[gmx-users] Re: distance_restraints

[maggin]

Hi, Justin,

You are right, I should first fix the bad geometry.

I check 1dx0.pdb, and the problematic areas are:
atom1 atom2
  1  N1+  (GLY124   N) 4 H  (GLY124  HT3) 
   181  C  (PRO137  CD)182 H  (PRO137  HD1)
   262  H  (PHE141  HD1)  263 C  (PHE141  CE2)
   296 O1-(ASP144  OD2)  297 C  (ASP144  C)
   685 O   (PRO165  O)  688 C  (VAL166 CA)

for these atoms bonds that rotated more than 30 degrees


1dx0.pdb is get from NMR.

So, for the initial structure , is there anyways to solve these LINCS
WARNING ?

Thank you very much!

maggin





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[gmx-users] Re: Genbox center of box

[Matt Bawn]

OK I found the problem. I had installed Surfnet the protein cavity finder a
few weeks ago, and it turns out this also has a function called genbox! so
my silly mistake.

I was wondering why centre and not center.


Thanks,

Matt




On Mon, Jun 10, 2013 at 6:23 PM, Justin Lemkul [via GROMACS] <
ml-node+s5086n5009004...@n6.nabble.com> wrote:

>
>
> On 6/10/13 3:26 PM, Matt Bawn wrote:
>
> >> I have never seen such a prompt, and I cannot reproduce the problem
> with
> > version
> >> 4.5.5 on my machine.  Did you install from source, or from some
> external
> > binary
> >> or package manager?  Are you running Gromacs directly, or are you using
> any
> > GUI
> >> interface of any sort?  Does the problem persist with a non-outdated
> > version
> >> like 4.6.2?
> >
> > I am running GROMACS that I installed and compiled myself via cygwin on
> a
> > windows machine. This prompt has only appeared recently and previously
> > following the tutorial instructions did not yield it. I went back to a
> > previous structure that had worked and the same prompt now also appears.
> I
> > can't think of anything that may have changed in the cygwin/gromacs
> > environment to cause this.
> >
>
> Got me stumped, and I don't have a Cygwin machine to test with, so I can't
> really help much more.  That prompt doesn't appear anywhere in the Gromacs
> source code, though, so it's really puzzling.  Testing with 4.6.2 would be
> useful.
>
> -Justin
>
> --
> 
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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> NAML
>



-- 
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Research Associate
Brooklyn** College CUNY




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Re: [gmx-users] [ defaults ] and nonbonded

[Justin Lemkul]

On 6/11/13 4:12 PM, Steven Neumann wrote:

Dear Gromacs Users,

I got really confused: In manual [defualts ]:

"nbfunc is the non-bonded function type. Use 1 (Lennard-Jones) or 2
(Buckingham)"

I want to use mdrun -table table.xvg with my own potential, which one I
should choose?

"gen-pairs - is for pair generation. The default is ‘no’, i.e. get 1-4
parameters from the pairtypes list. When parameters are not present in the
list, stop with a fatal error. Setting‘yes’ generates 1-4 parameters that
are not present in the pair list from normal Lennard-Jones parameters using
fudgeLJ"

I want to have all intramolecular atoms (within my chain) interacting (no
exclusions) with each other from [ atomtypes ] in ffnonbonded.itp
Does it mean "yes" with nrexcl =1 in my topology?

And sth I also got confused:

[ pairtypes ] are only 1-4 parameters or here I can specify parameters for
all atoms within my molecule? So [ atomtypes ] in ffnonbonded.itp also
correspond to intra molecular interactions?



These topics are discussed frequently.  Please search the archive; surely you 
will find relevant topics.


-Justin

--


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Blacksburg, VA
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Re: [gmx-users] Constraints of distance

[Justin Lemkul]

On 6/11/13 3:47 PM, Steven Neumann wrote:

Thank you Justin. So using nrexcl 0 or 1 (should be the same with
constraints) and type 1 will allow bonded atoms to interact (vdW) with each
other?



No, there will be differences for type 1 in this case.  Type 1 generates 
exclusions per nrexcl.  Using nrexcl = 0 will allow for all nonbonded 
interactions to be calculated, but nrexcl = 1 will exclude interactions with 
neighboring particles.  So the combination of nrexcl = 0 with type 1 
constraints, or any value of nrexcl with type 2 constraints will allow for all 
nonbonded interactions to be calculated.


-Justin



On Tue, Jun 11, 2013 at 6:10 PM, Justin Lemkul  wrote:




On 6/11/13 10:46 AM, Steven Neumann wrote:


I was not sure about the fucntion type (1 or 2). Once in manual it is
stated that function 1 is only for exclusions and another time it can be
used to miimc bonds. Both functions are working though.  Thanks anyway.



More precisely, constraints of type 1 generate exclusions between bonded
atoms within nrexcl (defined in the topology), whereas type 2 do not.
  Whether or not you need the constraints to do this depends on the nature
of the force field.


-Justin

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==**==

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Department of Biochemistry
Virginia Tech
Blacksburg, VA
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Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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[gmx-users] Re: gromacs 4.6.2 MPI distribution location problems

[sirishkaushik]

Note that this works fine with 4.5.5. 

when I installed using:

./configure CPPFLAGS="-I/home/kaushik/fftw-new/include"
LDFLAGS="-L/home/kaushik/fftw-new/lib" --enable-mpi --prefix
/home/kaushik/gromacs_executable/gromacs-old

ldd mdrun on the 4.5.5 version correctly points to the fftw and the mpi
locations:


linux-vdso.so.1 =>  (0x7fff6a302000)
libfftw3f.so.3 => /home/kaushik/fftw-new/lib/libfftw3f.so.3
(0x7f2e7a6e2000)
libmpi.so.1 => /usr/local/lib/libmpi.so.1 (0x7f2e7a34)
libnsl.so.1 => /lib/libnsl.so.1 (0x7f2e7a11b000)
libm.so.6 => /lib/libm.so.6 (0x7f2e79e99000)
libdl.so.2 => /lib/libdl.so.2 (0x7f2e79c95000)
libnuma.so.1 => /usr/lib/libnuma.so.1 (0x7f2e79a8c000)
librt.so.1 => /lib/librt.so.1 (0x7f2e79884000)
libutil.so.1 => /lib/libutil.so.1 (0x7f2e79681000)
libpthread.so.0 => /lib/libpthread.so.0 (0x7f2e79464000)
libc.so.6 => /lib/libc.so.6 (0x7f2e79102000)
libmpi.so.0 => /usr/lib/libmpi.so.0 (0x7f2e78e52000)
/lib64/ld-linux-x86-64.so.2 (0x7f2e7a9f4000)
libopen-rte.so.0 => /usr/lib/libopen-rte.so.0 (0x7f2e78c05000)
libopen-pal.so.0 => /usr/lib/libopen-pal.so.0 (0x7f2e789b)


However, with 4.6.2, when I install using:

cmake -DCMAKE_INSTALL_PREFIX=/home/kaushik/gromacs_executable/gromacs-mpi
-DGMX_THREADS=DGMX_X11=OFF -DGMX_MPI=ON
-DCMAKE_PREFIX_PATH=/home/kaushik/fftw-new -DGMX_DEFAULT_SUFFIX=OFF
-DMPI_INCLUDE_PATH=/usr/local/include -DMPI_COMPILER=/usr/local/bin/mpicxx

its now pointing to the wrong MPI libraries causing the crash with the
mpirun:

ldd mdrun:
linux-vdso.so.1 =>  (0x7fffba9ff000)
libfftw3f.so.3 => /home/kaushik/fftw-new/lib/libfftw3f.so.3
(0x7f32c6785000)
libmpi_cxx.so.0 => /usr/lib/libmpi_cxx.so.0 (0x7f32c655e000)
libmpi.so.0 => /usr/lib/libmpi.so.0 (0x7f32c62ae000)
libdl.so.2 => /lib/libdl.so.2 (0x7f32c60aa000)
libm.so.6 => /lib/libm.so.6 (0x7f32c5e27000)
libnuma.so.1 => /usr/lib/libnuma.so.1 (0x7f32c5c1f000)
librt.so.1 => /lib/librt.so.1 (0x7f32c5a17000)
libnsl.so.1 => /lib/libnsl.so.1 (0x7f32c57fe000)
libutil.so.1 => /lib/libutil.so.1 (0x7f32c55fb000)
libpthread.so.0 => /lib/libpthread.so.0 (0x7f32c53df000)
libgomp.so.1 => /usr/local/lib64/libgomp.so.1 (0x7f32c51d)
libc.so.6 => /lib/libc.so.6 (0x7f32c4e6e000)
libstdc++.so.6 => /usr/local/lib64/libstdc++.so.6 (0x7f32c4b67000)
libgcc_s.so.1 => /usr/local/lib64/libgcc_s.so.1 (0x7f32c4951000)
libopen-rte.so.0 => /usr/lib/libopen-rte.so.0 (0x7f32c4705000)
/lib64/ld-linux-x86-64.so.2 (0x7f32c6a97000)
libopen-pal.so.0 => /usr/lib/libopen-pal.so.0 (0x7f32c44af000)


Is this a potential bug, as in the gromacs compilation is picking up the
/usr/lib/ and /usr/include (old MPI locations) despite manually specifying
it using -DMPI_INCLUDE, etc?




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Aw: [gmx-users] Enthalpy Confusion

[lloyd riggs]

If you only want the total for the system or a delta for an entire run, indexed group there of, covarience (covar/aneig) does a good job.  I found neither actually fit, but the covarience does, or if you do it by hand using only LJ parmeters for the indexed sets, however I was using proteins, so for the fluid system ?, but it took some publication look ups that were quite old. (well not that old 1980's)

 

Stephan

 

Gesendet: Dienstag, 11. Juni 2013 um 20:09 Uhr
Von: "Jeffery Perkins" 
An: gmx-users@gromacs.org
Betreff: [gmx-users] Enthalpy Confusion

This may just be me not understanding what I'm looking at, but I'm trying to
get the Enthalpy of a simple test system of LJ fluid, running version 4.5.4
initially I've tried using the enthalpy option in g_energy but I noticed
that if i compare that value to H=U+pV using either the average or the
instantaneous values from g_energy switched over to SI so that there is no
issue there, the results are different (manual calculation is around 2x the
g_energy result).

So the question is, what am I overlooking in the analysis of the data i
have?



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[gmx-users] Re: Enthalpy Confusion

[Jeffery Perkins]

> >or should i be doing < U+*ref_p > = ? 

>More specifically,  + *ref_p = H 

> isn't really meaningful thing.  I mean, you can define something 
>such that  = H, but that's not really thermodynamics. 

sorry I always have issues deciding how to talk about this stuff, so thanks
for putting up with my terrible notation =)

>> example system gives  = -1168 kJ/mol and i find  = -725 kJ/mol
>> either 

>Interesting.  What material at what phase conditions?  For liquids, 
>the PV contribution should be very small.

I hadn't really thought about that... but the system is a monatomic
Lennard-Jones particle (uncharged sigma = 0.35 nm epsilon = 2 kJ/mol mass =
40 amu) which should be a liquid at the conditions I was looking at, P=1000
bar, T = 300 K using phase diagram in: Equation of state for the
Lennard-Jones fluid, J. J. Nicolas et al., MOLECULAR PHYSICS, 1979, VOL. 37,
No. 5, 1429-1454

the  is -1600 and the p is 880 when manually done, around 400 from
g_energy





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Re: [gmx-users] Re: mdrun segmentation fault for new build of gromacs 4.6.1

[Szilárd Páll]

Hi Amil,


On Mon, Jun 10, 2013 at 11:03 PM, Amil Anderson
 wrote:
> Szilárd,
>
> I tried the build using a PATH without the Intel compilers and NOT including 
> the directives -DGMX_EXTERNAL_BLAS=OFF and -DGMX_EXTERNAL_LAPACK=OFF and it 
> used the FFTW 3.2 wrappers to MKL.  Here is the output from mdrun -version:

Note that the aim of both workarounds is to stop the build system from
picking up the MKL BLAS/LAPACK libraries. Hence, I suspect that you
may have not been successful at preventing cmake to pick up the Intel
Compilers' location. I may very well be (have not looked at the code,
though) that the cmake find module looks at the standard installation
location (e.g. /opt/intel) and picks up automatically if something is
found there. Hence, removing MKL form the path may not help at all.

