[gmx-users] [solved] Problem compiling Gromacs 4.6 on BlueGene/Q

[Jernej Zidar]

>>
>> 1. Compile FFTW-3.3.2:
>> ./configure --prefix=/scratch/home/user/fftw-3.3.2
>> make && make install
>>
>
> This does not compile a single-precision FFTW (per generic GROMACS
> installation instructions).

Hi Mark,
  Thanks for pointing it out. I recompiled FFTW like so:
./configure --prefix=/scratch/home/user/fftw-3.3.2  --enable-float
--enable-threads

  The content of /scratch/home/user/fftw-3.3.2/lib is:
libfftw3f.la, libfftw3f.a, libfftw3f_threads.la, libfftw3f_threads.a

  Compiling Gromacs was a success:
 cmake ../gromacs-4.6.1 -DCMAKE_TOOLCHAIN_FILE=BlueGeneQ-static-XL-C
-DCMAKE_PREFIX_PATH=/scratch/home/user/fftw-3.3.2
make mdrun && make install-mdrun

  Cmake complained about the lack of SIMD instructions so I rebuilt
FFTW by adding "--enable-altivec". Gromacs compiled without any major
complaints.

Thank you!

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

[gmx-users] RE: About the binary identical results by restarting from the checkpoint file

[Cuiying Jian]

Hi GROMACS Users,
 
I am sorry if you are bothered by my second post about this topic. But the fact 
is that I tested restarting simulations with .cpt files by GROMACS 4.6.1.  and 
I still cannot get binary identical results from restarted simulations with 
those from continuous simulations. The command I used for restarting is as the 
following (e.g., only one processor is used during the simulations.):
mdrun -v -s md.tpr -cpt 0 -cpi md.cpt -deffnm md -reprod 
 
 
For further information, I attach my original .mdp file below:
constraints  =  all-bonds ; convert all bonds to constraints.
integrator =  md
dt  =  0.002  ; ps !
nsteps  =  1 ; total 2 ns.
nstcomm =  10; frequency for center of mass 
motion removal.
nstxout=  5  ; collect data every 10.0 ps.
nstxtcout =  5  ; frequency to write coordinate 
to xtc trajectory.
nstvout=  5  ; frequency to write 
velocities to output trajectory.
nstfout =  5  ; frequency to write forces 
to output trajectory.
nstlog   =  5  ; frequency to write 
energies to log file.
nstenergy=  5  ; frequency to write energies to 
energy file.
nstlist   =  1   ; frequency to update the 
neighbor list.
ns_type   =  grid
rlist   =  1.4
coulombtype  =  PME
rcoulomb=  1.4
vdwtype  =  cut-off
rvdw =  1.4
pme_order  =  8 ; use 6,8 or 10 when 
running in parallel
ewald_rtol   =  1e-5
optimize_fft=  yes
DispCorr   =  no ; don't apply any correction   
;open LINCS
constraint_algorithm = LINCS
lincs_order   = 4   ;highest order in the expansion 
of the constraint coupling matrix
lincs_warnangle  = 30 ;maximum angle that a bond can rotate 
before LINCS will complain
lincs_iter  = 1;number of iterations to 
correct for a rotational lengthening in LINCS
; Temperature coupling is on
Tcoupl  = v-rescale
tau_t = 0.1 
tc-grps  = HEP 
ref_t  =  300 
; Pressure  coupling is on
Pcoupl  = parrinello-rahman
Pcoupltype  = isotropic
tau_p= 1.0
compressibility   = 4.5e-5
ref_p = 1.0
; generate velocity is on at 300 K.
gen_vel  = yes
gen_temp  = 300.0
gen_seed   = -1
 
Is there something wrong with my .mdp file or my command? Thanks a lot. 
 
