Re: 答复: [gmx-users] topology file of ligand

[Justin Lemkul]

On 10/15/13 12:25 PM, sunyeping wrote:

Thank you Dr. Lemkul,

Could you recommand some primary literatures which are most usefule for me to 
understand the force field?



The ones cited in the Gromacs manual are a good start.  One should never attempt 
to use a force field without scrutinizing its history, assumptions, and 
parametrization methods...


-Justin

--
==

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441

==
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

答复: [gmx-users] topology file of ligand

[sunyeping]

Thank you Dr. Lemkul,
 
Could you recommand some primary literatures which are most usefule for me to 
understand the force field? 

Yeping Sun
Institute of Microbiology, Chinese Academy of Sciences

--发件人：Justin 
Lemkul 发送时间：2013年10月16日(星期三) 00:05收件人：gromacs 
主　题：Re: [gmx-users] topology file of ligandOn 10/15/13 
11:24 AM, sunyeping wrote:> Dear gromacs users,>> I am study the tutorial for 
protein-ligand complex system (gromacs tutorial 5: T4 lysozyme in complex with 
JZ4). The tutorial use PRODRG to produce the topology file. The author state 
that he immediately notice three things that are wrong with this topology, 
which include charge group, H atom charge, etc.> And the author then 
reconstructed a topology file. I don't understand how the charge group and 
charge of individual atom are correctly assigned. Could you explain it to 
me?>The Gromos96 parameter sets assign charges and charge groups based on 
chemical functional groups that are transferable between molecules. Spotting 
inaccuracies and knowing how to fix them come with understanding how the force 
field was derived (read the primary literature and study existing 
molecules).-Justin-- ==Justin 
A. Lemkul, Ph.D.Postdoctoral FellowDepartment of Pharmaceutical SciencesSchool 
of PharmacyHealth Sciences Facility II, Room 601University of Maryland, 
Baltimore20 Penn St.Baltimore, MD 21201jalem...@outerbanks.umaryland.edu | 
(410) 706-7441==-- gmx-users 
mailing list 
gmx-users@gromacs.orghttp://lists.gromacs.org/mailman/listinfo/gmx-users* 
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!* Please 
don't post (un)subscribe requests to the list. Use the www interface or send it 
to gmx-users-requ...@gromacs.org.* Can't post? Read 
http://www.gromacs.org/Support/Mailing_Lists
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] topology file of ligand

[Justin Lemkul]

On 10/15/13 11:24 AM, sunyeping wrote:

Dear gromacs users,

I am study the tutorial for protein-ligand complex system (gromacs tutorial 5: 
T4 lysozyme in complex with JZ4). The tutorial use PRODRG to produce the 
topology file. The author state that he  immediately notice three things that 
are wrong with this topology, which include charge group, H atom charge, etc.
  And the author then reconstructed a topology file.  I don't understand 
how the charge group and charge of individual atom are correctly assigned. 
Could you explain it to me?



The Gromos96 parameter sets assign charges and charge groups based on chemical 
functional groups that are transferable between molecules.  Spotting 
inaccuracies and knowing how to fix them come with understanding how the force 
field was derived (read the primary literature and study existing molecules).


-Justin

--
==

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441

==
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

[gmx-users] topology file of ligand

[sunyeping]

Dear gromacs users,
 
I am study the tutorial for protein-ligand complex system (gromacs tutorial 5: 
T4 lysozyme in complex with JZ4). The tutorial use PRODRG to produce the 
topology file. The author state that he  immediately notice three things that 
are wrong with this topology, which include charge group, H atom charge, etc. 
     And the author then reconstructed a topology file.  I don't understand how 
the charge group and charge of individual atom are correctly assigned. Could 
you explain it to me? 
 
Thanks.
 
Yeping Sun

Institute of Microbiology, Chinese Academy of Sciences

--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] jwe1050i + jwe0019i errors = SIGSEGV (Fujitsu)

[Mark Abraham]

On Thu, Oct 10, 2013 at 2:34 PM, James  wrote:

> Dear Mark,
>
> Thanks again for your response.
>
> Many of the regression tests seem to have passed:
>
> All 16 simple tests PASSED
> All 19 complex tests PASSED
> All 142 kernel tests PASSED
> All 9 freeenergy tests PASSED
> All 0 extra tests PASSED
> Error not all 42 pdb2gmx tests have been done successfully
> Only 0 energies in the log file
> pdb2gmx tests FAILED
>
> I'm not sure why pdb2gmx failed but I suppose it will not impact the
> crashing I'm experiencing.
>

No, that's fine. Probably they don't have sufficiently explicit guards to
stop people running the energy minimization with a more-than-useful number
of OpenMP threads.