In any case, I suppose this should be fixed in 4.6.2, but you should
wait for the imminent bugfix release, 4.6.3.

Cheers,
Szilard

>
> Program: mdrun
> Gromacs version:VERSION 4.6.1
> Precision:  single
> Memory model:   64 bit
> MPI library:thread_mpi
> OpenMP support: enabled
> GPU support:disabled
> invsqrt routine:gmx_software_invsqrt(x)
> CPU acceleration:   SSE4.1
> FFT library:FFTW 3.2 wrappers to MKL
> Large file support: enabled
> RDTSCP usage:   enabled
> Built on:   Mon Jun 10 15:34:03 CDT 2013
> Built by:   
> softwaremgmt@warp2-login.cluster 
> [CMAKE]
> Build OS/arch:  Linux 2.6.18-308.20.1.el5 x86_64
> Build CPU vendor:   GenuineIntel
> Build CPU brand:Intel(R) Xeon(R) CPU   E5520  @ 2.27GHz
> Build CPU family:   6   Model: 26   Stepping: 5
> Build CPU features: apic clfsh cmov cx8 cx16 htt lahf_lm mmx msr nonstop_tsc 
> pdcm popcnt pse rdtscp sse2 sse3 sse4.1 sse4.2 ssse3
> C compiler: /opt/centos/devtoolset-1.0/root/usr/bin/gcc GNU gcc (GCC) 
> 4.7.0 20120507 (Red Hat 4.7.0-5)
> C compiler flags:   -msse4.1   -Wextra -Wno-missing-field-initializers 
> -Wno-sign-compare -Wall -Wno-unused -Wunused-value   -fomit-frame-pointer 
> -funroll-all-loops -fexcess-precision=fast  -O3 -DNDEBUG
>
>
> All the regressiontests failed.  So it appears that, at least for my system, 
> I need to include the directives to not use the external BLAS/LAPACK.
>
> Amil
>
>
>
> On Jun 10, 2013, at 12:12 PM, Szilárd Páll [via GROMACS] wrote:
>
> Amil,
>
> It looks like there is a mixup in your software configuration and
> mdrun is linked against libguide.so, the OpenMP library part of the
> Intel compiler v11 which gets loaded early and is probably causing the
> crash. This library was probably pulled in implicitly by MKL which the
> build system detected and tried to use for BLAS/LAPACK (note that you
> have "FFT library:FFTW 3.2 wrappers to MKL" in the log and I
> assume you intended to use FFTW). I was under the impression that this
> issue was solved in 4.6.1 (http://redmine.gromacs.org/issues/1067),
> but perhaps that's not the case.
>
> I suggest you make sure that mdrun is not linked against any Intel
> library. The easiest way to achieve this is to either:
> - set -DGMX_EXTERNAL_BLAS=OFF and -DGMX_EXTERNAL_LAPACK=OFF so that
> the internal BLAS/LAPACK is used or
> - make sure that the Intel Compilers/MKL installation is not in the
> path so that the build system does not detect it.
>
> Check the mdrun -version output, specifically the reported "FFT
> library", after you recompile mdrun.
>
> Cheers,
> --
> Szilárd
>
>
> On Mon, Jun 10, 2013 at 4:57 PM, Amil Anderson <[hidden 
> email]> wrote:
>
>> Roland,
>>
>> Here is the output from the debug run with the stack trace:
>>
>> [aanderson@warp2-login gmxdemo]$ gdb mdrun
>> GNU gdb Fedora (6.8-27.el5)
>> Copyright (C) 2008 Free Software Foundation, Inc.
>> License GPLv3+: GNU GPL version 3 or later 
>> This is free software: you are free to change and redistribute it.
>> There is NO WARRANTY, to the extent permitted by law.  Type "show copying"
>> and "show warranty" for details.
>> This GDB was configured as "x86_64-redhat-linux-gnu"...
>> (gdb) run -nt 1 -s cpeptide_em -o cpeptide_em -c cpeptide_b4pr -v
>> Starting program: /shared/software/gromacs-4.6.1/bin/mdrun -nt 1 -s 
>> cpeptide_em -o cpeptide_em -c cpeptide_b4pr -v
>> [Thread debugging using libthread_db enabled]
>>  :-)  G  R  O  M  A  C  S  (-:
>>
>>   Gromacs Runs On Most of All Computer Systems
>>
>> :-)  VERSION 4.6.1  (-:
>> ...
>>
>> Back Off! I just backed up md.log to ./#md.log.18#
>> Reading file cpeptide_em.tpr, VERSION 4.6.1 (single precision)
>> Using 1 MPI thread
>> [New Thread 0x2b5fe6188ee0 (LWP 19572)]
>>
>> Program received signal SIGSEGV, Segmentation fault.
>> 0x2b5fe3865479 in omp_set_num_threads ()
>>from /shared/software/intel/Compiler/11.1/046/lib/intel64/libguide.so
>> (gdb) bt
>> #0  0x2b5fe3865479 in omp_set_num_threads ()
>>from 

Re: [gmx-users] Re: Enthalpy Confusion

[Michael Shirts]

> or should i be doing < U+*ref_p > = ?

More specifically,  + *ref_p = H

 isn't really meaningful thing.  I mean, you can define something
such that  = H, but that's not really thermodynamics.

> example system gives  = -1168 kJ/mol and i find  = -725 kJ/mol either

Interesting.  What material at what phase conditions?  For liquids,
the PV contribution should be very small.
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[gmx-users] Re: Enthalpy Confusion

[Jeffery Perkins]

>You should not use pV from g_energy though, as Michael explained, rather 
>you need ref_p times . This precludes that your system is in 
>equilibrium of course.

That is what I had initially thought, then take that with the  to get
?
or should i be doing < U+*ref_p > = ?

But even so I still get different values for H then g_energy returns

example system gives  = -1168 kJ/mol and i find  = -725 kJ/mol either
way
I was mostly using pV as a stand in for H as it seems to be where the
difference between manual calculation and g_energy lies

thanks again for taking the time to assist,

Jeffery



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Re: [gmx-users] Re: Enthalpy Confusion

[David van der Spoel]

On 2013-06-11 21:57, Jeffery Perkins wrote:

If you are computing enthaply in the NPT ensemble, P is constant, and
is the applied pressure.



The "pressure" quantity calculated from the KE and the virial is not
the pressure.  It is a quantity that when averaged over time is equal
the pressure.  Only the average is meaningful macroscopically.


Right, that's an easy one to miss but i don't think that's my problem here.


If you are computing enthalpy in another ensemble (which is possible,
though it may be harder to interpret) then you would use the average
pressure from this quantity


I'm running in NPT and was calcaulating H from ave. P, ave. U and ave. V for
the run
while i understand that this doesn't exactly equal average H it should be
close enough for me at this point, going back and redoing it with P set to
the reference value (which the average hits with small fluctuations)

the resultant H still doesn't line up properly for some example data:

"pV, g_energy"V, m^3  pV, J pV, kJ/mol
442.42  1.46E-26  1.46E-18884.07

P = 1000 bar = 100,000,000 Pa
and i see that my pV is around 2x g_energies pV, no values are scaled for
the # of items in the box at this point, this is all for moles of the system

  i think that's alright though


You should not use pV from g_energy though, as Michael explained, rather 
you need ref_p times . This precludes that your system is in 
equilibrium of course.






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Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
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[gmx-users] [ defaults ] and nonbonded

[Steven Neumann]

Dear Gromacs Users,

I got really confused: In manual [defualts ]:

"nbfunc is the non-bonded function type. Use 1 (Lennard-Jones) or 2
(Buckingham)"

I want to use mdrun -table table.xvg with my own potential, which one I
should choose?

"gen-pairs - is for pair generation. The default is ‘no’, i.e. get 1-4
parameters from the pairtypes list. When parameters are not present in the
list, stop with a fatal error. Setting‘yes’ generates 1-4 parameters that
are not present in the pair list from normal Lennard-Jones parameters using
fudgeLJ"

I want to have all intramolecular atoms (within my chain) interacting (no
exclusions) with each other from [ atomtypes ] in ffnonbonded.itp
Does it mean "yes" with nrexcl =1 in my topology?

And sth I also got confused:

[ pairtypes ] are only 1-4 parameters or here I can specify parameters for
all atoms within my molecule? So [ atomtypes ] in ffnonbonded.itp also
correspond to intra molecular interactions?


Thank you

Steven
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[gmx-users] Re: Enthalpy Confusion

[Jeffery Perkins]

>If you are computing enthaply in the NPT ensemble, P is constant, and 
>is the applied pressure. 

>The "pressure" quantity calculated from the KE and the virial is not 
>the pressure.  It is a quantity that when averaged over time is equal 
>the pressure.  Only the average is meaningful macroscopically. 

Right, that's an easy one to miss but i don't think that's my problem here. 

>If you are computing enthalpy in another ensemble (which is possible, 
>though it may be harder to interpret) then you would use the average 
>pressure from this quantity

I'm running in NPT and was calcaulating H from ave. P, ave. U and ave. V for
the run
while i understand that this doesn't exactly equal average H it should be
close enough for me at this point, going back and redoing it with P set to
the reference value (which the average hits with small fluctuations)

the resultant H still doesn't line up properly for some example data:

"pV, g_energy"V, m^3  pV, J pV, kJ/mol
442.42  1.46E-26  1.46E-18884.07

P = 1000 bar = 100,000,000 Pa
and i see that my pV is around 2x g_energies pV, no values are scaled for
the # of items in the box at this point, this is all for moles of the system

 i think that's alright though



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Re: [gmx-users] Constraints of distance

[Steven Neumann]

Thank you Justin. So using nrexcl 0 or 1 (should be the same with
constraints) and type 1 will allow bonded atoms to interact (vdW) with each
other?


On Tue, Jun 11, 2013 at 6:10 PM, Justin Lemkul  wrote:

>
>
> On 6/11/13 10:46 AM, Steven Neumann wrote:
>
>> I was not sure about the fucntion type (1 or 2). Once in manual it is
>> stated that function 1 is only for exclusions and another time it can be
>> used to miimc bonds. Both functions are working though.  Thanks anyway.
>>
>>
> More precisely, constraints of type 1 generate exclusions between bonded
> atoms within nrexcl (defined in the topology), whereas type 2 do not.
>  Whether or not you need the constraints to do this depends on the nature
> of the force field.
>
>
> -Justin
>
> --
> ==**==
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin
>
> ==**==
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[gmx-users] 2013 GROMACS USA Workshop and Conference

[Michael Shirts]

Dear GROMACS users list members:

We are pleased to announce the 2013 GROMACS USA Workshop and
Conference at the University of Virginia in Charlottesville, Virginia,
on September 13-15th.  This will be the first full GROMACS workshop
held here in the U.S.

The workshop and conference will consist of two days of tutorials,
discussions of future plans for GROMACS, face time with a large
percentage of the developers, plenary software and application
sessions, and a last day of development planning to which attendees
are also invited to help influence the future directions of GROMACS.

Please visit http://faculty.virginia.edu/gromacsworkshop for
registration and for much more information about the program.

For specific questions about registering or logistics after visiting
the website, please write to
gromacsworkshop-registrat...@virginia.edu.

Sincerely,
The 2013 GROMACS USA Workshop and Conference Steering Committee
Michael Shirts (chair)
Angel Garcia
Berk Hess
Yu-Shan Lin
Erik Lindahl
Peter Kasson
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Re: [gmx-users] Re: Enthalpy Confusion

[Michael Shirts]

If you are computing enthaply in the NPT ensemble, P is constant, and
is the applied pressure.