Cheers,
Cuiying
 
From: cuiying_j...@hotmail.com
To: gmx-users@gromacs.org
Subject: RE: About the binary identical results by restarting from the 
checkpoint file
Date: Mon, 3 Jun 2013 16:59:31 +




Hi Mark,
 
Thanks for your reply. I tested restarting simulations with .cpt files by 
GROMACS 4.6.1.  and the problems are still there, i.e. I cannot get binary 
identical results from restarted simulations with those from continuous 
simulations. The command I used for restarting is as the following (Only one 
processor is used during the simulations.):
mdrun -v -s md.tpr -cpt 0 -cpi md.cpt -deffnm md -reprod 
 
 
For further information, I attach my original .mdp file below:
constraints  =  all-bonds ; convert all bonds to constraints.
integrator =  md
dt  =  0.002  ; ps !
nsteps  =  1 ; total 2 ns.
nstcomm =  10; frequency for center of mass 
motion removal.
nstxout=  5  ; collect data every 10.0 ps.
nstxtcout =  5  ; frequency to write coordinate 
to xtc trajectory.
nstvout=  5  ; frequency to write 
velocities to output trajectory.
nstfout =  5  ; frequency to write forces 
to output trajectory.
nstlog   =  5  ; frequency to write 
energies to log file.
nstenergy=  5  ; frequency to write energies to 
energy file.
nstlist   =  1   ; frequency to update the 
neighbor list.
ns_type   =  grid
rlist   =  1.4
coulombtype  =  PME
rcoulomb=  1.4
vdwtype  =  cut-off
rvdw =  1.4
pme_order  =  8 ; use 6,8 or 10 when 
running in parallel
ewald_rtol   =  1e-5
optimize_fft=  yes
DispCorr   =  no

[gmx-users] System equilibrium problems

[Parker de Waal]

Hi everyone,

I recently tried to perform an 25 ns simulation on 12 nodes and was greeted
with this error around 3.2 ns into the run.

'3 particles communicated to PME node 9 are more than 2/3 times the cut-off
out of the domain decomposition cell of their charge group in dimension y.'

To my knowledge the system has reached equilibrium as shown by energy
minimization, nvt and npt runs prior to the md run. The only thing that
concerns me is the Pressure average of 1.9

Energy  Average   Err.Est.   RMSD  Tot-Drift
---
Potential   -921529  3200094074.9-214425
 (kJ/mol)

Energy  Average   Err.Est.   RMSD  Tot-Drift
---
Temperature 300.033   0.161.57434  -0.790469  (K)

Energy  Average   Err.Est.   RMSD  Tot-Drift
---
Pressure1.94649   0.3291.45451.28586  (bar)
Density 1012.96  0.037   0.778484 -0.0126246
 (kg/m^3)

Additionally here is a link to my md.mdp file
https://gist.github.com/ParkerdeWaal/d472bac58aa9cebfc23e#file-gistfile1-sh

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

[gmx-users] Tabulated Potentials

[O'Neill, David]

Hello Users,

Recently I have been trying to implement the use of tabulated potentials in 
GROMACS to an system of argon atoms.

I run a NVE simulation of 1000 argon atoms and then plot the potential energy 
from the output.

ar.itp :

[ defaults ]
; nbfunccomb-rule   gen-pairs   fudgeLJ fudgeQQ
  1 2   no  1.0 1.0

[ atomtypes ]
;name  at.num  masscharge   ptype   sigmaepsilon
   Ar   18  39.94  0.000   A  0.34  0.997

[ nonbond_params ]
  ; ij func  c6   c12
   Ar   Ar   1   0.340.997

Then I run the same simulation but with tabulated potentials.

ar.itp:

[ defaults ]
; nbfunccomb-rule   gen-pairs   fudgeLJ fudgeQQ
  1 2   no  1.0 1.0

[ atomtypes ]
;name  at.num  masscharge   ptype   sigmaepsilon
   Ar   18  39.94  0.000   A  1.000  1.000

[ nonbond_params ]
  ; ij func  c6   c12
   Ar   Ar   1  1.0001.000

The mdp file has changes of:

xtc-grps =
; Selection of energy groups
energygrps   = Ar
energygrp_table  = Ar Ar
coulombtype  = user
vdw-type = user

My table file (table_Ar_Ar.xvg) looks like this:

0.00e+00   0.00e+00 0.00e+00   0.00e+00 
0.00e+00   0.00e+00 0.00e+00
5.00e-04   0.00e+00 0.00e+00   0.00e+00 
0.00e+00   0.00e+00 0.00e+00
1.00e-03   0.00e+00 0.00e+00   0.00e+00 
0.00e+00   0.00e+00 0.00e+00
1.50e-03   0.00e+00 0.00e+00   0.00e+00 
0.00e+00   0.00e+00 0.00e+00
2.00e-03   0.00e+00 0.00e+00   0.00e+00 
0.00e+00   0.00e+00 0.00e+00
2.50e-03   0.00e+00 0.00e+00   0.00e+00 
0.00e+00   0.00e+00 0.00e+00
...
...
1.00e-01   1.00e+01 1.00e+02   -6.1606800110e+03 
-3.6964080066e+05   9.5170456866e+06 1.1420454824e+09
1.005000e-01   9.9502487562e+00 9.9007450311e+01   -5.9790513233e+03 
-3.5695828796e+05   8.9641561500e+06 1.0703470030e+09
1.01e-01   9.9009900990e+00 9.8029604941e+01   -5.8036392503e+03 
-3.4477064853e+05   8.4458948214e+06 1.0034726520e+09
1.015000e-01   9.8522167488e+00 9.7066174865e+01   -5.6342018047e+03 
-3.3305626432e+05   7.9599373058e+06 9.4107633173e+08
1.02e-01   9.8039215686e+00 9.6116878124e+01   -5.4705075446e+03 
-3.2179456145e+05   7.5041255756e+06 8.8283830301e+08
1.025000e-01   9.7560975610e+00 9.5181439619e+01   -5.3123350657e+03 
-3.1096595506e+05   7.0764553285e+06 8.2846306285e+08
...
...
1.897500e+00   5.2700922266e-01 2.7773872077e-01   -1.3198906261e-04 
-4.1735671970e-04   4.3683833118e-09 2.7626139521e-08
1.898000e+00   5.2687038988e-01 2.7759240774e-01   -1.3178057657e-04 
-4.1658770253e-04   4.3545938718e-09 2.7531678852e-08
1.898500e+00   5.2673163023e-01 2.7744621029e-01   -1.3157247463e-04 
-4.1582030435e-04   4.3408515750e-09 2.7437565921e-08
1.899000e+00   5.2659294365e-01 2.7730012831e-01   -1.3136475599e-04 
-4.1505452131e-04   4.3271562481e-09 2.7343799356e-08
1.899500e+00   5.2645433009e-01 2.7715416167e-01   -1.3115741984e-04 
-4.1429034960e-04   4.3135077182e-09 2.7250377793e-08
1.90e+00   5.2631578947e-01 2.7700831025e-01   -1.3095046538e-04 
-4.1352778540e-04   4.2999058130e-09 2.7157299872e-08

The potential energy is then plotted, but they are different for each system 
when they should be the same. I have spent quite some time on this checking the 
files looking for what I have done wrong, it is clear to me that it might be 
rather obvious but I just can't see it as I'm too far in. Anyone see my 
mistakes?

Regards,

Stream

--
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_Li

Re: [gmx-users] Problem in RMSD plot

[Justin Lemkul]

On 6/13/13 10:47 AM, Sainitin Donakonda wrote:

Hi,

Recently i ran 20ns protein ligand simulation ..in cluster ..I ran it in 2
parts first i ran 10ns and extended to another 10ns..

Then I got 2 .xtc files...i combined both these trajectories using
following command

trjcat -f 1.xtc 2.xtc -o combine.xtc -cat

Then using combine.xtc i plotted RMSD plot for protein back bone i got the
plot but it is strange there is a line from 0 ns passing as daignol

Here i attach that plot..

Can any body suggest how to solve this issue..



Attachments are not allowed by the list.  Please provide a URL to share an 
image.

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

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

Re: [gmx-users] Fw: charmm27 in gromacs- grompp error

[Justin Lemkul]

On 6/13/13 12:37 AM, Revthi Sanker wrote:




Dear all,
I am using charmm27 forcefield in gromacs for performing all atom simulations (system comprising of 
DOPC, cholesteryl ester and protein) .I got the itp file for dopc from the lipid book in which they 
have mentioned #include "charmm27.ff/ffbonded.itp" and  
"charmm27.ff/ffnonbonded.itp" to source to these for the parameters of each bond, angle 
dihedral etc based on the atom types instead of mentioning explicitly each numerical value from the 
gromacs directory.But it could not read the file and displayed:

Syntax error - File ffbonded.itp, line 2 Last line read: '[ atomtypes ]' 
Invalid order for directive defaults



ffbonded.itp should not be defining atomtypes, thus the directive is out of 
order in some way.



  When I commented those lines and again ran grompp, it generated the following 
error:
   No default Angle types
No default Ryckaert-Bell. types.

Kindly suggest me in this
  issue.



Something is badly wrong with the files you're using, but based on the limited 
information you have provided, there is nothing anyone can suggest but to refer 
to Chapter 5 of the manual for required topology hierarchy.  Certain directives 
must precede others.


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

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

[gmx-users] Problem in RMSD plot

[Sainitin Donakonda]

Hi,

Recently i ran 20ns protein ligand simulation ..in cluster ..I ran it in 2
parts first i ran 10ns and extended to another 10ns..

Then I got 2 .xtc files...i combined both these trajectories using
following command

trjcat -f 1.xtc 2.xtc -o combine.xtc -cat

Then using combine.xtc i plotted RMSD plot for protein back bone i got the
plot but it is strange there is a line from 0 ns passing as daignol

Here i attach that plot..

Can any body suggest how to solve this issue..

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

[gmx-users] Re: distance_restraints

[maggin]

 Hi, Tsjerk 

 I want equlibration enough time, so set NVT time 10ns , but  simulation
collapse at 7ns, protein have 7 fragments. Before NVT, I just do one time of
steep energy minimization.

So, I want first use constraint do steep, cg in vacuum, then add water, do
steep, cg with constraint, then again do steep, cg without constraint.

I hope after such steps my system will not collapse again in the next NVT,
NPT and MD.  

Good energy minimization will contribute to simulation a lot.

maggin

 



--
View this message in context: 
http://gromacs.5086.x6.nabble.com/distance-restraints-tp5008938p5009130.html
Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] Re: distance_restraints

[Tsjerk Wassenaar]

Hi Maggin,

Why do you run EM with constraints?

Cheers,

Tsjerk


On Thu, Jun 13, 2013 at 10:53 AM, maggin  wrote:

> Hi, Justin,
>
> It's seems no problem at steep energy minimization, except lose H atoms
> connect with C, the superposition are very well.
>
> When I use Pymol to  align the NMR structure and the structure after cg
> minimization, because cg is after steep, so same as steep, they lose H
> atoms
> that connect with C. but superposition is not so good with steep. It seems
> have some distanc and angles between problematic areas, and also as to good
> areas.
>
> problematic areas:
> atom1 atom2
>  1  N1+  (GLY124   N) 4 H  (GLY124  HT3)
> 
>
> atom1 atom2
> 181  C  (PRO137  CD)182 H  (PRO137  HD1)
> 
>
> atom1 atom2
>  262  H  (PHE141  HD1)  263 C  (PHE141  CE2)
> 
>
> atom1 atom2
>  296 O1-(ASP144  OD2)  297 C  (ASP144  C)
> 
>
> atom1 atom2
>   685 O   (PRO165  O)
> 
>
> atom1 atom2
>  685 O   (PRO165  O)  688 C  (VAL166 CA)
> 
>
> good area:
> PRO158
> 
>
> analysis:
> 1) 1  N1+  (GLY124   N) 4 H  (GLY124  HT3)
> because GLY124 is N-end, and have a positive charge, so after cg
> minimization, it move long range, so have LINCS WARNING
>
> 2)181  C  (PRO137  CD)182 H  (PRO137  HD1)
> because at steep minimization, it lose HD1, so at cg minimization, it also
> lost HD1, so actually they have no bond,
>
> 3) 262  H  (PHE141  HD1)  263 C  (PHE141  CE2)
> 296 O1-(ASP144  OD2)  297 C  (ASP144  C)
> 685 O   (PRO165  O)  688 C  (VAL166 CA)
> It seems for this group,  atoms are far away, they are not form bond, but
> it
> looks cg take they as bonds, so it cause LINCS WARNING
>
> At such situation, what is the best way to deal with these LINCS WARNINGS?
>
> Thank you very much!
>
> maggin
>
>
>
>
>
>
> --
> View this message in context:
> http://gromacs.5086.x6.nabble.com/distance-restraints-tp5008938p5009127.html
> Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
> --
> 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
>



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

Re: [gmx-users] Problem compiling Gromacs 4.6 on BlueGene/Q

[Mark Abraham]

On Thu, Jun 13, 2013 at 10:13 AM, Jernej Zidar wrote:

> Hi,
>   I'm trying to compile Gromacs 4.6 on a BlueGene cluster but I've
> stumbled upon something that looks like a bug.
>
>   Here's how I'm trying:
>
> 1. Compile FFTW-3.3.2:
> ./configure --prefix=/scratch/home/user/fftw-3.3.2
> make && make install
>

This does not compile a single-precision FFTW (per generic GROMACS
installation instructions).


> 2. Compile Gromacs 4.6 using instructions from Gromacs' page:
> cmake .. -DCMAKE_TOOLCHAIN_FILE=BlueGeneQ-static-XL-C \
>   -DCMAKE_PREFIX_PATH=/scratch/home/user/fftw-3.3.2
>
>   The cmake process completes without any error but make fails stating:
>
> Could not find fftw3f library named libfftw3f, please specify its
> location in CMAKE_PREFIX_PATH or FFTWF_LIBRARY by hand (e.g.
> -DFFTWF_LIBRARY='/path/to/libfftw3f.so')
> CMake Error at CMakeLists.txt:922 (MESSAGE):
>   Cannot find FFTW 3 (with correct precision - libfftw3f for
> single-precision
>   GROMACS or libfftw3 for double-precision GROMACS).  Either choose the
> right
>   precision, choose another FFT(W) library, enable the advanced option to
> let
>   GROMACS build FFTW 3 for you, or use the really slow GROMACS built-in
>   fftpack library.
>
> CMake Error: The following variables are used in this project, but
> they are set to NOTFOUND.
> Please set them or make sure they are set and tested correctly in the
> CMake files:
> FFTWF_INCLUDE_DIR (ADVANCED)
>
>   Problem 1: no shared objects are generated during the make phase of FFTW.
>

You probably want a static FFTW - the suggested solution is generic, though.

  Problem 2: even when setting the paths as instructed, the make fails
> with the same error. Looks like cmake is unable to "read" the path in
> "-DCMAKE_PREFIX_PATH".
>

I'd say it's more likely the single-precision libfftw3f.a file is not
there, so it can't be read :-)


>
>   I compiled Cmake myself using GNU compilers. Could this be the problem?
>

No.

Mark


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

[gmx-users] Re: distance_restraints

[maggin]

Hi, Justin,

It's seems no problem at steep energy minimization, except lose H atoms
connect with C, the superposition are very well.

When I use Pymol to  align the NMR structure and the structure after cg
minimization, because cg is after steep, so same as steep, they lose H atoms
that connect with C. but superposition is not so good with steep. It seems
have some distanc and angles between problematic areas, and also as to good
areas.
 
problematic areas:
atom1 atom2 
 1  N1+  (GLY124   N) 4 H  (GLY124  HT3)
 

atom1 atom2 
181  C  (PRO137  CD)182 H  (PRO137  HD1) 
 

atom1 atom2
 262  H  (PHE141  HD1)  263 C  (PHE141  CE2) 
 

atom1 atom2
 296 O1-(ASP144  OD2)  297 C  (ASP144  C) 
 

atom1 atom2
  685 O   (PRO165  O)  
 

atom1 atom2
 685 O   (PRO165  O)  688 C  (VAL166 CA) 
 

good area:
PRO158
 

analysis:
1) 1  N1+  (GLY124   N) 4 H  (GLY124  HT3)
because GLY124 is N-end, and have a positive charge, so after cg
minimization, it move long range, so have LINCS WARNING

2)181  C  (PRO137  CD)182 H  (PRO137  HD1) 
because at steep minimization, it lose HD1, so at cg minimization, it also
lost HD1, so actually they have no bond, 

3) 262  H  (PHE141  HD1)  263 C  (PHE141  CE2) 
296 O1-(ASP144  OD2)  297 C  (ASP144  C) 
685 O   (PRO165  O)  688 C  (VAL166 CA) 
It seems for this group,  atoms are far away, they are not form bond, but it
looks cg take they as bonds, so it cause LINCS WARNING

At such situation, what is the best way to deal with these LINCS WARNINGS? 

Thank you very much!

maggin


 



--
View this message in context: 
http://gromacs.5086.x6.nabble.com/distance-restraints-tp5008938p5009127.html
Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

[gmx-users] Problem compiling Gromacs 4.6 on BlueGene/Q

[Jernej Zidar]

Hi,
  I'm trying to compile Gromacs 4.6 on a BlueGene cluster but I've
stumbled upon something that looks like a bug.

  Here's how I'm trying:

1. Compile FFTW-3.3.2:
./configure --prefix=/scratch/home/user/fftw-3.3.2
make && make install
2. Compile Gromacs 4.6 using instructions from Gromacs' page:
cmake .. -DCMAKE_TOOLCHAIN_FILE=BlueGeneQ-static-XL-C \
  -DCMAKE_PREFIX_PATH=/scratch/home/user/fftw-3.3.2

  The cmake process completes without any error but make fails stating:

Could not find fftw3f library named libfftw3f, please specify its
location in CMAKE_PREFIX_PATH or FFTWF_LIBRARY by hand (e.g.
-DFFTWF_LIBRARY='/path/to/libfftw3f.so')
CMake Error at CMakeLists.txt:922 (MESSAGE):
  Cannot find FFTW 3 (with correct precision - libfftw3f for single-precision
  GROMACS or libfftw3 for double-precision GROMACS).  Either choose the right
  precision, choose another FFT(W) library, enable the advanced option to let
  GROMACS build FFTW 3 for you, or use the really slow GROMACS built-in
  fftpack library.

CMake Error: The following variables are used in this project, but
they are set to NOTFOUND.
Please set them or make sure they are set and tested correctly in the
CMake files:
FFTWF_INCLUDE_DIR (ADVANCED)

  Problem 1: no shared objects are generated during the make phase of FFTW.

  Problem 2: even when setting the paths as instructed, the make fails
with the same error. Looks like cmake is unable to "read" the path in
"-DCMAKE_PREFIX_PATH".

  I compiled Cmake myself using GNU compilers. Could this be the problem?

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

[gmx-users] Re: distance_restraints

[maggin]

Hi, Justin,

I use Pymol to align the NMR structure and the structure after steep
minimization, find problematic areas are superposition very well, while all
the problematic areas have same character, that after steep minimization,
Amino acid will lose some H atoms  connect with C

 

 

 

 

 

 

When I check other place, find they are same with the problematic areas,
amino acid lose some H atoms  connect with C

So, it's unlike lose H atomes cause these LINCS WARNING.

maggin





--
View this message in context: 
http://gromacs.5086.x6.nabble.com/distance-restraints-tp5008938p5009124.html
Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
-- 
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