPILER=/share/apps/computer/openmpi-2.0.1/bin/mpic++
> -DCMAKE_PREFIX_PATH=/share/apps/chemistry/gromacs-5.1
> -DBUILD_SHARED_LIBS=off
>
> please note that I didn't use -DGMX_MPI=on
> Just want to be sure that everything is fine. Do you agree with that?
>
> Regards,
> Mahmood
> --
> Gromacs Users mailing list
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Re: [gmx-users] gromacs build options

2016-10-08 Thread Mahmood Naderan

OK. I ran

/share/apps/computer/cmake-3.2.3-Linux-x86_64/bin/cmake ..
-DCMAKE_C_COMPILER=/share/apps/computer/openmpi-2.0.1/bin/mpicc
-DCMAKE_CXX_COMPILER=/share/apps/computer/openmpi-2.0.1/bin/mpic++
-DCMAKE_PREFIX_PATH=/share/apps/chemistry/gromacs-5.1
-DBUILD_SHARED_LIBS=off

please note that I didn't use -DGMX_MPI=on
Just want to be sure that everything is fine. Do you agree with that?

Regards,
Mahmood
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Re: [gmx-users] principal component analysis chain break (Tsjerk Wassenaar)

2016-10-08 Thread Tsjerk Wassenaar

Hi Jie,

Knowing a few words is not yet knowing the language :)
It's a bit odd that the extreme projections, or any projection for that
matter, has breaks where the original has bonds. Projecting on any subset
of principal components is a reduction of dimensionality and distances
between particles can thus only become smaller. Have you visually checked
the trajectory? What's the difference between md_backbone.xtc and
md1_backbone.xtc?

Cheers,

Tsjerk



On Sat, Oct 8, 2016 at 3:33 PM, 胡杰  wrote:

> Hi Tsjerk,
> Thanks for your reply. It's amazing you know my language!
> I'm sure PBC is processed, and the input trajectory is whole. But, chain
> do break in extreme projection.
> By the way could you please give me some suggestions about meaningful PCA
> output.
> Sincerely yours
> Jie
>
>
> > -原始邮件-
> > 发件人: gromacs.org_gmx-users-requ...@maillist.sys.kth.se
> > 发送时间: 2016年10月7日 星期五
> > 收件人: gromacs.org_gmx-users@maillist.sys.kth.se
> > 抄送:
> > 主题: gromacs.org_gmx-users Digest, Vol 150, Issue 35
> >
> > Send gromacs.org_gmx-users mailing list submissions to
> >  gromacs.org_gmx-users@maillist.sys.kth.se
> >
> > To subscribe or unsubscribe via the World Wide Web, visit
> >  https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> > or, via email, send a message with subject or body 'help' to
> >  gromacs.org_gmx-users-requ...@maillist.sys.kth.se
> >
> > You can reach the person managing the list at
> >  gromacs.org_gmx-users-ow...@maillist.sys.kth.se
> >
> > When replying, please edit your Subject line so it is more specific
> > than "Re: Contents of gromacs.org_gmx-users digest..."
> >
> >
> > Today's Topics:
> >
> >1. Umbrella sampling tutorial (gozde ergin)
> >2. principal  component analysis chain break (??)
> >3. Re: principal component analysis chain break (Tsjerk Wassenaar)
> >
> >
> > --
> >
> > Message: 1
> > Date: Fri, 7 Oct 2016 10:41:36 +0200
> > From: gozde ergin 
> > To: gromacs.org_gmx-users@maillist.sys.kth.se
> > Subject: [gmx-users] Umbrella sampling tutorial
> > Message-ID: 
> > Content-Type: text/plain; charset=utf-8
> >
> > Dear all,
> >
> > I would like to ask a question about Justin?s tutorial.
> > By using the POSRES_B, a restraint is applied on chain B in order to
> immobile it. Is the effect of this restraint removed during the WHAM?
> >
> > I want to do a similar thing by applying restraint force on the organic
> molecule on the bulk water in order to inhibit their movement inside the
> bulk. Should I consider the removing of the restraint in PMF?
> >
> > Thanks in advance.
> >
> > --
> >
> > Message: 2
> > Date: Fri, 7 Oct 2016 17:20:53 +0800 (GMT+08:00)
> > From: ?? 
> > To: gmx-us...@gromacs.org
> > Subject: [gmx-users] principal  component analysis chain break
> > Message-ID:
> >  <612918.790a.1579e71fe59.coremail.huji...@mails.ucas.ac.cn>
> > Content-Type: text/plain; charset=GBK
> >
> > Dear Gromacs community,
> >
> > It's a question about principal  component analysis(PCA).
> > Starting with a tRNA trajectory xtc file and a reference pdb file I use
> the following command, :
> > 1. g_covar -s ref_backbone.pdb -f md_backbone.xtc
> > 2. g_anaeig -s ref_backbone.pdb -f md1_backbone.xtc -extr extreme1.pdb
> -first 1 -last 1 -nframes 30
> >
> > extreme1.pdb is what I want, but the chain of the structure break at
> some place showing from PLMOL or VMD. What's the matter. Could you please
> tell me how to get the compelet structure of extreme1.pdb.
> >
> > best regards
> > Jie
> >
> >
> >
> >
> >
> >
> >
> > --
> >
> > Message: 3
> > Date: Fri, 7 Oct 2016 11:34:46 +0200
> > From: Tsjerk Wassenaar 
> > To: Discussion list for GROMACS users 
> > Subject: Re: [gmx-users] principal component analysis chain break
> > Message-ID:
> >