The "pressure" quantity calculated from the KE and the virial is not
the pressure.  It is a quantity that when averaged over time is equal
the pressure.  Only the average is meaningful macroscopically.

If you are computing enthalpy in another ensemble (which is possible,
though it may be harder to interpret) then you would use the average
pressure from this quantity.



On Tue, Jun 11, 2013 at 3:08 PM, Jeffery Perkins  wrote:
> that's what i thought, and what i tried to do, my pressure is a bit higher
> then that, we want a Lennard-Jones liquid so it's running at 1000+ bar, and
> while I agree that gromacs is giving H as Etot + pV it appears that when i
> calculate pV i get a different value from what g_energy returns for it I did
> p in Pa, V in m^3, as the whole box, to get J of energy, and then multiply
> by 6.02E23 to get J/mol of my box, and then convert down to kJ/mol to be the
> same units as g_energy.
>
> When you say the applied pressure you mean that p = ref_p? or the calculated
> pressure from the virial and Ke?
>
> Thanks for the help,
>
> Jeffery
>
>
>
> --
> View this message in context: 
> http://gromacs.5086.x6.nabble.com/Enthalpy-Confusion-tp5009053p5009058.html
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[gmx-users] Re: Enthalpy Confusion

[Jeffery Perkins]

that's what i thought, and what i tried to do, my pressure is a bit higher
then that, we want a Lennard-Jones liquid so it's running at 1000+ bar, and
while I agree that gromacs is giving H as Etot + pV it appears that when i
calculate pV i get a different value from what g_energy returns for it I did
p in Pa, V in m^3, as the whole box, to get J of energy, and then multiply
by 6.02E23 to get J/mol of my box, and then convert down to kJ/mol to be the
same units as g_energy.

When you say the applied pressure you mean that p = ref_p? or the calculated
pressure from the virial and Ke?

Thanks for the help,

Jeffery



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Re: [gmx-users] Enthalpy Confusion

[David van der Spoel]

On 2013-06-11 20:09, Jeffery Perkins wrote:

This may just be me not understanding what I'm looking at, but I'm trying to
get the Enthalpy of a simple test system of LJ fluid, running version 4.5.4
initially I've tried using the enthalpy option in g_energy but I noticed
that if i compare that value to H=U+pV using either the average  or the
instantaneous values from g_energy switched over to SI so that there is no
issue there, the results are different (manual calculation is around 2x the
g_energy result).

So the question is, what am I overlooking in the analysis of the data i
have?

The calculation is done inside mdrun and it provides
H = Etot + pV

where p is the applied pressure (typically 1 bar).
Is this the same that you did?




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Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
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Re: [gmx-users] System does not heat up to 300K.

[Marc Hoemberger]

Thanks, I must have confused the units for the simulated annealing
parameters.


On Tue, Jun 11, 2013 at 2:12 PM, Dr. Vitaly Chaban wrote:

> According to your MD parameters, your system should attain T=300K at the
> 300th
> nanosecond.
>
> Since you have run only for 50 * 0.002 ps = 1ns, you got T=1K, since
> temperature elevates linearly, based on your setup.
>
>
> Dr. Vitaly Chaban
>
>
>
>
> On Tue, Jun 11, 2013 at 8:07 PM, Marc Hömberger  wrote:
>
> > Hi,
> >
> > I have a system setup (minimized etc.) and wanted to heat this system
> > gradually with simulated annealing. I set up the mdp file as you can see
> > below (simulated annealing part is marked bold). But when the heating is
> > finished, the log file tells me that the temperature of the system is
> only
> > 1K (see below).
> >
> > Can someone tell me what I am doing wrong?
> >
> >
> > Best,
> > Marc
> >
> > ; PREPROCESSING *
> > ;include=
> > ;define =
> > ; RUN CONTROL ***
> > dt  = 0.002 ; timestep, 2 fs
> > integrator  = md; leap-frog integrator
> > nsteps  = 50 ; 2 * 50 = 1000 ps
> > tinit   = 0 ; starting time, ps
> > init_step   = 0 ; starting step
> > comm-mode   = linear; remove COM translation
> > nstcomm = 10; freq steps comm-mode
> > comm-grps   = system; groups COM removal ; protein
> > nstcalcenergy   = -1; freq calc ener; default =
> nstlist
> > ; DYNAMICS **
> > ;### Initial velocity assignment
> > gen_vel = yes   ; assign velocities from Maxwell
> > distribution
> > gen_temp= 300   ; temperature for Maxwell
> > distribution
> > gen_seed= -1; random generator seed; -1 from
> > job ID
> > ; OUTPUT CONTROL 
> > ;### xtc
> > nstxtcout   = 2500  ; .xtc freq write coor
> > xtc-precision   = 1000  ; .xtc precision
> > xtc_grps= system; .xtc saved groups
> > ;### trr
> > nstxout = 50; .trr freq write coor
> > nstvout = 50; .trr freq write vel
> > nstfout = 0 ; .trr freq write forces
> > ;### log
> > nstlog  = 2500  ; .log freq write ener
> > ;### edr
> > nstenergy   = 2500  ; .edr freq write ener; =
> > i*nstcalcenergy
> > energygrps  = protein non-protein   ; .edr saved groups
> > ; NON-BONDED INTERACTIONS ***
> > ns_type = grid  ; search neighbor grid cells
> > nstlist = 10; freq update NB list
> >
> > vdwtype = switch; switching function for VdW
> > coulombtype = PME   ; PME for long-range
> electrostatics
> > rvdw_switch = 0.9   ; switching dist VdW
> > rvdw= 1.0   ; cutoff VdW
> > rcoulomb= 1.2   ; cutoff elec
> > rlist   = 1.2   ; cutoff NB list; must = rcoulomb
> > when PME
> >
> > epsilon-r   = 1 ; dielectric const
> > DispCorr= EnerPres  ; Long-range VdW dispersion
> > correction
> >
> > ;### PME & Ewald
> > ewald_rtol  = 1.0e-5; direct space tolerance;
> > 1.0e-6/2.2e-5
> > fourierspacing  = 0.12  ; max grid spacing for FFT
> > pme_order   = 6 ; interpolation order; depends on
> > cutoff
> > ewald_geometry  = 3d; Ewald in 3d
> > epsilon_surface = 0 ; dipole correction for 3d Ewald
> > optimize_fft= yes   ; start-up FFT grid optimization
> > ; BOUNDARY CONTROL **
> > pbc = xyz   ; 3-D PBC
> > ; CONSTRAINTS CONTROL ***
> > constraints = all-bonds ; all bonds (even heavy atom-H
> > bonds) constrained
> > continuation= no; constraints applied to initial
> > conf
> > constraint_algorithm = lincs; holonomic constraints
> > lincs_iter  = 1 ; accuracy of LINCS
> > lincs_order = 4 ; also related to accuracy
> > lincs_warnangle = 30; max allowed bond angle before
> > warning
> > ; TEMPERATURE CONTROL ***
> > tcoupl  = nose-hoover   ; Nose-Hoover T-coupling;
> v-rescale
> > tc-grps = s

Re: [gmx-users] System does not heat up to 300K.

[Dr. Vitaly Chaban]

According to your MD parameters, your system should attain T=300K at the 300th
nanosecond.

Since you have run only for 50 * 0.002 ps = 1ns, you got T=1K, since
temperature elevates linearly, based on your setup.


Dr. Vitaly Chaban




On Tue, Jun 11, 2013 at 8:07 PM, Marc Hömberger  wrote:

> Hi,
>
> I have a system setup (minimized etc.) and wanted to heat this system
> gradually with simulated annealing. I set up the mdp file as you can see
> below (simulated annealing part is marked bold). But when the heating is
> finished, the log file tells me that the temperature of the system is only
> 1K (see below).
>
> Can someone tell me what I am doing wrong?
>
>
> Best,
> Marc
>
> ; PREPROCESSING *
> ;include=
> ;define =
> ; RUN CONTROL ***
> dt  = 0.002 ; timestep, 2 fs
> integrator  = md; leap-frog integrator
> nsteps  = 50 ; 2 * 50 = 1000 ps
> tinit   = 0 ; starting time, ps
> init_step   = 0 ; starting step
> comm-mode   = linear; remove COM translation
> nstcomm = 10; freq steps comm-mode
> comm-grps   = system; groups COM removal ; protein
> nstcalcenergy   = -1; freq calc ener; default = nstlist
> ; DYNAMICS **
> ;### Initial velocity assignment
> gen_vel = yes   ; assign velocities from Maxwell
> distribution
> gen_temp= 300   ; temperature for Maxwell
> distribution
> gen_seed= -1; random generator seed; -1 from
> job ID
> ; OUTPUT CONTROL 
> ;### xtc
> nstxtcout   = 2500  ; .xtc freq write coor
> xtc-precision   = 1000  ; .xtc precision
> xtc_grps= system; .xtc saved groups
> ;### trr
> nstxout = 50; .trr freq write coor
> nstvout = 50; .trr freq write vel
> nstfout = 0 ; .trr freq write forces
> ;### log
> nstlog  = 2500  ; .log freq write ener
> ;### edr
> nstenergy   = 2500  ; .edr freq write ener; =
> i*nstcalcenergy
> energygrps  = protein non-protein   ; .edr saved groups
> ; NON-BONDED INTERACTIONS ***
> ns_type = grid  ; search neighbor grid cells
> nstlist = 10; freq update NB list
>
> vdwtype = switch; switching function for VdW
> coulombtype = PME   ; PME for long-range electrostatics
> rvdw_switch = 0.9   ; switching dist VdW
> rvdw= 1.0   ; cutoff VdW
> rcoulomb= 1.2   ; cutoff elec
> rlist   = 1.2   ; cutoff NB list; must = rcoulomb
> when PME
>
> epsilon-r   = 1 ; dielectric const
> DispCorr= EnerPres  ; Long-range VdW dispersion
> correction
>
> ;### PME & Ewald
> ewald_rtol  = 1.0e-5; direct space tolerance;
> 1.0e-6/2.2e-5
> fourierspacing  = 0.12  ; max grid spacing for FFT
> pme_order   = 6 ; interpolation order; depends on
> cutoff
> ewald_geometry  = 3d; Ewald in 3d
> epsilon_surface = 0 ; dipole correction for 3d Ewald
> optimize_fft= yes   ; start-up FFT grid optimization
> ; BOUNDARY CONTROL **
> pbc = xyz   ; 3-D PBC
> ; CONSTRAINTS CONTROL ***
> constraints = all-bonds ; all bonds (even heavy atom-H
> bonds) constrained
> continuation= no; constraints applied to initial
> conf
> constraint_algorithm = lincs; holonomic constraints
> lincs_iter  = 1 ; accuracy of LINCS
> lincs_order = 4 ; also related to accuracy
> lincs_warnangle = 30; max allowed bond angle before
> warning
> ; TEMPERATURE CONTROL ***
> tcoupl  = nose-hoover   ; Nose-Hoover T-coupling; v-rescale
> tc-grps = system; two coupling groups - more
> accurate
> tau_t   = 0.6   ; coupling time constant at equil,
> in ps
> ref_t   = 300   ; reference temperature, one for
> each group, in K
> ; PRESSURE CONTROL **
> pcoupl  = Parrinello-Rah

Re: [gmx-users] System does not heat up to 300K.

[Justin Lemkul]

On 6/11/13 2:07 PM, Marc Hömberger wrote:

Hi,

I have a system setup (minimized etc.) and wanted to heat this system
gradually with simulated annealing. I set up the mdp file as you can see
below (simulated annealing part is marked bold). But when the heating is
finished, the log file tells me that the temperature of the system is only
1K (see below).

Can someone tell me what I am doing wrong?



You've specified heating to 300K over 300,000 ps (300 ns), thus 1 K per 1 ns. 
Your simulation calls for 1 ns of time, thus 1 K should be achieved.


-Justin



Best,
Marc

; PREPROCESSING *
;include=
;define =
; RUN CONTROL ***
dt  = 0.002 ; timestep, 2 fs
integrator  = md; leap-frog integrator
nsteps  = 50 ; 2 * 50 = 1000 ps
tinit   = 0 ; starting time, ps
init_step   = 0 ; starting step
comm-mode   = linear; remove COM translation
nstcomm = 10; freq steps comm-mode
comm-grps   = system; groups COM removal ; protein
nstcalcenergy   = -1; freq calc ener; default = nstlist
; DYNAMICS **
;### Initial velocity assignment
gen_vel = yes   ; assign velocities from Maxwell
distribution
gen_temp= 300   ; temperature for Maxwell
distribution
gen_seed= -1; random generator seed; -1 from
job ID
; OUTPUT CONTROL 
;### xtc
nstxtcout   = 2500  ; .xtc freq write coor
xtc-precision   = 1000  ; .xtc precision
xtc_grps= system; .xtc saved groups
;### trr
nstxout = 50; .trr freq write coor
nstvout = 50; .trr freq write vel
nstfout = 0 ; .trr freq write forces
;### log
nstlog  = 2500  ; .log freq write ener
;### edr
nstenergy   = 2500  ; .edr freq write ener; =
i*nstcalcenergy
energygrps  = protein non-protein   ; .edr saved groups
; NON-BONDED INTERACTIONS ***
ns_type = grid  ; search neighbor grid cells
nstlist = 10; freq update NB list

vdwtype = switch; switching function for VdW
coulombtype = PME   ; PME for long-range electrostatics
rvdw_switch = 0.9   ; switching dist VdW
rvdw= 1.0   ; cutoff VdW
rcoulomb= 1.2   ; cutoff elec
rlist   = 1.2   ; cutoff NB list; must = rcoulomb
when PME

epsilon-r   = 1 ; dielectric const
DispCorr= EnerPres  ; Long-range VdW dispersion
correction

;### PME & Ewald
ewald_rtol  = 1.0e-5; direct space tolerance;
1.0e-6/2.2e-5
fourierspacing  = 0.12  ; max grid spacing for FFT
pme_order   = 6 ; interpolation order; depends on
cutoff
ewald_geometry  = 3d; Ewald in 3d
epsilon_surface = 0 ; dipole correction for 3d Ewald
optimize_fft= yes   ; start-up FFT grid optimization
; BOUNDARY CONTROL **
pbc = xyz   ; 3-D PBC
; CONSTRAINTS CONTROL ***
constraints = all-bonds ; all bonds (even heavy atom-H
bonds) constrained
continuation= no; constraints applied to initial
conf
constraint_algorithm = lincs; holonomic constraints
lincs_iter  = 1 ; accuracy of LINCS
lincs_order = 4 ; also related to accuracy
lincs_warnangle = 30; max allowed bond angle before
warning
; TEMPERATURE CONTROL ***
tcoupl  = nose-hoover   ; Nose-Hoover T-coupling; v-rescale
tc-grps = system; two coupling groups - more
accurate
tau_t   = 0.6   ; coupling time constant at equil,
in ps
ref_t   = 300   ; reference temperature, one for
each group, in K
; PRESSURE CONTROL **
pcoupl  = Parrinello-Rahman ; Pressure coupling on in
NPT
pcoupltype  = isotropic ; uniform scaling of box vectors
tau_p   = 1.0   ; coupling time constant at equil,
in ps
ref_p   = 1.0   ; reference pressure, in bar
compressibility

[gmx-users] Enthalpy Confusion

[Jeffery Perkins]

This may just be me not understanding what I'm looking at, but I'm trying to
get the Enthalpy of a simple test system of LJ fluid, running version 4.5.4
initially I've tried using the enthalpy option in g_energy but I noticed
that if i compare that value to H=U+pV using either the average  or the
instantaneous values from g_energy switched over to SI so that there is no
issue there, the results are different (manual calculation is around 2x the
g_energy result).

So the question is, what am I overlooking in the analysis of the data i
have?



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[gmx-users] System does not heat up to 300K.

[Marc Hömberger]

Hi,

I have a system setup (minimized etc.) and wanted to heat this system
gradually with simulated annealing. I set up the mdp file as you can see
below (simulated annealing part is marked bold). But when the heating is
finished, the log file tells me that the temperature of the system is only
1K (see below).

Can someone tell me what I am doing wrong?


Best,
Marc

; PREPROCESSING *
;include=
;define =
; RUN CONTROL ***
dt  = 0.002 ; timestep, 2 fs
integrator  = md; leap-frog integrator
nsteps  = 50 ; 2 * 50 = 1000 ps
tinit   = 0 ; starting time, ps
init_step   = 0 ; starting step
comm-mode   = linear; remove COM translation
nstcomm = 10; freq steps comm-mode
comm-grps   = system; groups COM removal ; protein
nstcalcenergy   = -1; freq calc ener; default = nstlist
; DYNAMICS **
;### Initial velocity assignment
gen_vel = yes   ; assign velocities from Maxwell
distribution
gen_temp= 300   ; temperature for Maxwell
distribution
gen_seed= -1; random generator seed; -1 from
job ID
; OUTPUT CONTROL 
;### xtc
nstxtcout   = 2500  ; .xtc freq write coor
xtc-precision   = 1000  ; .xtc precision
xtc_grps= system; .xtc saved groups
;### trr
nstxout = 50; .trr freq write coor
nstvout = 50; .trr freq write vel
nstfout = 0 ; .trr freq write forces
;### log
nstlog  = 2500  ; .log freq write ener
;### edr
nstenergy   = 2500  ; .edr freq write ener; =
i*nstcalcenergy
energygrps  = protein non-protein   ; .edr saved groups
; NON-BONDED INTERACTIONS ***
ns_type = grid  ; search neighbor grid cells
nstlist = 10; freq update NB list

vdwtype = switch; switching function for VdW
coulombtype = PME   ; PME for long-range electrostatics
rvdw_switch = 0.9   ; switching dist VdW
rvdw= 1.0   ; cutoff VdW
rcoulomb= 1.2   ; cutoff elec
rlist   = 1.2   ; cutoff NB list; must = rcoulomb
when PME

epsilon-r   = 1 ; dielectric const
DispCorr= EnerPres  ; Long-range VdW dispersion
correction

;### PME & Ewald
ewald_rtol  = 1.0e-5; direct space tolerance;
1.0e-6/2.2e-5
fourierspacing  = 0.12  ; max grid spacing for FFT
pme_order   = 6 ; interpolation order; depends on
cutoff
ewald_geometry  = 3d; Ewald in 3d
epsilon_surface = 0 ; dipole correction for 3d Ewald
optimize_fft= yes   ; start-up FFT grid optimization
; BOUNDARY CONTROL **
pbc = xyz   ; 3-D PBC
; CONSTRAINTS CONTROL ***
constraints = all-bonds ; all bonds (even heavy atom-H
bonds) constrained
continuation= no; constraints applied to initial
conf
constraint_algorithm = lincs; holonomic constraints
lincs_iter  = 1 ; accuracy of LINCS
lincs_order = 4 ; also related to accuracy
lincs_warnangle = 30; max allowed bond angle before
warning
; TEMPERATURE CONTROL ***
tcoupl  = nose-hoover   ; Nose-Hoover T-coupling; v-rescale
tc-grps = system; two coupling groups - more
accurate
tau_t   = 0.6   ; coupling time constant at equil,
in ps
ref_t   = 300   ; reference temperature, one for
each group, in K
; PRESSURE CONTROL **
pcoupl  = Parrinello-Rahman ; Pressure coupling on in
NPT
pcoupltype  = isotropic ; uniform scaling of box vectors
tau_p   = 1.0   ; coupling time constant at equil,
in ps
ref_p   = 1.0   ; reference pressure, in bar
compressibility = 4.5e-5; isothermal compressibility of
water at 1 atm, bar^-1
; SIMULATED ANNEALING **
*annealing   = single; type of 

[gmx-users] Re: Membrane Equilibration

[Neha]

Hi,

I am using the Martini field for those who wanted to know.

My values for the mdp file for ref_p were inspired from this paper as it
says pressure was coupled anisotropically to 0 bar in all directions. 

http://www.sciencedirect.com/science/article/pii/S0005273611002045

I think I will try to set gen_vel = no and see what happens. If it doesn't
work I will experiment with altering the ref_p values and surface tension
etc. Thank you all for the help!



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[gmx-users] Re: Membrane Equilibration

[JW Gibbs]

Is there a reason you would like to keep it at 105K? Just curious which
forcefield are you using? 

Also, for proper surface tension, there is an option called 

pcoupltype = surface-tension. 

I think you should check that out. 



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Re: [gmx-users] Re: Membrane Equilibration

[Justin Lemkul]

On 6/11/13 1:25 PM, Neha wrote:

Hi everybody,

Thank you so much for taking the time to read this.
I thought ref_p would need to be 0.0 and 0.0 if I wanted zero surface
tension. How else could I get a tensionless membrane?



As far as I understand, surface tension is only applied when using "pcoupl = 
surface-tension" and then ref_p specifies the value of surface tension in 
bar-nm.  Normally, ref_p specifies the reference pressure for an NPT ensemble.



As for the generating velocities, I completely forgot that would ruin the
equilibrium. Would you recommend saying gen_vel = no or simply raising the
gen_temp closer to the required value? If the second how close do you think
I should keep it? Sorry for bombarding you guys with so many questions!



gen_temp is irrelevant when gen_vel is set to "no."


Also no one has commented on this so I'm guessing using the structure file
from the Berendsen run is an okay way to do what I want?



The configuration alone is insufficient.  You should preserve the previous 
ensemble by passing the final .cpt file to grompp -t.


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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[gmx-users] Re: Membrane Equilibration

[JW Gibbs]

Exactly so. I think Gromacs issues a warning when you try to initialize
velocities with Parrinello-Rahman barostat. But if you performed your
equilibration at 105K using Berendsen barostat, I think it should be okay
and you should put gen-vel = no. 



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[gmx-users] Re: Membrane Equilibration

[Neha]

Hi everybody,

Thank you so much for taking the time to read this. 
I thought ref_p would need to be 0.0 and 0.0 if I wanted zero surface
tension. How else could I get a tensionless membrane?

As for the generating velocities, I completely forgot that would ruin the
equilibrium. Would you recommend saying gen_vel = no or simply raising the
gen_temp closer to the required value? If the second how close do you think
I should keep it? Sorry for bombarding you guys with so many questions!

Also no one has commented on this so I'm guessing using the structure file
from the Berendsen run is an okay way to do what I want?

Again thanks for the help!


Justin Lemkul wrote
> On 6/11/13 1:13 PM, HANNIBAL LECTER wrote:
>> ref_p= 0.0  0.0 ??
>>
>> Are you sure about this??
>>
> 
> That's a likely culprit.  See below for another.
> 
> 
>>>
>>> On Tue, Jun 11, 2013 at 5:22 PM, Neha <

> nshafique@

> > wrote:
>>>
 Hi everybody,

 I am trying to simulate a lipid bilayer and wanted to use Parrinello
>>> Rahman
 coupling. However, I read that Parinello-Rahman is not great for
 equilibration so I thought I would do a small run using the Berendsen
 barostat to decrease the chances of large oscillations. I then used the
 .gro
 file obtained from that run to start a new run using Parrinello-Rahman.
 I
 am
 not sure if that's the correct way to go about doing what I want to do.

 My Parrinello run also terminated a little while in, with the error
 that
>>> 2
 of my atoms have moved further apart than the cut-off distance. A part
 of
 my
 mdp file is pasted below and I was wondering if anyone had any
>>> suggestions
 as to stop that from happening. My time step is 0.02 ps and I thought
 increasing tau-p might work. I am using the compressibility from the
 map
 file on the Martini website and am worried that might be too large. Any
 help
 will be super useful! Let me know if you need any more information.


 ; OPTIONS FOR WEAK COUPLING ALGORITHMS =
 ; Temperature coupling   =
 tcoupl   = nose-hoover
 ; Groups to couple separately =
 tc-grps  = DPPC W
 ; Time constant (ps) and reference temperature (K) =
 tau_t= 1.0 1.0
 ref_t= 320 320
 nsttcouple   = 1
 ; Pressure coupling  =
 Pcoupl   = Parrinello-Rahman
 Pcoupltype   = semiisotropic
 ; Time constant (ps), compressibility (1/bar) and reference P (bar) =
 tau_p= 5.0  5.0
 compressibility  = 3e-4 3e-4
 ref_p= 0.0  0.0
 nstpcouple   = 5

 ; GENERATE VELOCITIES FOR STARTUP RUN =
 gen_vel  = yes
 gen_temp = 105
> 
> Here is another issue.  You're re-generating velocities (destroying the
> previous 
> equilibration) with a barostat that doesn't usually play nice under such 
> circumstances, and you're generating velocities for a temperature well
> below the 
> target defined in ref_t.  That can cause the thermostat to go haywire,
> which 
> then has negative effects on the pressure (which comes from kinetic energy
> and 
> the virial), which can lead to collapse.
> 
> -Justin
> 
> -- 
> 
> 
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
> 
> -- 
> gmx-users mailing list

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Re: [gmx-users] Membrane Equilibration

[Justin Lemkul]

On 6/11/13 1:13 PM, HANNIBAL LECTER wrote:

ref_p= 0.0  0.0 ??

Are you sure about this??



That's a likely culprit.  See below for another.



On Tue, Jun 11, 2013 at 12:08 PM, Dr. Vitaly Chaban wrote:


what happens to your energy before the observed crash? does the crash
happen at the same time-step each time?


Dr. Vitaly Chaban


On Tue, Jun 11, 2013 at 5:22 PM, Neha  wrote:


Hi everybody,

I am trying to simulate a lipid bilayer and wanted to use Parrinello

Rahman

coupling. However, I read that Parinello-Rahman is not great for
equilibration so I thought I would do a small run using the Berendsen
barostat to decrease the chances of large oscillations. I then used the
.gro
file obtained from that run to start a new run using Parrinello-Rahman. I
am
not sure if that's the correct way to go about doing what I want to do.

My Parrinello run also terminated a little while in, with the error that

2

of my atoms have moved further apart than the cut-off distance. A part of
my
mdp file is pasted below and I was wondering if anyone had any

suggestions

as to stop that from happening. My time step is 0.02 ps and I thought
increasing tau-p might work. I am using the compressibility from the map
file on the Martini website and am worried that might be too large. Any
help
will be super useful! Let me know if you need any more information.


; OPTIONS FOR WEAK COUPLING ALGORITHMS =
; Temperature coupling   =
tcoupl   = nose-hoover
; Groups to couple separately =
tc-grps  = DPPC W
; Time constant (ps) and reference temperature (K) =
tau_t= 1.0 1.0
ref_t= 320 320
nsttcouple   = 1
; Pressure coupling  =
Pcoupl   = Parrinello-Rahman
Pcoupltype   = semiisotropic
; Time constant (ps), compressibility (1/bar) and reference P (bar) =
tau_p= 5.0  5.0
compressibility  = 3e-4 3e-4
ref_p= 0.0  0.0
nstpcouple   = 5

; GENERATE VELOCITIES FOR STARTUP RUN =
gen_vel  = yes
gen_temp = 105


Here is another issue.  You're re-generating velocities (destroying the previous 
equilibration) with a barostat that doesn't usually play nice under such 
circumstances, and you're generating velocities for a temperature well below the 
target defined in ref_t.  That can cause the thermostat to go haywire, which 
then has negative effects on the pressure (which comes from kinetic energy and 
the virial), which can lead to collapse.


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] A charge group moved too far between two domain decomposition steps

[Justin Lemkul]

On 6/11/13 10:55 AM, Dr. Vitaly Chaban wrote:




On Tue, Jun 11, 2013 at 3:52 PM, Justin Lemkul mailto:jalem...@vt.edu>> wrote:



On 6/11/13 9:27 AM, Dr. Vitaly Chaban wrote:

This problem indeed happens from time to time. With versions 4.5+ it is
more frequent than with versions up to 4.0.7. It is not always 
connected to
blowing up in the sense of bad contacts, positive potential energy, etc.
The more cores you use per job, the more likely this error to appear. 
The
larger *spatially) system you simulate, the more likely it to appear.


People generally reported more crashes in 4.5.x than in 4.0.x that we
determined arise from nsttcouple and nstpcouple being set incorrectly.
  There's a thread somewhere about it, but in general, the same principles
are always true - adequate equilibration and sensible .mdp settings should
lead to stable integration later on.



I can send you a couple of systems, which spontaneously crash. Not at the
beginning and not at the end, just unpredictably every few dozens of
nanoseconds. The systems are not strictly in the thermodynamic equilibrium
state, but they are not exploding in the common sense of this term. Another
coordinate files, executed with the same MDP file, never crash, however. I do
not really know the reason, but it is not as simple as good or bad set of MD
parameters. Maybe, something is connected with (deprecated) versions of external
libraries, since at my workstation, where I control everything, crashes occur
more rarely than at the cluster.



If there is a viable test case in one of those systems, upload a bug report to 
redmine.gromacs.org.  That's the only way the development team will know if 
anything needs to be fixed.  There were a lot of claims of instability early in 
the 4.5 development cycle, some bugs and others not, but since then there has 
been relative silence on the topic, so it was assumed all was well.  If it's 
not, we need to know, especially if version 4.6.2 still produces the problem 
(since 4.5.x is pretty much over with in terms of active development).





The simple advice is to reduce the time-step, but it is not to be
understood as a universal treatment.

Of course, you can reinitialize your charge groups, as this is better
connected with the below error message.


What does this mean?  Charge groups are a fixed element of the force field;
how would you propose adjusting them to make the error go away?




Really? How many force fields can you enumerate, where the developers say how we
should distribute atoms among the charge groups?



Nearly all of them.  AMBER and CHARMM obviously don't use charge groups (in the 
sense of a "group" being multiple atoms) and thus each atom is a "group."  The 
GROMOS parameter sets have defined charge groups that originate in the GROMOS 
software and distributed files, as all the parameters came from model compounds 
with definable (and transferable) functional groups.


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] Membrane Equilibration

[HANNIBAL LECTER]

ref_p= 0.0  0.0 ??

Are you sure about this??


On Tue, Jun 11, 2013 at 12:08 PM, Dr. Vitaly Chaban wrote:

> what happens to your energy before the observed crash? does the crash
> happen at the same time-step each time?
>
>
> Dr. Vitaly Chaban
>
>
> On Tue, Jun 11, 2013 at 5:22 PM, Neha  wrote:
>
> > Hi everybody,
> >
> > I am trying to simulate a lipid bilayer and wanted to use Parrinello
> Rahman
> > coupling. However, I read that Parinello-Rahman is not great for
> > equilibration so I thought I would do a small run using the Berendsen
> > barostat to decrease the chances of large oscillations. I then used the
> > .gro
> > file obtained from that run to start a new run using Parrinello-Rahman. I
> > am
> > not sure if that's the correct way to go about doing what I want to do.
> >
> > My Parrinello run also terminated a little while in, with the error that
> 2
> > of my atoms have moved further apart than the cut-off distance. A part of
> > my
> > mdp file is pasted below and I was wondering if anyone had any
> suggestions
> > as to stop that from happening. My time step is 0.02 ps and I thought
> > increasing tau-p might work. I am using the compressibility from the map
> > file on the Martini website and am worried that might be too large. Any
> > help
> > will be super useful! Let me know if you need any more information.
> >
> >
> > ; OPTIONS FOR WEAK COUPLING ALGORITHMS =
> > ; Temperature coupling   =
> > tcoupl   = nose-hoover
> > ; Groups to couple separately =
> > tc-grps  = DPPC W
> > ; Time constant (ps) and reference temperature (K) =
> > tau_t= 1.0 1.0
> > ref_t= 320 320
> > nsttcouple   = 1
> > ; Pressure coupling  =
> > Pcoupl   = Parrinello-Rahman
> > Pcoupltype   = semiisotropic
> > ; Time constant (ps), compressibility (1/bar) and reference P (bar) =
> > tau_p= 5.0  5.0
> > compressibility  = 3e-4 3e-4
> > ref_p= 0.0  0.0
> > nstpcouple   = 5
> >
> > ; GENERATE VELOCITIES FOR STARTUP RUN =
> > gen_vel  = yes
> > gen_temp = 105
> > gen_seed = 473529
> >
> >
> >
> > --
> > View this message in context:
> > http://gromacs.5086.x6.nabble.com/Membrane-Equilibration-tp5009038.html
> > Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
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Re: [gmx-users] Constraints of distance

[Justin Lemkul]

On 6/11/13 10:46 AM, Steven Neumann wrote:

I was not sure about the fucntion type (1 or 2). Once in manual it is
stated that function 1 is only for exclusions and another time it can be
used to miimc bonds. Both functions are working though.  Thanks anyway.



More precisely, constraints of type 1 generate exclusions between bonded atoms 
within nrexcl (defined in the topology), whereas type 2 do not.  Whether or not 
you need the constraints to do this depends on the nature of the force field.


-Justin

--


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Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] Membrane Equilibration

[Dr. Vitaly Chaban]

what happens to your energy before the observed crash? does the crash
happen at the same time-step each time?


Dr. Vitaly Chaban


On Tue, Jun 11, 2013 at 5:22 PM, Neha  wrote:

> Hi everybody,
>
> I am trying to simulate a lipid bilayer and wanted to use Parrinello Rahman
> coupling. However, I read that Parinello-Rahman is not great for
> equilibration so I thought I would do a small run using the Berendsen
> barostat to decrease the chances of large oscillations. I then used the
> .gro
> file obtained from that run to start a new run using Parrinello-Rahman. I
> am
> not sure if that's the correct way to go about doing what I want to do.
>
> My Parrinello run also terminated a little while in, with the error that 2
> of my atoms have moved further apart than the cut-off distance. A part of
> my
> mdp file is pasted below and I was wondering if anyone had any suggestions
> as to stop that from happening. My time step is 0.02 ps and I thought
> increasing tau-p might work. I am using the compressibility from the map
> file on the Martini website and am worried that might be too large. Any
> help
> will be super useful! Let me know if you need any more information.
>
>
> ; OPTIONS FOR WEAK COUPLING ALGORITHMS =
> ; Temperature coupling   =
> tcoupl   = nose-hoover
> ; Groups to couple separately =
> tc-grps  = DPPC W
> ; Time constant (ps) and reference temperature (K) =
> tau_t= 1.0 1.0
> ref_t= 320 320
> nsttcouple   = 1
> ; Pressure coupling  =
> Pcoupl   = Parrinello-Rahman
> Pcoupltype   = semiisotropic
> ; Time constant (ps), compressibility (1/bar) and reference P (bar) =
> tau_p= 5.0  5.0
> compressibility  = 3e-4 3e-4
> ref_p= 0.0  0.0
> nstpcouple   = 5
>
> ; GENERATE VELOCITIES FOR STARTUP RUN =
> gen_vel  = yes
> gen_temp = 105
> gen_seed = 473529
>
>
>
> --
> View this message in context:
> http://gromacs.5086.x6.nabble.com/Membrane-Equilibration-tp5009038.html
> Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
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[gmx-users] Membrane Equilibration

[Neha]

Hi everybody,

I am trying to simulate a lipid bilayer and wanted to use Parrinello Rahman
coupling. However, I read that Parinello-Rahman is not great for
equilibration so I thought I would do a small run using the Berendsen
barostat to decrease the chances of large oscillations. I then used the .gro
file obtained from that run to start a new run using Parrinello-Rahman. I am
not sure if that's the correct way to go about doing what I want to do.

My Parrinello run also terminated a little while in, with the error that 2
of my atoms have moved further apart than the cut-off distance. A part of my
mdp file is pasted below and I was wondering if anyone had any suggestions
as to stop that from happening. My time step is 0.02 ps and I thought
increasing tau-p might work. I am using the compressibility from the map
file on the Martini website and am worried that might be too large. Any help
will be super useful! Let me know if you need any more information.


; OPTIONS FOR WEAK COUPLING ALGORITHMS =
; Temperature coupling   =
tcoupl   = nose-hoover
; Groups to couple separately =
tc-grps  = DPPC W
; Time constant (ps) and reference temperature (K) =
tau_t= 1.0 1.0
ref_t= 320 320
nsttcouple   = 1
; Pressure coupling  =
Pcoupl   = Parrinello-Rahman
Pcoupltype   = semiisotropic
; Time constant (ps), compressibility (1/bar) and reference P (bar) =
tau_p= 5.0  5.0
compressibility  = 3e-4 3e-4
ref_p= 0.0  0.0
nstpcouple   = 5

; GENERATE VELOCITIES FOR STARTUP RUN =
gen_vel  = yes
gen_temp = 105
gen_seed = 473529



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Re: [gmx-users] Constraints of distance

[Dr. Vitaly Chaban]

Steven -

I probably know nothing about "function #2", but "function 1" is used just
everywhere. It does constrain intramolecular distances.

Good luck. Vitaly


Dr. Vitaly Chaban


On Tue, Jun 11, 2013 at 4:46 PM, Steven Neumann wrote:

> I was not sure about the fucntion type (1 or 2). Once in manual it is
> stated that function 1 is only for exclusions and another time it can be
> used to miimc bonds. Both functions are working though.  Thanks anyway.
>
> Steven
>
>
> On Tue, Jun 11, 2013 at 2:18 PM, Dr. Vitaly Chaban wrote:
>
>> I think all is correct.
>>
>> Why are you asking? People normally report problems.
>>
>> Dr. Vitaly Chaban
>>
>>
>>
>>
>>
>>
>> On Tue, Jun 11, 2013 at 12:30 PM, Steven Neumann > >wrote:
>>
>> > Dear Gmx Users,
>> >
>> > I am running CG simulation and I wish my beads to be constraint - one
>> away
>> > from each other of 0.4 nm. I wan to use Lincs for this purpose. I do not
>> > have any bonds in my topology or rtp entry. I just add:
>> >
>> > [ constraints ]
>> > 1 2  1  0.4
>> > 2 3  1  0.4
>> > ...
>> > 31   32 1  0.4
>> >
>> > constraints = none
>> > constraint_algorithm = Lincs
>> >
>> >
>> > Is that correct? I used function 1, is that right?
>> >
>> > Shall I specify something else?
>> >
>> >
>> > Steven
>> > --
>> > 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
>> >
>> --
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>> http://lists.gromacs.org/mailman/listinfo/gmx-users
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>>
>
>
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Re: [gmx-users] A charge group moved too far between two domain decomposition steps

[Dr. Vitaly Chaban]

On Tue, Jun 11, 2013 at 3:52 PM, Justin Lemkul  wrote:

>
>
> On 6/11/13 9:27 AM, Dr. Vitaly Chaban wrote:
>
>> This problem indeed happens from time to time. With versions 4.5+ it is
>> more frequent than with versions up to 4.0.7. It is not always connected
>> to
>> blowing up in the sense of bad contacts, positive potential energy, etc.
>> The more cores you use per job, the more likely this error to appear. The
>> larger *spatially) system you simulate, the more likely it to appear.
>>
>>
> People generally reported more crashes in 4.5.x than in 4.0.x that we
> determined arise from nsttcouple and nstpcouple being set incorrectly.
>  There's a thread somewhere about it, but in general, the same principles
> are always true - adequate equilibration and sensible .mdp settings should
> lead to stable integration later on.
>


I can send you a couple of systems, which spontaneously crash. Not at the
beginning and not at the end, just unpredictably every few dozens of
nanoseconds. The systems are not strictly in the thermodynamic equilibrium
state, but they are not exploding in the common sense of this term. Another
coordinate files, executed with the same MDP file, never crash, however. I
do not really know the reason, but it is not as simple as good or bad set
of MD parameters. Maybe, something is connected with (deprecated) versions
of external libraries, since at my workstation, where I control everything,
crashes occur more rarely than at the cluster.




>
>  The simple advice is to reduce the time-step, but it is not to be
>> understood as a universal treatment.
>>
>> Of course, you can reinitialize your charge groups, as this is better
>> connected with the below error message.
>>
>>
> What does this mean?  Charge groups are a fixed element of the force
> field; how would you propose adjusting them to make the error go away?
>
>


Really? How many force fields can you enumerate, where the developers say
how we should distribute atoms among the charge groups?

Not all MD codes use charge group mechanism, by the way.

Anyways, this is not my thread. Perhaps, the starter really has a simple
problem with blowing up.


Dr. Vitaly Chaban












> -Justin
>
> --
> ==**==
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin
>
> ==**==
>
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Re: [gmx-users] Constraints of distance

[Steven Neumann]

I was not sure about the fucntion type (1 or 2). Once in manual it is
stated that function 1 is only for exclusions and another time it can be
used to miimc bonds. Both functions are working though.  Thanks anyway.

Steven


On Tue, Jun 11, 2013 at 2:18 PM, Dr. Vitaly Chaban wrote:

> I think all is correct.
>
> Why are you asking? People normally report problems.
>
> Dr. Vitaly Chaban
>
>
>
>
>
>
> On Tue, Jun 11, 2013 at 12:30 PM, Steven Neumann  >wrote:
>
> > Dear Gmx Users,
> >
> > I am running CG simulation and I wish my beads to be constraint - one
> away
> > from each other of 0.4 nm. I wan to use Lincs for this purpose. I do not
> > have any bonds in my topology or rtp entry. I just add:
> >
> > [ constraints ]
> > 1 2  1  0.4
> > 2 3  1  0.4
> > ...
> > 31   32 1  0.4
> >
> > constraints = none
> > constraint_algorithm = Lincs
> >
> >
> > Is that correct? I used function 1, is that right?
> >
> > Shall I specify something else?
> >
> >
> > Steven
> > --
> > 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
> >
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Re: [gmx-users] A charge group moved too far between two domain decomposition steps

[Justin Lemkul]

On 6/11/13 9:27 AM, Dr. Vitaly Chaban wrote:

This problem indeed happens from time to time. With versions 4.5+ it is
more frequent than with versions up to 4.0.7. It is not always connected to
blowing up in the sense of bad contacts, positive potential energy, etc.
The more cores you use per job, the more likely this error to appear. The
larger *spatially) system you simulate, the more likely it to appear.



People generally reported more crashes in 4.5.x than in 4.0.x that we determined 
arise from nsttcouple and nstpcouple being set incorrectly.  There's a thread 
somewhere about it, but in general, the same principles are always true - 
adequate equilibration and sensible .mdp settings should lead to stable 
integration later on.



The simple advice is to reduce the time-step, but it is not to be
understood as a universal treatment.

Of course, you can reinitialize your charge groups, as this is better
connected with the below error message.



What does this mean?  Charge groups are a fixed element of the force field; how 
would you propose adjusting them to make the error go away?


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Fwd: Re: [gmx-users] restraints on water oxygen atoms

[Justin Lemkul]

I was having issues with my email earlier today, so some things did not go 
through.  Apologies if this is a multiple post, but I wanted to make sure it got 
through, especially since it provides resolution to a very long-running thread:


On 6/11/13 7:46 AM, Shima Arasteh wrote:

I put the output file of shrinking steps after 32 iterations:

https://jumpshare.com/b/5Y6WUGv7OT1sOFzsrWgN



I see it now.  Your protein is very small.  InflateGRO works by deleting lipids
based on the distance between C-alpha and P atoms.  Your protein isn't even in
the plane of the P atoms (as most proteins are) and thus very few are likely
deleted.  There is probably atomic overlap in the first (inflated) structure.

Increase the deletion radius in the inflation step, and inspect very carefully
using the visualization software of choice.  If the initial (inflated) structure
is devoid of clashes, so too should any structures in the shrinking steps.

-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin




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Re: [gmx-users] Re: restraints on water oxygen atoms

[Justin Lemkul]

On 6/11/13 9:38 AM, JW Gibbs wrote:

Hi,

As Justin had already suggested, restraints will lead to nasty atomic
clashes. Looking at the gro file you have provided, it seems that the system
is very poorly equilibrated.

I had a similar issue. If the forcefield you are using is accurate enough,
follow the steps as follows:

1. Take the system and increase the box size in all the directions. Run
energy minimization. This will give a somewhat better starting point for the
membrane.

2. Now play around with the box size, such that the x-y dimensions conform
to the reported APL value. Eg., suppose for POPC, you have 48 Lipids per
leaflet and say the experimental APL is about 5.7 nm^2 then the
x=y=sqrt(48*5.7) nm. Adjust the z direction according to what thickness of
water you would want to have.



Doing this assumes that the force field will reproduce experimental APL and, 
more often than not, introduces stress on the membrane.  The membrane will 
probably adjust, but I think this is going to slow equilibration more than anything.



3. Solvate the system (using genbox maybe?). Albeit some water molecules
will penetrate the lipids. Do not worry about that. If your forcefield is
accurate enough, water molecules would diffuse to the top after you follow
steps 4.



Again, this is a barrier to equilibration.  I outline one possible solvation 
mechanism in my tutorial, and there are water removal scripts on the Gromacs 
website.  Water diffusion can be very slow and can seriously perturb the lipids.



4. Position restraint the membrane and then use semi-isotropic pressure
coupling but DO NOT position restraint water. Run NPT for maybe 4-5 ns. You
would see that water has diffused to the top and that you have a very good
initial condition.

As I said, it all depends on the correctness of the forcefield that you are
using, but I think any Lipid forcefield will be parameterized such that the
tails would have hydrophobic characteristics and you would not have to worry
about water penetrating the bilayer.



Not always the case, but generally true enough.

-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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[gmx-users] Re: restraints on water oxygen atoms

[JW Gibbs]

Hi, 

As Justin had already suggested, restraints will lead to nasty atomic
clashes. Looking at the gro file you have provided, it seems that the system
is very poorly equilibrated. 

I had a similar issue. If the forcefield you are using is accurate enough,
follow the steps as follows:

1. Take the system and increase the box size in all the directions. Run
energy minimization. This will give a somewhat better starting point for the
membrane. 

2. Now play around with the box size, such that the x-y dimensions conform
to the reported APL value. Eg., suppose for POPC, you have 48 Lipids per
leaflet and say the experimental APL is about 5.7 nm^2 then the
x=y=sqrt(48*5.7) nm. Adjust the z direction according to what thickness of
water you would want to have. 

3. Solvate the system (using genbox maybe?). Albeit some water molecules
will penetrate the lipids. Do not worry about that. If your forcefield is
accurate enough, water molecules would diffuse to the top after you follow
steps 4. 

4. Position restraint the membrane and then use semi-isotropic pressure
coupling but DO NOT position restraint water. Run NPT for maybe 4-5 ns. You
would see that water has diffused to the top and that you have a very good
initial condition. 

As I said, it all depends on the correctness of the forcefield that you are
using, but I think any Lipid forcefield will be parameterized such that the
tails would have hydrophobic characteristics and you would not have to worry
about water penetrating the bilayer. 



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Re: [gmx-users] stay at some temperature during annealing

[Dr. Vitaly Chaban]

On Tue, Jun 11, 2013 at 12:52 PM, Justin Lemkul  wrote:

>
>
> On 6/11/13 1:11 AM, mu xiaojia wrote:
>
>> Hi guys,
>>
>> I am using simulated annealing for my protein+water+Ion system, I tried to
>> let the system stay at some temperature for a while, e.g.: stay at 600k
>> from 3000ps to 1 ps, then gradually cool it down to 298k, so my mdp is
>> like:
>>
>> annealing_time = 0 3000 1 2 0 3000 1 2 0 3000 1 2
>> annealing_temp = 298 600 600 298 298 600 600 298  298 600 600 298
>>
>>
>> however, error message is:
>>
>> Found 12 annealing_time values, wanter 9
>>
>> apparently, the "600 600" does not work, does anyone have any suggestion,
>> or I could only separate the simulation? Thanks very much!
>>
>>


There is a problem with the number of temperature coupling groups. You have
defined less than you expect, as the program requests only 9 values. So,
refer to the number of points to T annealing, which you do not list here.


Dr. Vitaly Chaban
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Re: [gmx-users] A charge group moved too far between two domain decomposition steps

[Dr. Vitaly Chaban]

This problem indeed happens from time to time. With versions 4.5+ it is
more frequent than with versions up to 4.0.7. It is not always connected to
blowing up in the sense of bad contacts, positive potential energy, etc.
The more cores you use per job, the more likely this error to appear. The
larger *spatially) system you simulate, the more likely it to appear.

The simple advice is to reduce the time-step, but it is not to be
understood as a universal treatment.

Of course, you can reinitialize your charge groups, as this is better
connected with the below error message.


Dr. Vitaly Chaban






On Tue, Jun 11, 2013 at 12:54 PM, Justin Lemkul  wrote:

>
>
> On 6/11/13 1:30 AM, Souilem Safa wrote:
>
>> Dear Gromacs users,
>> I tried to do the simulation of a single molecule in cyclohexane, I'm
>> using
>> gromos 53a6 force field for both molecules.
>> i did all the minimization steps. After npt, I runned for 25 000 000
>> steps.
>>   just after around 100 000 steps, the system stops and i got this fatal
>> error:
>>
>>
>> Fatal error:
>> A charge group moved too far between two domain decomposition steps
>> This usually means that your system is not well equilibrated
>>
>>
>> Then I back again to npt step to equilibrate for longer time as the error
>> message said to me, I equilibrate for 500 000 steps instead of 25
>> steps
>> setted in the mdp file, but again I got the same error.
>>
>> What should I do to overcome this problem?
>>
>
> http://www.gromacs.org/**Documentation/Terminology/**Blowing_Up
>
> There are plenty of possible problems within your topology or .mdp
> settings. Unfortunately, you provided neither, but everything there is to
> say is fairly well summarized in the link.
>
> -Justin
>
> --
> ==**==
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin
>
> ==**==
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Re: [gmx-users] Constraints of distance

[Dr. Vitaly Chaban]

I think all is correct.

Why are you asking? People normally report problems.

Dr. Vitaly Chaban






On Tue, Jun 11, 2013 at 12:30 PM, Steven Neumann wrote:

> Dear Gmx Users,
>
> I am running CG simulation and I wish my beads to be constraint - one away
> from each other of 0.4 nm. I wan to use Lincs for this purpose. I do not
> have any bonds in my topology or rtp entry. I just add:
>
> [ constraints ]
> 1 2  1  0.4
> 2 3  1  0.4
> ...
> 31   32 1  0.4
>
> constraints = none
> constraint_algorithm = Lincs
>
>
> Is that correct? I used function 1, is that right?
>
> Shall I specify something else?
>
>
> Steven
> --
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Re: [gmx-users] restraints on water oxygen atoms

[Shima Arasteh]

I put the output file of shrinking steps after 32 iterations:

https://jumpshare.com/b/5Y6WUGv7OT1sOFzsrWgN 

 
Sincerely,
Shima


- Original Message -
From: Justin Lemkul 
To: Shima Arasteh ; Discussion list for GROMACS 
users 
Cc: 
Sent: Tuesday, June 11, 2013 3:25 PM
Subject: Re: [gmx-users] restraints on water oxygen atoms



On 6/11/13 2:05 AM, Shima Arasteh wrote:
> These are the all commands to do iteration:
> After generating topology
> -    concatenate the protein and bilayer structure files:
>
>       #cat dimer-newbox.gro popc-whole.gro > system.gro
>        ( Remove unnecessary lines and update the second line of the 
>coordinate file (total number of atoms) accordingly )
>
> -    Use a very strong position-restraining force on protein heavy atoms to 
> ensure that the position of the protein does not change during EM :
>       Adding these lines to topology file:
>       ; Strong position restraints for InflateGRO
>       #include "topol_Protein_A.itp"
>       #ifdef POSRE
>       #include "strong_posre.itp"
>       #endif
>       #include "topol_Protein_B.itp"
>       #ifdef POSRE
>       #include "strong_posre.itp"
>       #endif
>
> -    Now, generate this new position restraint file using genrestr:
>       #genrestr -f dimer-newbox.gro -o strong_posre.itp -fc 10 10 
>10
>
> -    In the .mdp file used for the minimizations, add a line "define = 
> -DSTRONG_POSRES" to make use of these new position restraints.
>
> -    Scale the lipid positions by a factor of 4:
>       #perl inflategro.pl system.gro 6 POPC 14 system_inflated.gro 5 area.dat
>
>        Updating the .top file and adding POPC 238 to it.
> ITERATION
>      1.
>       Energy minimization with restrained protein
>       #grompp -f minim.mdp -c system_inflated.gro -p topol.top -o em.tpr
>       #mdrun -deffnm em
>
>    Steepest Descents converged to Fmax < 1000 in 137 steps
>
> Steepest Descents converged to Fmax < 100 in 4998 steps
> Potential Energy  =  1.1410846e+04
> Maximum force     =  9.4570084e+01 on atom 8800
> Norm of force     =  3.2672191e+00
>
>
>       scale down the lipids by a factor of 0.95
>       #perl inflategro.pl em.gro 0.95 POPC 0 em_shrink1.gro 5 area_shrink1.dat
>
>      2.
>      #grompp -f minim.mdp -c em_shrink1.gro -p topol.top -o em_shrink1.tpr
>      # perl inflategro.pl em_shrink1.gro 0.95 POPC 0 em_shrink2.gro 5 
>area_shrink2.dat
>
>      3.
>      # grompp -f minim.mdp -c em_shrink2.gro -p topol.top -o em_shrink2.tpr
>      # perl inflategro.pl em_shrink2.gro 0.95 POPC 0 em_shrink3.gro 5 
>area_shrink3.dat
>
>      .
>      .
>      .
>      .
>
>
>
>
> Then, after 32 iterations, the APL reaches the value of 10% higher than the 
> experimental value. So, I use the last gro file em_shrink32.gro as the 
> initial configuration to solvate and next steps. But when I check the 
> overlaps in  em_shrink32.gro, there are many improper overlaps and acyl 
> penetration to the protein, disgusting!
>

Please provide a link to an image or images that illustrate what's going on.  
If 
molecules are truly overlapping this badly, it sounds like something is very 
wrong with the force field, since such interactions normally cannot arise 
without the system blowing up.

-Justin

-- 


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin



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Re: [gmx-users] Angles not read

[Justin Lemkul]

On 6/11/13 5:59 AM, Steven Neumann wrote:

On Mon, Jun 10, 2013 at 1:44 PM, Justin Lemkul  wrote:




On 6/10/13 8:42 AM, Justin Lemkul wrote:




On 6/10/13 8:40 AM, Steven Neumann wrote:


On Mon, Jun 10, 2013 at 1:27 PM, Justin Lemkul  wrote:




On 6/10/13 8:23 AM, Steven Neumann wrote:

  Dear Gmx Users,


I created my own CG force field and i process my structure to pdb2gmx.
I
process 3 beads I created to check whether the topology is properly
created:


Using the CG force field in directory ./CG.ff

No file 'watermodels.dat' found, will not include a water model
Reading 60central_Carbons.pdb...
Read 3 atoms
Analyzing pdb file
Splitting chemical chains based on TER records or chain id changing.
There are 1 chains and 0 blocks of water and 3 residues with 3 atoms

 chain  #res #atoms
 1 'X' 3  3

All occupancy fields zero. This is probably not an X-Ray structure
Opening force field file ./CG.ff/atomtypes.atp
Atomtype 1
Reading residue database... (CG)
Opening force field file ./CG.ff/aminoacids.rtp
Reading .rtp file without '[ bondedtypes ]' directive,
Will proceed as if the entry


[ bondedtypes ]
; bonds  angles  dihedrals  impropers all_dihedrals nr_exclusions HH14
remove_dih
1   1  1  2 0 3
1
1
Residue 13t at the beginning of ./CG.ff/aminoacids.rtp
Sorting it all out...

Back Off! I just backed up topol.top to ./#topol.top.2#
Processing chain 1 'X' (3 atoms, 3 residues)
Identified residue MET1 as a starting terminus.
Identified residue VAL3 as a ending terminus.
8 out of 8 lines of specbond.dat converted successfully
Checking for duplicate atoms
Now there are 3 residues with 3 atoms
Making bonds...
No bonds
Generating angles, dihedrals and pairs...
Making cmap torsions...There are0 dihedrals,0 impropers,0
angles
0 pairs,0 bonds and 0 virtual sites
Total mass 319.420 a.m.u.
Total charge 1.000 e
Writing topology

Back Off! I just backed up posre.itp to ./#posre.itp.2#

Writing coordinate file...

Back Off! I just backed up 60proc.pdb to ./#60proc.pdb.2#
   - PLEASE NOTE 
You have successfully generated a topology from:3Carbons.pdb.
The CG force field is used.
   - ETON ESAELP 

gcq#304: "Gabba Gabba Hey!" (The Ramones)

It stated that there are no angles.
However in my ffbonded.itp which i ncluded in my forcefield.itp

[ angletypes ]
; i  j  k funct th0  C0  C1  C2  C3  C4
CMECSECVA600.0680894-0.0328291000590330
-46.313

How Gromacs can read this angle?


  [angletypes] simply define possible interactions, but are not used

unless
there are [angles] in the .rtp that use them.  pdb2gmx writes angles
based
on bonds, but if you note above, there are zero bonds, so pdb2gmx cannot
write any angles.  Does your .rtp entry specify [angles] but no [bonds]?




I want to use constraints with SHAKE as bonds...no harmonic bonds. In
this
case pdb2gmx will never create angles? Shall I also manually add [
angles ]
to my top then?



Yes, because in the absence of bonds, even [angles] in .rtp entries are
ignored.



Thinking a bit more though, it's probably a lot easier to define bonds and
let pdb2gmx do the work for you.  Using:

constraints = all-bonds
constraint-algorithm = shake

will turn all bonds in the topology into constraints, which sounds like
exactly what you want to do.


-Justin



I want my atoms to be constrained. I specified in my topology

[ constraints ]
1 2 0.4
2 3 0.4
etc.
  Shall use?



You're missing a function type.


constraints = none
constraint-algorithm = shake

I do not have [ bonds ] in my topology



Presumably it should work (pending the correction noted above).  Try it and see.

-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] Constraints of distance

[Justin Lemkul]

On 6/11/13 6:30 AM, Steven Neumann wrote:

Dear Gmx Users,

I am running CG simulation and I wish my beads to be constraint - one away
from each other of 0.4 nm. I wan to use Lincs for this purpose. I do not
have any bonds in my topology or rtp entry. I just add:

[ constraints ]
1 2  1  0.4
2 3  1  0.4
...
31   32 1  0.4

constraints = none
constraint_algorithm = Lincs


Is that correct? I used function 1, is that right?

Shall I specify something else?



Is there a reason you suspect a problem?  Have you tried it or are we just 
checking your work?  Giving it a shot is going to be a lot faster than waiting 
for an email :)


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] restraints on water oxygen atoms

[Justin Lemkul]

On 6/11/13 2:05 AM, Shima Arasteh wrote:

These are the all commands to do iteration:
After generating topology
-concatenate the protein and bilayer structure files:

  #cat dimer-newbox.gro popc-whole.gro > system.gro
   ( Remove unnecessary lines and update the second line of the coordinate 
file (total number of atoms) accordingly )

-Use a very strong position-restraining force on protein heavy atoms to 
ensure that the position of the protein does not change during EM :
  Adding these lines to topology file:
  ; Strong position restraints for InflateGRO
  #include "topol_Protein_A.itp"
  #ifdef POSRE
  #include "strong_posre.itp"
  #endif
  #include "topol_Protein_B.itp"
  #ifdef POSRE
  #include "strong_posre.itp"
  #endif

-Now, generate this new position restraint file using genrestr:
  #genrestr -f dimer-newbox.gro -o strong_posre.itp -fc 10 10 10

-In the .mdp file used for the minimizations, add a line "define = 
-DSTRONG_POSRES" to make use of these new position restraints.

-Scale the lipid positions by a factor of 4:
  #perl inflategro.pl system.gro 6 POPC 14 system_inflated.gro 5 area.dat

   Updating the .top file and adding POPC 238 to it.
ITERATION
 1.
  Energy minimization with restrained protein
  #grompp -f minim.mdp -c system_inflated.gro -p topol.top -o em.tpr
  #mdrun -deffnm em

   Steepest Descents converged to Fmax < 1000 in 137 steps

Steepest Descents converged to Fmax < 100 in 4998 steps
Potential Energy  =  1.1410846e+04
Maximum force =  9.4570084e+01 on atom 8800
Norm of force =  3.2672191e+00


  scale down the lipids by a factor of 0.95
  #perl inflategro.pl em.gro 0.95 POPC 0 em_shrink1.gro 5 area_shrink1.dat

 2.
 #grompp -f minim.mdp -c em_shrink1.gro -p topol.top -o em_shrink1.tpr
 # perl inflategro.pl em_shrink1.gro 0.95 POPC 0 em_shrink2.gro 5 
area_shrink2.dat

 3.
 # grompp -f minim.mdp -c em_shrink2.gro -p topol.top -o em_shrink2.tpr
 # perl inflategro.pl em_shrink2.gro 0.95 POPC 0 em_shrink3.gro 5 
area_shrink3.dat

 .
 .
 .
 .




Then, after 32 iterations, the APL reaches the value of 10% higher than the 
experimental value. So, I use the last gro file em_shrink32.gro as the initial 
configuration to solvate and next steps. But when I check the overlaps in  
em_shrink32.gro, there are many improper overlaps and acyl penetration to the 
protein, disgusting!



Please provide a link to an image or images that illustrate what's going on.  If 
molecules are truly overlapping this badly, it sounds like something is very 
wrong with the force field, since such interactions normally cannot arise 
without the system blowing up.


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] A charge group moved too far between two domain decomposition steps

[Justin Lemkul]

On 6/11/13 1:30 AM, Souilem Safa wrote:

Dear Gromacs users,
I tried to do the simulation of a single molecule in cyclohexane, I'm using
gromos 53a6 force field for both molecules.
i did all the minimization steps. After npt, I runned for 25 000 000 steps.
  just after around 100 000 steps, the system stops and i got this fatal
error:


Fatal error:
A charge group moved too far between two domain decomposition steps
This usually means that your system is not well equilibrated


Then I back again to npt step to equilibrate for longer time as the error
message said to me, I equilibrate for 500 000 steps instead of 25 steps
setted in the mdp file, but again I got the same error.

What should I do to overcome this problem?


http://www.gromacs.org/Documentation/Terminology/Blowing_Up

There are plenty of possible problems within your topology or .mdp settings. 
Unfortunately, you provided neither, but everything there is to say is fairly 
well summarized in the link.


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] stay at some temperature during annealing

[Justin Lemkul]

On 6/11/13 1:11 AM, mu xiaojia wrote:

Hi guys,

I am using simulated annealing for my protein+water+Ion system, I tried to
let the system stay at some temperature for a while, e.g.: stay at 600k
from 3000ps to 1 ps, then gradually cool it down to 298k, so my mdp is
like:

annealing_time = 0 3000 1 2 0 3000 1 2 0 3000 1 2
annealing_temp = 298 600 600 298 298 600 600 298  298 600 600 298


however, error message is:

Found 12 annealing_time values, wanter 9

apparently, the "600 600" does not work, does anyone have any suggestion,
or I could only separate the simulation? Thanks very much!



The approach should work, but is also dependent upon other settings.  Can you 
please provide a full .mdp file?


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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[gmx-users] Constraints of distance

[Steven Neumann]

Dear Gmx Users,

I am running CG simulation and I wish my beads to be constraint - one away
from each other of 0.4 nm. I wan to use Lincs for this purpose. I do not
have any bonds in my topology or rtp entry. I just add:

[ constraints ]
1 2  1  0.4
2 3  1  0.4
...
31   32 1  0.4

constraints = none
constraint_algorithm = Lincs


Is that correct? I used function 1, is that right?

Shall I specify something else?


Steven
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[gmx-users] equilibration error

[Souilem Safa]

Dear Gromacs users,
I tried to do the simulation of a single molecule in cyclohexane, I'm using
gromos 53a6 force field for both molecules.
i did all the minimization steps. After npt, I runned for 25 000 000 steps.
 just after around 100 000 steps, the system stops and i got this fatal
error:


Fatal error:
A charge group moved too far between two domain decomposition steps
This usually means that your system is not well equilibrated


Then I back again to npt step to equilibrate for longer time as the error
message said to me, I equilibrate for 500 000 steps instead of 25 steps
setted in the mdp file, but again I got the same error.

What should I do to overcome this problem?
Thank you very much
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Re: [gmx-users] Angles not read

[Steven Neumann]

On Mon, Jun 10, 2013 at 1:44 PM, Justin Lemkul  wrote:

>
>
> On 6/10/13 8:42 AM, Justin Lemkul wrote:
>
>>
>>
>> On 6/10/13 8:40 AM, Steven Neumann wrote:
>>
>>> On Mon, Jun 10, 2013 at 1:27 PM, Justin Lemkul  wrote:
>>>
>>>

 On 6/10/13 8:23 AM, Steven Neumann wrote:

  Dear Gmx Users,
>
> I created my own CG force field and i process my structure to pdb2gmx.
> I
> process 3 beads I created to check whether the topology is properly
> created:
>
>
> Using the CG force field in directory ./CG.ff
>
> No file 'watermodels.dat' found, will not include a water model
> Reading 60central_Carbons.pdb...
> Read 3 atoms
> Analyzing pdb file
> Splitting chemical chains based on TER records or chain id changing.
> There are 1 chains and 0 blocks of water and 3 residues with 3 atoms
>
> chain  #res #atoms
> 1 'X' 3  3
>
> All occupancy fields zero. This is probably not an X-Ray structure
> Opening force field file ./CG.ff/atomtypes.atp
> Atomtype 1
> Reading residue database... (CG)
> Opening force field file ./CG.ff/aminoacids.rtp
> Reading .rtp file without '[ bondedtypes ]' directive,
> Will proceed as if the entry
>
>
> [ bondedtypes ]
> ; bonds  angles  dihedrals  impropers all_dihedrals nr_exclusions HH14
> remove_dih
>1   1  1  2 0 3
> 1
> 1
> Residue 13t at the beginning of ./CG.ff/aminoacids.rtp
> Sorting it all out...
>
> Back Off! I just backed up topol.top to ./#topol.top.2#
> Processing chain 1 'X' (3 atoms, 3 residues)
> Identified residue MET1 as a starting terminus.
> Identified residue VAL3 as a ending terminus.
> 8 out of 8 lines of specbond.dat converted successfully
> Checking for duplicate atoms
> Now there are 3 residues with 3 atoms
> Making bonds...
> No bonds
> Generating angles, dihedrals and pairs...
> Making cmap torsions...There are0 dihedrals,0 impropers,0
> angles
>0 pairs,0 bonds and 0 virtual sites
> Total mass 319.420 a.m.u.
> Total charge 1.000 e
> Writing topology
>
> Back Off! I just backed up posre.itp to ./#posre.itp.2#
>
> Writing coordinate file...
>
> Back Off! I just backed up 60proc.pdb to ./#60proc.pdb.2#
>   - PLEASE NOTE 
> You have successfully generated a topology from:3Carbons.pdb.
> The CG force field is used.
>   - ETON ESAELP 
>
> gcq#304: "Gabba Gabba Hey!" (The Ramones)
>
> It stated that there are no angles.
> However in my ffbonded.itp which i ncluded in my forcefield.itp
>
> [ angletypes ]
> ; i  j  k funct th0  C0  C1  C2  C3  C4
> CMECSECVA600.0680894-0.0328291000590330
> -46.313
>
> How Gromacs can read this angle?
>
>
>  [angletypes] simply define possible interactions, but are not used
 unless
 there are [angles] in the .rtp that use them.  pdb2gmx writes angles
 based
 on bonds, but if you note above, there are zero bonds, so pdb2gmx cannot
 write any angles.  Does your .rtp entry specify [angles] but no [bonds]?

>>>
>>>
>>> I want to use constraints with SHAKE as bonds...no harmonic bonds. In
>>> this
>>> case pdb2gmx will never create angles? Shall I also manually add [
>>> angles ]
>>> to my top then?
>>>
>>>
>> Yes, because in the absence of bonds, even [angles] in .rtp entries are
>> ignored.
>>
>>
> Thinking a bit more though, it's probably a lot easier to define bonds and
> let pdb2gmx do the work for you.  Using:
>
> constraints = all-bonds
> constraint-algorithm = shake
>
> will turn all bonds in the topology into constraints, which sounds like
> exactly what you want to do.
>
>
> -Justin
>

I want my atoms to be constrained. I specified in my topology

[ constraints ]
1 2 0.4
2 3 0.4
etc.
 Shall use?

constraints = none
constraint-algorithm = shake

I do not have [ bonds ] in my topology


> --
> ==**==
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin
>
> ==**==
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Re: [gmx-users] shall we use double precision?

[Dr. Vitaly Chaban]

It is *desirable*.

In many cases of free energy calculations, single precision is still
reliable.

Dr. Vitaly Chaban






On Tue, Jun 11, 2013 at 7:35 AM, Albert  wrote:

> Hello :
>
>  I am going to use Gromacs with PLUMD plugin to perform Metadynamics.
> Since this methods involved in free energy calculations, I am just
> wondering is it necessary to introduce double precision Gromacs?
>
> thank you very much
>
> Albert
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Re: [gmx-users] site-site Coulombic force

[Mark Abraham]

Not directly. Code that permitted doing so during the actual simulation
would be far too inefficient. You can use tpbconv and trjconv to make
matching subsets of your .tpr and output trajectory, and pass those through
mdrun -rerun. Or, depending what you actually want, you may need to make an
.mdp file with energy groups to generate an equivalent .tpr, from which to
make the subset.

Mark


On Mon, Jun 10, 2013 at 1:32 PM, biki  wrote:

> Hi all,
>
> Is it possible in GROMACS to print  the individual site-site Coulombic
> force along with respective co-ordinates of the sites in each time step as
> output e.g. for simulation of rigid water.
>
> Thanks,
> Best regards
> Biki
>
>
>
>
> --
> View this message in context:
> http://gromacs.5086.x6.nabble.com/site-site-Coulombic-force-tp5008961.html
> Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
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Re: [gmx-users] shall we use double precision?

[Albert]

HI Mark:

 thank you for kind reply. I found the following in the documentations:

Installations:

Example.
This is the procedure for compiling the serial version of GROMACS, using 
the GNU compilers.

tar zxf gromacs-4.0.5.tar.gz
cd gromacs-4.0.5
export plumedir="PLUMED root"
cp $plumedir/patches/plumedpatch gromacs 4.0.4.sh .
CC=gcc CXX=g++ ./configure
./plumedpatch gromacs 4.0.4.sh -patch
make
make install


However, in the test section, it said the following:

For GROMACS users only. Please note that:
 The tests for GROMACS are designed for and should be executed with
the double-precision version of the code;
 Biasxmd, ptmetad, dd and pd are designed for the parallel version of
GROMACS. The user should specify in the test script the location of
the parallel executable and the version of GROMACS used. These tests
will fail if the parallel version of GROMACS has not been compiled.


thank you very much

Albert



On 06/11/2013 08:55 AM, Mark Abraham wrote:

Probably not. What does PLUMED documentation recommend?

Mark


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