> Regarding the stack trace showing line numbers, what is the best way to go
> about this, in this context? I'm not really experienced in that aspect.
>

That's a matter of compiling in debug mode (use cmake ..
-DCMAKE_BUILD_TYPE=Debug), and hopefully observing the same crash with an
error message that has more useful information. The debug mode annotates
the executable so that a finger can be pointed at the code line that caused
the segfault. Hopefully the compiler does this properly, but support for
this in OpenMP is a corner compiler writers might cut ;-) Depending on the
details, loading a core dump in a debugger can also be necessary, but your
local sysadmins are the people to talk to there.

Mark

Thanks again for your help!
>
> Best regards,
>
> James
>
>
> On 21 September 2013 23:12, Mark Abraham  wrote:
>
> > On Sat, Sep 21, 2013 at 2:45 PM, James 
> wrote:
> > > Dear Mark and the rest of the Gromacs team,
> > >
> > > Thanks a lot for your response. I have been trying to isolate the
> problem
> > > and have also been in discussion with the support staff. They suggested
> > it
> > > may be a bug in the gromacs code, and I have tried to isolate the
> problem
> > > more precisely.
> >
> > First, do the GROMACS regression tests for Verlet kernels pass? (Run
> > them all, but those with nbnxn prefix are of interest here.) They
> > likely won't scale to 16 OMP threads, but you can vary OMP_NUM_THREADS
> > environment variable to see what you can see.
> >
> > > Considering that the calculation is run under MPI with 16 OpenMP cores
> > per
> > > MPI node, the error seems to occur under the following conditions:
> > >
> > > A few thousand atoms: 1 or 2 MPI nodes: OK
> > > Double the number of atoms (~15,000): 1 MPI node: OK, 2 MPI nodes:
> > SIGSEGV
> > > error described below.
> > >
> > > So it seems that the error occurs for relatively large systems which
> use
> > > MPI.
> >
> > ~500 atoms per core (thread) is a system in the normal GROMACS scaling
> > regime. 16 OMP threads is more than is useful on other HPC systems,
> > but since we don't know what your hardware is, whether you are
> > investigating something useful is your decision.
> >
> > > The crash mentions the "calc_cell_indices" function (see below). Is
> this
> > > somehow a problem with memory not being sufficient at the MPI interface
> > at
> > > this function? I'm not sure how to proceed further. Any help would be
> > > greatly appreciated.
> >
> > If there is a problem with GROMACS (which so far I doubt), we'd need a
> > stack trace that shows a line number (rather than addresses) in order
> > to start to locate it.
> >
> > Mark
> >
> > > Gromacs version is 4.6.3.
> > >
> > > Thank you very much for your time.
> > >
> > > James
> > >
> > >
> > > On 4 September 2013 16:05, Mark Abraham 
> > wrote:
> > >
> > >> On Sep 4, 2013 7:59 AM, "James"  wrote:
> > >> >
> > >> > Dear all,
> > >> >
> > >> > I'm trying to run Gromacs on a Fujitsu supercomputer but the
> software
> > is
> > >> > crashing.
> > >> >
> > >> > I run grompp:
> > >> >
> > >> > grompp_mpi_d -f parameters.mdp -c system.pdb -p overthe.top
> > >> >
> > >> > and it produces the error:
> > >> >
> > >> > jwe1050i-w The hardware barrier couldn't be used and continues
> > processing
> > >> > using the software barrier.
> > >> > taken to (standard) corrective action, execution continuing.
> > >> > error summary (Fortran)
> > >> > error number error level error count
> > >> > jwe1050i w 1
> > >> > total error count = 1
> > >> >
> > >> > but still outputs topol.tpr so I can continue.
> > >>
> > >> There's no value in compiling grompp with MPI or in double precision.
> > >>
> > >> > I then run with
> > >> >
> > >> > export FLIB_FASTOMP=FALSE
> > >> > source /home/username/Gromacs463/bin/GMXRC.bash
> > >> > mpiexec mdrun_mpi_d -ntomp 16 -v
> > >> >
> > >> > but it crashes:
> > >> >
> > >> > starting mdrun 'testrun'
> > >> > 5 steps, 100.0 ps.
> > >> > jwe0019i-u The program was terminated abnormally with signal number
> > >> SIGSEGV.
> > >> > signal identifier = SEGV_MAPERR, address not mapped to object
> > >> > error occurs at calc_cell_indices._OMP_1 loc 00233474 offset
> > >> > 03b4
> > >> > calc_cell_indices._OMP_1 at loc 002330c0 called from loc
> > >> > 02088fa0 in