Re: [gmx-users] principal component analysis chain break (Tsjerk Wassenaar)

2016-10-08 Thread 胡杰

Hi Tsjerk,
Thanks for your reply. It's amazing you know my language!
I'm sure PBC is processed, and the input trajectory is whole. But, chain do 
break in extreme projection.
By the way could you please give me some suggestions about meaningful PCA 
output. 
Sincerely yours
Jie


> -原始邮件-
> 发件人: gromacs.org_gmx-users-requ...@maillist.sys.kth.se
> 发送时间: 2016年10月7日 星期五
> 收件人: gromacs.org_gmx-users@maillist.sys.kth.se
> 抄送: 
> 主题: gromacs.org_gmx-users Digest, Vol 150, Issue 35
> 
> Send gromacs.org_gmx-users mailing list submissions to
>  gromacs.org_gmx-users@maillist.sys.kth.se
> 
> To subscribe or unsubscribe via the World Wide Web, visit
>  https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> or, via email, send a message with subject or body 'help' to
>  gromacs.org_gmx-users-requ...@maillist.sys.kth.se
> 
> You can reach the person managing the list at
>  gromacs.org_gmx-users-ow...@maillist.sys.kth.se
> 
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of gromacs.org_gmx-users digest..."
> 
> 
> Today's Topics:
> 
>1. Umbrella sampling tutorial (gozde ergin)
>2. principal  component analysis chain break (??)
>3. Re: principal component analysis chain break (Tsjerk Wassenaar)
> 
> 
> --
> 
> Message: 1
> Date: Fri, 7 Oct 2016 10:41:36 +0200
> From: gozde ergin 
> To: gromacs.org_gmx-users@maillist.sys.kth.se
> Subject: [gmx-users] Umbrella sampling tutorial
> Message-ID: 
> Content-Type: text/plain; charset=utf-8
> 
> Dear all,
> 
> I would like to ask a question about Justin?s tutorial.
> By using the POSRES_B, a restraint is applied on chain B in order to immobile 
> it. Is the effect of this restraint removed during the WHAM? 
> 
> I want to do a similar thing by applying restraint force on the organic 
> molecule on the bulk water in order to inhibit their movement inside the 
> bulk. Should I consider the removing of the restraint in PMF?
> 
> Thanks in advance.
> 
> --
> 
> Message: 2
> Date: Fri, 7 Oct 2016 17:20:53 +0800 (GMT+08:00)
> From: ?? 
> To: gmx-us...@gromacs.org
> Subject: [gmx-users] principal  component analysis chain break
> Message-ID:
>  <612918.790a.1579e71fe59.coremail.huji...@mails.ucas.ac.cn>
> Content-Type: text/plain; charset=GBK
> 
> Dear Gromacs community,
> 
> It's a question about principal  component analysis(PCA).
> Starting with a tRNA trajectory xtc file and a reference pdb file I use the 
> following command, :
> 1. g_covar -s ref_backbone.pdb -f md_backbone.xtc
> 2. g_anaeig -s ref_backbone.pdb -f md1_backbone.xtc -extr extreme1.pdb -first 
> 1 -last 1 -nframes 30
> 
> extreme1.pdb is what I want, but the chain of the structure break at some 
> place showing from PLMOL or VMD. What's the matter. Could you please tell me 
> how to get the compelet structure of extreme1.pdb.
> 
> best regards
> Jie
> 
> 
> 
> 
> 
> 
> 
> --
> 
> Message: 3
> Date: Fri, 7 Oct 2016 11:34:46 +0200
> From: Tsjerk Wassenaar 
> To: Discussion list for GROMACS users 
> Subject: Re: [gmx-users] principal component analysis chain break
> Message-ID:
>

Re: [gmx-users] Unknown bond_atomtype CAY

2016-10-08 Thread Justin Lemkul




On 10/8/16 2:58 AM, Sameer Edirisinghe wrote:

Dear gromacs users, Dr. Justin,

I managed to run md simulation with the aid of your helps here . As the
next step I'm trying to create a crystal from polymer molecule so i can put
several molecules to the same box and do a simulation. What approach should
I take here ?



gmx genconf, gmx insert-molecules, etc.  See the manual.

If you're going to start doing something different, please start a new thread 
rather than dig up an old one that's not really related.


-Justin


Regards
Sameera Edirisinghe

On Sep 22, 2016 00:41, "Justin Lemkul"  wrote:




On 9/21/16 7:42 AM, Sameer Edirisinghe wrote:


Dear Dr. Justin,

Thanks for the explanation. Now i got the point you mentioned here. Then i
checked the bonds i have mentioned in .rtp file and then i found the
relevant bonded type. then i checked the ffbonded.itp file and i found
that
bond type is already in there.
As an example,

CAY  HA1 ; this is one of bond i have in .rtp file. and for that bond,
relevant bond type (mentioned as below) was already in ffbonded.itp file
CTHC  10.10900   284512.0

But still following error is occurring while running grompp.

1) ERROR 1 [file topol.top, line 108]:
  No default Bond types

2) ERROR 2 [file topol.top, line 168]:
  No default Angle types

3) ERROR 3 [file topol.top, line 426]:
  No default Ryckaert-Bell. types

How do i refer particular bond types in ffbonded.itp file to my current
.gro file or any other relevant file ?



grompp won't complain about parameters being missing if they're actually
there. You're probably looking at the wrong line.

-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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--
==

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] Errors during energy minimization of POPC membrane

2016-10-08 Thread Justin Lemkul




On 10/7/16 11:07 PM, Roshan Shrestha wrote:

Thanks Justin, but I am not sure how can that be since I downloaded
the force field from Mackerell Lab, did not show any errors while
using it for equilibrating my peptide. How can it show errors for my
bilayer though?



Without seeing the topology itself, I can't possibly tell.  But if it came from 
CHARMM-GUI, there's no reason I can think of that it wouldn't work.


-Justin


On 10/7/16, Roshan Shrestha  wrote:

I created a POPC membrane using CHARMM membrane builder, added some water
into it using gromacs, did not add any ions since it was already neutral,
then I ran its energy minimization using minim.mdp of lysozyme tutorial.
However, I ended up with lots of errors like these below after using
grompp:




















































*ERROR 9779 [file topol.top, line 161668]:  No default U-B typesERROR 9780
[file topol.top, line 161669]:  No default U-B typesERROR 9781 [file
topol.top, line 161671]:  No default U-B typesERROR 9782 [file topol.top,
line 161672]:  No default U-B typesERROR 9783 [file topol.top, line
161674]:  No default U-B typesERROR 9784 [file topol.top, line 161675]:  No
default U-B typesERROR 9785 [file topol.top, line 161677]:  No default U-B
typesERROR 9786 [file topol.top, line 161678]:  No default U-B typesERROR
9787 [file topol.top, line 161680]:  No default U-B typesERROR 9788 [file
topol.top, line 161681]:  No default U-B typesExcluding 3 bonded neighbours
molecule type 'Other'Excluding 2 bonded neighbours molecule type
'SOL'Removing all charge groups because cutoff-scheme=VerletThere was 1
note---Program gmx
grompp, VERSION 5.1.3Source code file:
/home/roshan/Downloads/gromacs-5.1.3/src/gromacs/gmxpreprocess/grompp.c,
line: 1738Fatal error:There were 9788 errors in input file(s)*

--
Roshan Shrestha
Graduate Student
Central Department of Physics,Tribhuvan University
Kathmandu,Nepal






--
==

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] Installation of gromacs 5.1.4 in a windows system

2016-10-08 Thread Arnauld Robert Tapa

Hi, I need seriously help to install gromacs 5.1.4 in a system windows 
7-64bits. All the videos I've found on youtube are talking about Linux system 
ignoring windows. I could just install a Borland C/C++ compiler. For the cmake 
and gromacs itself I have all the problems. Please to help me ( A youtube link 
of installation of gromacs in a windows system will be preferred )
Regards
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Re: [gmx-users] gromacs build options

2016-10-08 Thread Mark Abraham

Hi,

This is the job of the wrapper compiler I've been telling you to use. Do
any setup it requires, then

cmake -DCMAKE_C_COMPILER=/path/to/mpicc -DCMAKE_CXX_COMPILER=/path/to/mpic++

It doesn't make sense to consider trying to use the same cmake option that
you use to tell cmake where GROMACS will later be installed, to be the path
where it should find MPI to build with. Not even configure --prefix works
like that :-)

Mark

On Sat, Oct 8, 2016 at 1:32 PM Mahmood Naderan  wrote:

> OMPI-2.0.1 is installed on the system. I want to tell gromacs that mpifort
> (or other wrappers) are in /share/apps/openmpi-2.0.1/bin and libraries are
> in /share/apps/opnempi-2.0.1/lib
>
> How can I tell that to cmake?
>
> Regards,
> Mahmood
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Re: [gmx-users] gromacs build options

2016-10-08 Thread Mahmood Naderan

OMPI-2.0.1 is installed on the system. I want to tell gromacs that mpifort
(or other wrappers) are in /share/apps/openmpi-2.0.1/bin and libraries are
in /share/apps/opnempi-2.0.1/lib

How can I tell that to cmake?

Regards,
Mahmood
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Re: [gmx-users] gromacs build options

2016-10-08 Thread Mark Abraham

Hi,

If you're trying to install OpenMPI, please read its docs. That's a
completely separate thing from installing GROMACS, and one you have to
accomplish before e.g. trying to build GROMACS with support for that
OpenMPI library, by using the newly installed wrapper compiler.

Mark

On Sat, Oct 8, 2016 at 1:04 PM Mahmood Naderan  wrote:

> Excuse me, what I understood from the manual is that
> -DCMAKE_INSTALL_PREFIX is the same as --prefix in ./configure script. Do
> you mean that I can give multiple location with that option? One for the
> gromacs itself and the other for the MPI?
>
> I mean
> -DCMAKE_INSTALL_PREFIX=/share/apps/gromacs-5.1
> -DCMAKE_INSTALL_PREFIX=/share/apps/openmpi-2.0.1
>
>
>
> Regards,
> Mahmood
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Re: [gmx-users] gromacs build options

2016-10-08 Thread Mahmood Naderan

Excuse me, what I understood from the manual is that
-DCMAKE_INSTALL_PREFIX is the same as --prefix in ./configure script. Do
you mean that I can give multiple location with that option? One for the
gromacs itself and the other for the MPI?

I mean
-DCMAKE_INSTALL_PREFIX=/share/apps/gromacs-5.1
-DCMAKE_INSTALL_PREFIX=/share/apps/openmpi-2.0.1



Regards,
Mahmood
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Re: [gmx-users] gromacs build options

2016-10-08 Thread Mark Abraham

Hi,

These are covered in the install guide... cmake
-DCMAKE_INSTALL_PREFIX=/what/ever/you/want, and run whichever MPI wrapper
compilers that you want (GROMACS doesn't care where they are located).

Mark

On Sat, Oct 8, 2016 at 12:14 PM Mahmood Naderan 
wrote:

> Hi,
> I am trying to install gromacs-5.1 from the source. What are the proper
> cmake options for the following things:
>
> 1- Installing to a custom location and not /usr/local
> 2- Using a customized installation of MPI and not /usr/local
>
>
> Regards,
> Mahmood
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[gmx-users] gromacs build options

2016-10-08 Thread Mahmood Naderan

Hi,
I am trying to install gromacs-5.1 from the source. What are the proper
cmake options for the following things:

1- Installing to a custom location and not /usr/local
2- Using a customized installation of MPI and not /usr/local


Regards,
Mahmood
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Re: [gmx-users] Unknown bond_atomtype CAY

2016-10-08 Thread Sameer Edirisinghe

Dear gromacs users, Dr. Justin,

I managed to run md simulation with the aid of your helps here . As the
next step I'm trying to create a crystal from polymer molecule so i can put
several molecules to the same box and do a simulation. What approach should
I take here ?

Regards
Sameera Edirisinghe

On Sep 22, 2016 00:41, "Justin Lemkul"  wrote:

>
>
> On 9/21/16 7:42 AM, Sameer Edirisinghe wrote:
>
>> Dear Dr. Justin,
>>
>> Thanks for the explanation. Now i got the point you mentioned here. Then i
>> checked the bonds i have mentioned in .rtp file and then i found the
>> relevant bonded type. then i checked the ffbonded.itp file and i found
>> that
>> bond type is already in there.
>> As an example,
>>
>> CAY  HA1 ; this is one of bond i have in .rtp file. and for that bond,
>> relevant bond type (mentioned as below) was already in ffbonded.itp file
>> CTHC  10.10900   284512.0
>>
>> But still following error is occurring while running grompp.
>>
>> 1) ERROR 1 [file topol.top, line 108]:
>>   No default Bond types
>>
>> 2) ERROR 2 [file topol.top, line 168]:
>>   No default Angle types
>>
>> 3) ERROR 3 [file topol.top, line 426]:
>>   No default Ryckaert-Bell. types
>>
>> How do i refer particular bond types in ffbonded.itp file to my current
>> .gro file or any other relevant file ?
>>
>>
> grompp won't complain about parameters being missing if they're actually
> there. You're probably looking at the wrong line.
>
> -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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