Re: [gmx-users] genion doubt

[Justin A. Lemkul]

Bharath.K. Chakravarthi wrote:

HI
I'm not sure about this kind of error but as per my knowledge the 
problem might be with the parameter cpp in mdp file.

In my mdp file it is as follows



The problem is unrelated to cpp, since the error complained about the use of 
"warnings" in the .mdp file.  Further, if we are to assume Gromacs 4.0.x, the 
cpp setting is ignored, as Gromacs has its own C pre-processor now.



title = ecoli_nusG
cpp = /usr/bin/cpp
define = -DPOSRES
constraints = all-bonds
integrator = md
dt = 0.001 ; ps !
nsteps = 10 ; total 100 ps.
nstcomm = 1
..
..

and somewhere i read the nsteps should be between 5-10 for pr 
dynamics.


In general, yes, to obtain good equilibration you would certainly want to run 
for more than 1.0 ps, but I would say there is no absolute setting that should 
be applied.


-Justin

search gromacs tutorial for better clue... 

On Sat, May 15, 2010 at 6:03 AM, manjula kasinathan > wrote:



hi snip

Thank u. as per ur suggestion i added sodium ions to my
protein. then i carried out mdrun for energy minimization nsteps
3000 but i runs only for 1108 steps. then i went to position
restrain steps the command i gave

grompp -f pr.mdp -c em.gro -p top.top -o pr.tpr

i got a fatal error
Too many warnings (1), grompp terminated.
If you are sure all warnings are harmless, use the
-maxwarn option

WARNING 1 [file pr.mdp, line unknown]:
  Unknown or double left-hand 'warnings' in parameter file

y i'm getting this error.how can i correct this could any one help plz.

my pr.mdp file

title   = FWS
warnings= 10
cpp = /usr/local/gromacs/share/gromacs/cpp
define  = -DPOSRES
constraints = all-bonds
integrator  = md
dt  = 0.002 ; ps !
nsteps  = 500 ; total 1.0 ps.
nstcomm = 1
nstxout = 250 ; collect data every 0.5 ps
nstvout = 1000
nstfout = 0
nstlog  = 10
nstenergy   = 10
nstlist = 10
ns_type = grid
rlist   = 1.0
coulombtype = PME
rcoulomb= 1.0
vdwtype = cut-off
rvdw= 1.4
fourierspacing  = 0.12
fourier_nx  = 0
fourier_ny  = 0
fourier_nz  = 0
pme_order   = 4
ewald_rtol  = 1e-5
optimize_fft= yes
; Berendsen temperature coupling is on
Tcoupl  = v-rescale
tau_t   = 0.1 0.1
tc-grps = protein non-protein
ref_t   = 300 300
; Pressure coupling is on
Pcoupl  = parrinello-rahman
Pcoupltype  = isotropic
tau_p   = 0.5
compressibility = 4.5e-5
ref_p   = 1.0
; Generate velocites is on at 300 K.
gen_vel = yes
gen_temp= 300.0
gen_seed= 173529

with this warnings i proceeded with mdrun but i get the following
LINCS warnnings

starting mdrun 'Protein in water'
500 steps,  1.0 ps.
step 300, will finish Sat May 15 08:57:23 2010
Step 394, time 0.788 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000103, max 0.001028 (between atoms 4478 and 4480)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
   4478   4480   33.40.1081   0.1091  0.1090
Step 423, time 0.846 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.442275, max 40.666431 (between atoms 8211 and 8212)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
   8473   8476   88.60.1527   0.2741  0.1522
   8473   8475   89.90.1094   3.6185  0.1090
   8473   8474   89.50.1094   0.2778  0.1090
   8471   8473   87.20.1455   0.2548  0.1449
   8471   8472   33.20.1013   0.1241  0.1010
   8215   8217   32.80.1090   0.1240  0.1090
   8215   8216   39.20.1091   0.1282  0.1090
   8211   8215   45.80.1536   0.1603  0.1529
   8211   8213   44.00.1425   0.1645  0.1410
   8211   8212   90.20.4225   4.5416  0.1090
   8209   8211   45.60.1511   0.1348  0.1529
   8209   8210   32.40.1098   0.1199  0.1090
   8207   8209   33.30.1482   0.1823  0.1449
   7224   7225   30.40.1013   0.1010  0.1010
   5296   5297   30.50.1093   0.1092  0.1090
Warning: 1-4 interaction between 8208 and 8213 at distance 4.720
which is larger than the 1-4 table size 2.400 nm
These are ignored for the rest of the simulation
This usually mean

Re: [gmx-users] genion doubt

[Justin A. Lemkul]

manjula kasinathan wrote:


hi snip

Thank u. as per ur suggestion i added sodium ions to my protein. 
then i carried out mdrun for energy minimization nsteps 3000 but i runs 
only for 1108 steps. then i went to position restrain steps the command 
i gave


grompp -f pr.mdp -c em.gro -p top.top -o pr.tpr

i got a fatal error
Too many warnings (1), grompp terminated.
If you are sure all warnings are harmless, use the -maxwarn 
option


WARNING 1 [file pr.mdp, line unknown]:
  Unknown or double left-hand 'warnings' in parameter file

y i'm getting this error.how can i correct this could any one help plz.



http://www.gromacs.org/Documentation/Errors#Unknown_left-hand__in_parameter_file

Read the manual - there is no such setting as "warnings."


my pr.mdp file

title   = FWS
warnings= 10
cpp = /usr/local/gromacs/share/gromacs/cpp
define  = -DPOSRES
constraints = all-bonds
integrator  = md
dt  = 0.002 ; ps !
nsteps  = 500 ; total 1.0 ps.
nstcomm = 1
nstxout = 250 ; collect data every 0.5 ps
nstvout = 1000
nstfout = 0
nstlog  = 10
nstenergy   = 10
nstlist = 10
ns_type = grid
rlist   = 1.0
coulombtype = PME
rcoulomb= 1.0
vdwtype = cut-off
rvdw= 1.4
fourierspacing  = 0.12
fourier_nx  = 0
fourier_ny  = 0
fourier_nz  = 0
pme_order   = 4
ewald_rtol  = 1e-5
optimize_fft= yes
; Berendsen temperature coupling is on
Tcoupl  = v-rescale
tau_t   = 0.1 0.1
tc-grps = protein non-protein
ref_t   = 300 300
; Pressure coupling is on
Pcoupl  = parrinello-rahman
Pcoupltype  = isotropic
tau_p   = 0.5
compressibility = 4.5e-5
ref_p   = 1.0
; Generate velocites is on at 300 K.
gen_vel = yes
gen_temp= 300.0
gen_seed= 173529

with this warnings i proceeded with mdrun but i get the following LINCS 
warnnings


starting mdrun 'Protein in water'
500 steps,  1.0 ps.
step 300, will finish Sat May 15 08:57:23 2010
Step 394, time 0.788 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000103, max 0.001028 (between atoms 4478 and 4480)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
   4478   4480   33.40.1081   0.1091  0.1090
Step 423, time 0.846 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.442275, max 40.666431 (between atoms 8211 and 8212)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
   8473   8476   88.60.1527   0.2741  0.1522
   8473   8475   89.90.1094   3.6185  0.1090
   8473   8474   89.50.1094   0.2778  0.1090
   8471   8473   87.20.1455   0.2548  0.1449
   8471   8472   33.20.1013   0.1241  0.1010
   8215   8217   32.80.1090   0.1240  0.1090
   8215   8216   39.20.1091   0.1282  0.1090
   8211   8215   45.80.1536   0.1603  0.1529
   8211   8213   44.00.1425   0.1645  0.1410
   8211   8212   90.20.4225   4.5416  0.1090
   8209   8211   45.60.1511   0.1348  0.1529
   8209   8210   32.40.1098   0.1199  0.1090
   8207   8209   33.30.1482   0.1823  0.1449
   7224   7225   30.40.1013   0.1010  0.1010
   5296   5297   30.50.1093   0.1092  0.1090
Warning: 1-4 interaction between 8208 and 8213 at distance 4.720 which 
is larger than the 1-4 table size 2.400 nm

These are ignored for the rest of the simulation
This usually means your system is exploding,
if not, you should increase table-extension in your mdp file
or with user tables increase the table size

Step 424, time 0.848 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 171806.092017, max 19412182.00 (between atoms 8235 and 8236)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
   8507   8508   90.00.1011   0.2179  0.1010
   8497   8499   39.80.1460   0.2065  0.1449
   8497   8498   59.80.1009   0.1923  0.1010
   8495   8497   44.00.1354 729.7847  0.1335
   8495   8496   94.40.1235 729.7617  0.1229
   8491   8493   89.70.1091   0.2077  0.1090
   8487   8489   89.80.1091   0.5344  0.1090
   8485   8491   32.70.1531   0.1890  0.1529
   8485   8486   47.40.1091   0.1421  0.1090
   8482   8485   50.70.1536 215.0330  0.1529
   8482   8484   71.00.1094 214.9777  0.1090
   8482   8483   92.60.1091 215.0566  0.1090
   8480   8495   77.10.1633 417.3555  0.1522
   8480   8482   84.20.1556 871.1644  0.1529
   8480   8481   80.70.1078 911.5953 

Re: [gmx-users] genion doubt

[Bharath.K. Chakravarthi]

HI
I'm not sure about this kind of error but as per my knowledge the problem
might be with the parameter cpp in mdp file.
In my mdp file it is as follows

title = ecoli_nusG
cpp = /usr/bin/cpp
define = -DPOSRES
constraints = all-bonds
integrator = md
dt = 0.001 ; ps !
nsteps = 10 ; total 100 ps.
nstcomm = 1
..
..

and somewhere i read the nsteps should be between 5-10 for pr
dynamics.
search gromacs tutorial for better clue... [?]

On Sat, May 15, 2010 at 6:03 AM, manjula kasinathan wrote:

>
> hi snip
>
> Thank u. as per ur suggestion i added sodium ions to my protein.
> then i carried out mdrun for energy minimization nsteps 3000 but i runs only
> for 1108 steps. then i went to position restrain steps the command i gave
>
> grompp -f pr.mdp -c em.gro -p top.top -o pr.tpr
>
> i got a fatal error
> Too many warnings (1), grompp terminated.
> If you are sure all warnings are harmless, use the -maxwarn
> option
>
> WARNING 1 [file pr.mdp, line unknown]:
>   Unknown or double left-hand 'warnings' in parameter file
>
> y i'm getting this error.how can i correct this could any one help plz.
>
> my pr.mdp file
>
> title   = FWS
> warnings= 10
> cpp = /usr/local/gromacs/share/gromacs/cpp
> define  = -DPOSRES
> constraints = all-bonds
> integrator  = md
> dt  = 0.002 ; ps !
> nsteps  = 500 ; total 1.0 ps.
> nstcomm = 1
> nstxout = 250 ; collect data every 0.5 ps
> nstvout = 1000
> nstfout = 0
> nstlog  = 10
> nstenergy   = 10
> nstlist = 10
> ns_type = grid
> rlist   = 1.0
> coulombtype = PME
> rcoulomb= 1.0
> vdwtype = cut-off
> rvdw= 1.4
> fourierspacing  = 0.12
> fourier_nx  = 0
> fourier_ny  = 0
> fourier_nz  = 0
> pme_order   = 4
> ewald_rtol  = 1e-5
> optimize_fft= yes
> ; Berendsen temperature coupling is on
> Tcoupl  = v-rescale
> tau_t   = 0.1 0.1
> tc-grps = protein non-protein
> ref_t   = 300 300
> ; Pressure coupling is on
> Pcoupl  = parrinello-rahman
> Pcoupltype  = isotropic
> tau_p   = 0.5
> compressibility = 4.5e-5
> ref_p   = 1.0
> ; Generate velocites is on at 300 K.
> gen_vel = yes
> gen_temp= 300.0
> gen_seed= 173529
>
> with this warnings i proceeded with mdrun but i get the following LINCS
> warnnings
>
> starting mdrun 'Protein in water'
> 500 steps,  1.0 ps.
> step 300, will finish Sat May 15 08:57:23 2010
> Step 394, time 0.788 (ps)  LINCS WARNING
> relative constraint deviation after LINCS:
> rms 0.000103, max 0.001028 (between atoms 4478 and 4480)
> bonds that rotated more than 30 degrees:
>  atom 1 atom 2  angle  previous, current, constraint length
>4478   4480   33.40.1081   0.1091  0.1090
> Step 423, time 0.846 (ps)  LINCS WARNING
> relative constraint deviation after LINCS:
> rms 0.442275, max 40.666431 (between atoms 8211 and 8212)
> bonds that rotated more than 30 degrees:
>  atom 1 atom 2  angle  previous, current, constraint length
>8473   8476   88.60.1527   0.2741  0.1522
>8473   8475   89.90.1094   3.6185  0.1090
>8473   8474   89.50.1094   0.2778  0.1090
>8471   8473   87.20.1455   0.2548  0.1449
>8471   8472   33.20.1013   0.1241  0.1010
>8215   8217   32.80.1090   0.1240  0.1090
>8215   8216   39.20.1091   0.1282  0.1090
>8211   8215   45.80.1536   0.1603  0.1529
>8211   8213   44.00.1425   0.1645  0.1410
>8211   8212   90.20.4225   4.5416  0.1090
>8209   8211   45.60.1511   0.1348  0.1529
>8209   8210   32.40.1098   0.1199  0.1090
>8207   8209   33.30.1482   0.1823  0.1449
>7224   7225   30.40.1013   0.1010  0.1010
>5296   5297   30.50.1093   0.1092  0.1090
> Warning: 1-4 interaction between 8208 and 8213 at distance 4.720 which is
> larger than the 1-4 table size 2.400 nm
> These are ignored for the rest of the simulation
> This usually means your system is exploding,
> if not, you should increase table-extension in your mdp file
> or with user tables increase the table size
>
> Step 424, time 0.848 (ps)  LINCS WARNING
> relative constraint deviation after LINCS:
> rms 171806.092017, max 19412182.00 (between atoms 8235 and 8236)
> bonds that rotated more than 30 degrees:
>  atom 1 atom 2  angle  previous, current, constraint length
>8507   8508   90.00.1011   0.2179  0.1010
>8497   8499   39.80.1460   0.2065  0.1449
>8497   8498   59.80.1009   0.1923  0.1010
>8495   8497   44.00.1354 729.7847  0.1335
>8495   8496   94.40.123