Re: [gmx-users] Number of ligand contacts over the trajectories

[anu chandra]

Thanks a lot for reply.


On Mon, Oct 14, 2013 at 12:34 PM, bipin singh  wrote:

> g_mindist with -on and -d option.
>
>
> On Mon, Oct 14, 2013 at 11:37 AM, anu chandra  wrote:
>
> > Dear Gromacs users,
> >
> > I am working with protein-ligand interaction. I would like to calculate
> the
> > number of contacts ligand make with the protein within a specific cut
> off (
> > say within 3.5 to 4.5 angstroms), along the simulation trajectories. Is
> > there any Gromacs analysis script, which can help me with doing this
> > calculation?
> >
> > Thanks in advance
> >
> > Regards
> > Anu
> > --
> > gmx-users mailing listgmx-users@gromacs.org
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> > * Please don't post (un)subscribe requests to the list. Use the
> > www interface or send it to gmx-users-requ...@gromacs.org.
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
>
>
>
> --
> *---
> Thanks and Regards,
> Bipin Singh*
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> * Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-requ...@gromacs.org.
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] recalculating .trr from .xtc

[XAvier Periole]

Interactions will be off, especially the bonded terms. 

> On Oct 15, 2013, at 7:21, Mark Abraham  wrote:
> 
> Also, the precision was selected when the xtc file was written, ie in the
> mdp file.
> 
> Mark
>> On Oct 15, 2013 3:24 AM, "Justin Lemkul"  wrote:
>> 
>> 
>> 
>>> On 10/14/13 7:56 PM, Leandro Bortot wrote:
>>> 
>>> Dear GROMACS users,
>>> 
>>>  Does anyone know how significant is the difference between the
>>> "original" .trr file from a simulation and a "recalculated" .trr from a
>>> whole system .xtc (mdrun -rerun traj.xtc -o traj.trr)?
>>>  I mean... do you know how big would be the error induced by this
>>> "recalculation" procedure?
>>> 
>>>  I'm not interested in calculating autocorrelation functions. Most of
>>> my analysis are related to the atom positions over time and free energy
>>> calculations.
>> Position-related quantities should be impacted very little.  Given that
>> you can't acquire precision though, I see no point in even generating a
>> .trr file - the .xtc has the same information while occupying less disk
>> space.
>> 
>> -Justin
>> 
>> --
>> ==**
>> 
>> Justin A. Lemkul, Ph.D.
>> Postdoctoral Fellow
>> 
>> Department of Pharmaceutical Sciences
>> School of Pharmacy
>> Health Sciences Facility II, Room 601
>> University of Maryland, Baltimore
>> 20 Penn St.
>> Baltimore, MD 21201
>> 
>> jalemkul@outerbanks.umaryland.**edu  |
>> (410) 706-7441
>> 
>> ==**
>> --
>> gmx-users mailing listgmx-users@gromacs.org
>> http://lists.gromacs.org/**mailman/listinfo/gmx-users
>> * Please search the archive at http://www.gromacs.org/**
>> Support/Mailing_Lists/Searchbefore
>>  posting!
>> * Please don't post (un)subscribe requests to the list. Use the www
>> interface or send it to gmx-users-requ...@gromacs.org.
>> * Can't post? Read 
>> http://www.gromacs.org/**Support/Mailing_Lists
> -- 
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> * Please search the archive at 
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> * Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-requ...@gromacs.org.
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists