Re: [gmx-users] mdp file warnings

[Eduardo Oliveira]

Ok,

Thanks a lot!



 De: Justin Lemkul 
Para: Discussion list for GROMACS users  
Enviadas: Segunda-feira, 17 de Dezembro de 2012 12:08
Assunto: Re: [gmx-users] mdp file warnings
 


On 12/17/12 9:06 AM, Eduardo Oliveira wrote:
> OK, so if i got this right all I have to do is add another line in the mdp 
> file
> with refcoord_scaling = com?  I thought that i had to make a substitution in 
> one
> of the existing terms.
> 

Right, it's a new term entirely (see the manual).  All keywords have a default 
setting that is accepted if not explicitly given in the .mdp file.  For 
refcoord_scaling, the default is "no," which will trigger the warning you got 
when used with position restraints.

-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] mdp file warnings

[Justin Lemkul]

On 12/17/12 9:06 AM, Eduardo Oliveira wrote:

OK, so if i got this right all I have to do is add another line in the mdp file
with refcoord_scaling = com?  I thought that i had to make a substitution in one
of the existing terms.



Right, it's a new term entirely (see the manual).  All keywords have a default 
setting that is accepted if not explicitly given in the .mdp file.  For 
refcoord_scaling, the default is "no," which will trigger the warning you got 
when used with position restraints.


-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] mdp file warnings

[Eduardo Oliveira]

OK, so if i got this right all I have to do is add another line in the mdp file 
with refcoord_scaling = com?  I thought that i had to make a substitution in 
one of the existing terms.

Thanks.



 De: Justin Lemkul 
Para: Eduardo Oliveira ; Discussion list for GROMACS 
users  
Enviadas: Segunda-feira, 17 de Dezembro de 2012 11:57
Assunto: Re: [gmx-users] mdp file warnings
 


On 12/17/12 8:55 AM, Eduardo Oliveira wrote:
> Hi,
>
> I'm setting my system but when I run grompp I get a warning and the program 
> terminates.  It says the following:
>
> You are using  pressure coupling with absolute position restraints, this will 
> give artifacts. Use refcoord_scaling option.
>
>
> I want to try it but i don't know where to change this term in the mdp file. 
> Any help?
>

Location within the file is irrelevant.  For most cases, you want 
"refcoord_scaling = com."  See the numerous discussions on this topic in the 
list archive.

-Justin

> title                    = 500ps_pr_fixo
> cpp                      = /lib/cpp
> define                   = -DPOSRES
> integrator               = md
> tinit                    = 0
> dt                       = 0.002
> nsteps                   = 25 ; total 500 ps
> comm-mode                = Linear
> nstcomm                  = 1
> nstxout                  = 500
> nstvout                  = 2
> nstfout                  = 2
> nstlog                   = 1000
> nstenergy                = 100
> nstxtcout                = 500
> xtc-precision            = 1000
> energygrps               = Protein SOL NA
> nstlist                  = 5
> ns_type                  = grid
> pbc                      = xyz
> rlist                    = 1.0
> domain-decomposition     = no
> coulombtype              = PME
> rcoulomb                 = 1.0
> epsilon-r                = 1
> vdw-type                 = Cut-off
> rvdw                     = 1.4
> DispCorr                 = EnerPres
> optimize_fft             = yes
> Tcoupl                   = V-rescale ;berendsen
> tc-grps                  = Protein Non-protein
> tau-t                    = .1 .1
> ref-t                    = 310 310
> gen_vel                  = yes
> gen_temp                 = 310
> gen_seed                 = 173529
> Pcoupl                   = berendsen
> Pcoupltype               = Isotropic
> tau-p                    = 1
> compressibility          = 4.5e-5
> ref-p                    = 1
> constraints              = all-bonds
> constraint-algorithm     = Lincs
> unconstrained-start      = no
> Shake-SOR                = no
> shake-tol                = 1e-04
> lincs-order              = 4
> lincs-warnangle          = 30
> morse                    = no
>

-- 


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] mdp file warnings

[Justin Lemkul]

On 12/17/12 8:55 AM, Eduardo Oliveira wrote:

Hi,

I'm setting my system but when I run grompp I get a warning and the program 
terminates.  It says the following:

You are using  pressure coupling with absolute position restraints, this will 
give artifacts. Use refcoord_scaling option.


I want to try it but i don't know where to change this term in the mdp file. 
Any help?



Location within the file is irrelevant.  For most cases, you want 
"refcoord_scaling = com."  See the numerous discussions on this topic in the 
list archive.


-Justin


title= 500ps_pr_fixo
cpp  = /lib/cpp
define   = -DPOSRES
integrator   = md
tinit= 0
dt   = 0.002
nsteps   = 25 ; total 500 ps
comm-mode= Linear
nstcomm  = 1
nstxout  = 500
nstvout  = 2
nstfout  = 2
nstlog   = 1000
nstenergy= 100
nstxtcout= 500
xtc-precision= 1000
energygrps   = Protein SOL NA
nstlist  = 5
ns_type  = grid
pbc  = xyz
rlist= 1.0
domain-decomposition = no
coulombtype  = PME
rcoulomb = 1.0
epsilon-r= 1
vdw-type = Cut-off
rvdw = 1.4
DispCorr = EnerPres
optimize_fft = yes
Tcoupl   = V-rescale ;berendsen
tc-grps  = Protein Non-protein
tau-t= .1 .1
ref-t= 310 310
gen_vel  = yes
gen_temp = 310
gen_seed = 173529
Pcoupl   = berendsen
Pcoupltype   = Isotropic
tau-p= 1
compressibility  = 4.5e-5
ref-p= 1
constraints  = all-bonds
constraint-algorithm = Lincs
unconstrained-start  = no
Shake-SOR= no
shake-tol= 1e-04
lincs-order  = 4
lincs-warnangle  = 30
morse= no



--


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] mdp file problem

[Justin A. Lemkul]

madhumita das wrote:

Thanks Justin,

I must inform you that my pdb file has a modified cysteine residue 
having a mercury atom attached to the sulphur atom next to the residue 
having the atom 2700. Is the murcury atom creating any problem? I want 


Probably.  Parameterizing such a species properly is not trivial, if it can even 
be done in a non-polarizable MM force field.


http://www.gromacs.org/Documentation/How-tos/Parameterization#Exotic_Species


to also know can I use amber forcefield in GROMACS for pdb files of lipid?



Lipids probably aren't built in, but could potentially be added if you provide 
the proper parameters.  CHARMM is probably a better choice.  CHARMM27 is built 
into Gromacs already, and CHARMM36 is available as a download from the website.


-Justin

On Tue, Nov 8, 2011 at 5:56 PM, Justin A. Lemkul > wrote:




madhumita das wrote:


Hi GROMACS users,

   i am in the midst of simulating  a protein in water.  I have
modified  a residue  in my  pdb file at position  182,  using
amber and then acpype.py.  But  after running  the energy
minimization step,using  em.mdp file  generated from acpype ,
following error comes.

Steepest Descents:
  Tolerance (Fmax)   =  1.0e+03
  Number of steps= 5000
Step=   17, Dmax= 1.5e-06 nm, Epot=  9.89827e+17 Fmax=
inf, atom= 2700

Stepsize too small, or no change in energy.
Converged to machine precision,
but not to the requested precision Fmax < 1000

Double precision normally gives you higher accuracy.

writing lowest energy coordinates.

Steepest Descents converged to machine precision in 18 steps,
but did not reach the requested Fmax < 1000.
Potential Energy  =  9.8982703e+17
Maximum force =inf on atom 2700
Norm of force =  1.7474532e+19


An infinite force suggests severe atomic overlap.  Check the
starting structure, paying close attention to atom 2700 and its
surrounding environment.

-Justin

-- 
==__==


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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] mdp file problem

[madhumita das]

Thanks Justin,

I must inform you that my pdb file has a modified cysteine residue having a
mercury atom attached to the sulphur atom next to the residue having the
atom 2700. Is the murcury atom creating any problem? I want to also know
can I use amber forcefield in GROMACS for pdb files of lipid?

On Tue, Nov 8, 2011 at 5:56 PM, Justin A. Lemkul  wrote:

>
>
> madhumita das wrote:
>
>>
>> Hi GROMACS users,
>>
>>i am in the midst of simulating  a protein in water.  I have modified
>>  a residue  in my  pdb file at position  182,  using amber and then
>> acpype.py.  But  after running  the energy minimization step,using  em.mdp
>> file  generated from acpype , following error comes.
>>
>> Steepest Descents:
>>   Tolerance (Fmax)   =  1.0e+03
>>   Number of steps= 5000
>> Step=   17, Dmax= 1.5e-06 nm, Epot=  9.89827e+17 Fmax= inf, atom=
>> 2700
>> Stepsize too small, or no change in energy.
>> Converged to machine precision,
>> but not to the requested precision Fmax < 1000
>>
>> Double precision normally gives you higher accuracy.
>>
>> writing lowest energy coordinates.
>>
>> Steepest Descents converged to machine precision in 18 steps,
>> but did not reach the requested Fmax < 1000.
>> Potential Energy  =  9.8982703e+17
>> Maximum force =inf on atom 2700
>> Norm of force =  1.7474532e+19
>>
>
> An infinite force suggests severe atomic overlap.  Check the starting
> structure, paying close attention to atom 2700 and its surrounding
> environment.
>
> -Justin
>
> --
> ==**==
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> 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] mdp file problem

[Justin A. Lemkul]

madhumita das wrote:


Hi GROMACS users,

i am in the midst of simulating  a protein in water.  I have 
modified  a residue  in my  pdb file at position  182,  using amber and 
then acpype.py.  But  after running  the energy minimization step,using  
em.mdp file  generated from acpype , following error comes.


Steepest Descents:
   Tolerance (Fmax)   =  1.0e+03
   Number of steps= 5000
Step=   17, Dmax= 1.5e-06 nm, Epot=  9.89827e+17 Fmax= inf, 
atom= 2700

Stepsize too small, or no change in energy.
Converged to machine precision,
but not to the requested precision Fmax < 1000

Double precision normally gives you higher accuracy.

writing lowest energy coordinates.

Steepest Descents converged to machine precision in 18 steps,
but did not reach the requested Fmax < 1000.
Potential Energy  =  9.8982703e+17
Maximum force =inf on atom 2700
Norm of force =  1.7474532e+19


An infinite force suggests severe atomic overlap.  Check the starting structure, 
paying close attention to atom 2700 and its surrounding environment.


-Justin

--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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] .mdp file

[datta sarma]

Dear Mark,
  Excellent suggestion, i'll also follow it to be a good gromacs
user. Perhaps reading books, literature, searching on-line resources, go
through tutorial or manual is always evergreen idea, but a bit hard work
needed (To be an expert).
Thanks a lot.
Best Regards
sharma

On Tue, Aug 9, 2011 at 2:11 PM, Mark Abraham wrote:

>  On 9/08/2011 5:26 PM, manoj damale wrote:
>
>   Hey hi
> i want to do gromacs tutorial and for that i required the .mdp file for
> where i can get that file
>
>
> The tutorial will tell you how to get it or create it.
>
>
>   and what type of modification should i do in that file
>
>
> Whatever the tutorial suggests. What modifications are best suited for your
> own work later is something you will have to judge with the experience you
> have gained. Do all the tutorial material you can find, read textbooks and
> read current literature widely. Then think hard and test carefully.
>
> Mark
>
> --
> gmx-users mailing listgmx-users@gromacs.org
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Re: [gmx-users] .mdp file

[Mark Abraham]

On 9/08/2011 5:26 PM, manoj damale wrote:

Hey hi
i want to do gromacs tutorial and for that i required the .mdp file 
for where i can get that file




The tutorial will tell you how to get it or create it.


and what type of modification should i do in that file



Whatever the tutorial suggests. What modifications are best suited for 
your own work later is something you will have to judge with the 
experience you have gained. Do all the tutorial material you can find, 
read textbooks and read current literature widely. Then think hard and 
test carefully.


Mark
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Re: [gmx-users] mdp file settings for PME

[Justin A. Lemkul]

jojo J wrote:

Dear experts,

I posted this message before but I think you did not see it since I 
noticed messages after this have been replied. I have a hydrocarbon 


Messages do not receive replies in any sort of order.  Probably no one has had 
any relevant comments yet, or they live in a time zone where they are not awake :)


system with no charged particles. Today In one of the GROMACS tutorials 
I saw the following setting in em.mdp file:

fourierspacing  =  0.12
;fourier_nx  =   0
;fourier_ny  =   0
;fourier_nz  =   0
;pme_order  =   4
;ewald_rtol =  1e-5
;optimize_fft  =  yes

has been used for PME . Sofar I did not even include coulombtype=PME in 
my em.mdp file. What I had was:

constraints =  all-bonds
integrator  =  steep
dt  =  0.002; ps !
nsteps  =  200
nstlist =  10
ns_type =  grid
rlist   =  1.0
rcoulomb=  1.0
rvdw=  1.0
;
;   Energy minimizing stuff
;
emtol   =  1000.0

Can you please guide me whether it is necessary to include these lines 
in em file for system having only partial charges like hydrocarbon 
(alkane). Also, in md.mdp file I have only coulombtype=PME and not the 


This contradicts your statement above.  You said you had only uncharged 
particles, but clearly this is not the case.


above Ewald settings. Do you recommend to include those settings? 


For energy minimization, the effects of plain cutoffs may or may not be 
significant.  Using plain cutoffs for actual simulation is a bad idea.  The 
artifacts are well-documented and for modern simulations any good reviewer 
should raise an immediate concern if plain cutoffs were used and not thoroughly 
justified.  A method like PME is significantly more accurate, but you can also 
achieve reasonable results using switch, shift, etc.  Read about the relevant 
mechanics of the force field you're using for what might be appropriate.


Without the mentioned lines I am getting reasonabel results (potential 
energy, kinetic, ,, also T coupling works perfectly). If I had better to 
unclude them what is the best value for fourierspacing?




I don't think there's ever been any sort of systematic study on the effects of 
Fourier grid spacing.  The trade-off is between speed and accuracy.  Larger 
values speed up calculations, but make PME less accurate.  Smaller values have 
the opposite effect.  You could do a small test for yourself (0.12, 0.16, 
0.18...) to see if there are any adverse effects.


-Justin


Thank you,



--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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] mdp file

[XAvier Periole]

On May 15, 2010, at 9:28, shahab shariati   
wrote:



Hi gromacs users

I want compare simulation of protein with simulation of protein-dna.

should conditions (mdp file[T, P, dt, steps, ..] and box size)  
be same in two simulations?
Besides the box size, which be reduced, all the rest should be the  
same except for partilar purpose.


thanks alot
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Re: [gmx-users] mdp file

[Mark Abraham]

leila karami wrote:

dear Mark

thanks for your attention. is this mdp file true for energy minimization 
(100 steps by steepest descent and 100 steps by/ conjugate gradient/)?


define=  -DFLEX_SPC
constraints =  none
*integrator  =  steep
nsteps   =  100
integrator  =  cg
nsteps   =  100*
emtol =  2000
emstep  =  0.01
nstcomm   =  1
ns_type =  grid
rlist   =  1
rcoulomb   =  1.0
rvdw =  1.0
Tcoupl  =  no
Pcoupl  =  no
gen_vel =  no


No - you should have tried it to see what you got. grompp probably gives 
an error because you cannot define integrator twice. You need to have 
two mdp files and do a pair of (grompp - mdrun) operations.


Mark
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Re: [gmx-users] mdp file

[Mark Abraham]

leila karami wrote:

Hi
I want to creat mdp file for energy minimization (em.mdp). if I want to 
minimize my system (pr+dna), by steepest descent and conjugate gradient 
such as for example 100 steps by steepest descent and 100 steps by 
conjugate gradient, how I can  creat  mdp file?


For example, take one from a tutorial, consider whether each parameter 
is suitable for your needs, change as suitable, use.


Mark
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Re: [gmx-users] mdp file for monitoring pair groups

[Justin A. Lemkul]

Ragnarok sdf wrote:

The problem is that the .tpr file tells me that the monitoring is
being made between all pairs. I want only the pairs aminoacid1-ligand,
aminoacid2-ligand etc and not aminoacid1-aminoacid2. This kind of
monitoring, i.e., between all possible pairs, gives me .edr files that
are 1Gb or more in size. That is a problem since I need to do the same
type of analysis for 61 more complexes.
So, again, I need to monitor only the pairs in which one of the
members is the LIGAND and the other is one of the aminoacids of that
huge list I posted in the energygrps.



Gromacs is working as it should.  I don't believe there is any way to specify an 
"energy pair" as you want it.  To consider 200+ interactions, you have the side 
effect of getting a 200x200 matrix of interactions.


Does your ligand really interact with 200 amino acids, or does it potentially 
interact with 200 amino acids?  If you run the trajectory to see which amino 
acids are actually interacting, you can -rerun with substantially less energy 
groups defined.


-Justin


what is not working exactly?

This should give you as output all the pair interacts and you can
select the ones you want ... ?!

On Jul 17, 2009, at 4:23 PM, Ragnarok sdf wrote:


I have created an mdp file with 202 groups for monitoring in the
energygrps string. Being 201 of these aminoacids which interact with
the 202nd which is the ligand. The problem is that I found out that
this does not work properly, and also does not work the way I thought
it would work. Well, the deal is that I want to monitor each of the
pair interactions, i.e., aminoacid1-ligand, aminoacid2-ligand,
aminoacid3-ligand etc. Is there a way I can do this with a single mdp
file, or should I create 202 different mdp files and -rerun 202 times
the same simulation (which sounds just as crazy as the idea i had
before)?
Here is what I have written for the energygrps:
energygrps  =  _S r_29 r_30 r_61 r_63 r_64 r_65 r_66 r_67 r_68
r_69 r_70 r_71 r_72 r_73 r_74 r_75 r_76 r_77 r_78 r_79 r_80 r_81 r_82
r_83 r_84 r_85 r_86 r_87 r_88 r_92 r_94 r_95 r_96 r_98 r_111 r_112
r_113 r_114 r_115 r_116 r_117 r_118 r_119 r_120 r_121 r_122 r_123
r_124 r_125 r_126 r_127 r_128 r_129 r_130 r_131 r_132 r_133 r_134
r_142 r_143 r_144 r_145 r_146 r_147 r_148 r_149 r_150 r_151 r_152
r_154 r_172 r_195 r_196 r_197 r_198 r_199 r_200 r_201 r_202 r_203
r_222 r_223 r_224 r_225 r_226 r_227 r_228 r_231 r_232 r_233 r_234
r_243 r_246 r_247 r_249 r_250 r_251 r_275 r_277 r_278 r_279 r_280
r_281 r_282 r_283 r_284 r_285 r_286 r_287 r_288 r_289 r_290 r_291
r_292 r_293 r_294 r_295 r_296 r_297 r_325 r_326 r_327 r_328 r_329
r_330 r_331 r_332 r_333 r_334 r_335 r_336 r_337 r_338 r_339 r_340
r_341 r_342 r_343 r_344 r_345 r_346 r_354 r_355 r_356 r_357 r_358
r_359 r_360 r_361 r_362 r_363 r_364 r_365 r_367 r_368 r_369 r_370
r_371 r_378 r_395 r_396 r_397 r_398 r_399 r_401 r_402 r_403 r_424
r_426 r_430 r_432 r_433 r_434 r_435 r_438 r_439 r_440 r_441 r_442
r_443 r_444 r_445 r_446 r_447 r_448 r_449 r_450 r_451 r_452 r_453
r_456 r_458 r_459 r_460 r_461 r_476 r_521 r_536 r_537 r_538 r_539

I would like some advice on the matter.
Thank you in advance
Fabrício Bracht

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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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] mdp file for monitoring pair groups

[Ragnarok sdf]

The problem is that the .tpr file tells me that the monitoring is
being made between all pairs. I want only the pairs aminoacid1-ligand,
aminoacid2-ligand etc and not aminoacid1-aminoacid2. This kind of
monitoring, i.e., between all possible pairs, gives me .edr files that
are 1Gb or more in size. That is a problem since I need to do the same
type of analysis for 61 more complexes.
So, again, I need to monitor only the pairs in which one of the
members is the LIGAND and the other is one of the aminoacids of that
huge list I posted in the energygrps.

>what is not working exactly?
>
>This should give you as output all the pair interacts and you can
>select the ones you want ... ?!
>
>On Jul 17, 2009, at 4:23 PM, Ragnarok sdf wrote:
>
>> I have created an mdp file with 202 groups for monitoring in the
>>energygrps string. Being 201 of these aminoacids which interact with
>>the 202nd which is the ligand. The problem is that I found out that
>> this does not work properly, and also does not work the way I thought
>> it would work. Well, the deal is that I want to monitor each of the
>> pair interactions, i.e., aminoacid1-ligand, aminoacid2-ligand,
>> aminoacid3-ligand etc. Is there a way I can do this with a single mdp
>> file, or should I create 202 different mdp files and -rerun 202 times
>> the same simulation (which sounds just as crazy as the idea i had
>> before)?
>> Here is what I have written for the energygrps:
>> energygrps  =  _S r_29 r_30 r_61 r_63 r_64 r_65 r_66 r_67 r_68
>> r_69 r_70 r_71 r_72 r_73 r_74 r_75 r_76 r_77 r_78 r_79 r_80 r_81 r_82
>> r_83 r_84 r_85 r_86 r_87 r_88 r_92 r_94 r_95 r_96 r_98 r_111 r_112
>> r_113 r_114 r_115 r_116 r_117 r_118 r_119 r_120 r_121 r_122 r_123
>> r_124 r_125 r_126 r_127 r_128 r_129 r_130 r_131 r_132 r_133 r_134
>> r_142 r_143 r_144 r_145 r_146 r_147 r_148 r_149 r_150 r_151 r_152
>> r_154 r_172 r_195 r_196 r_197 r_198 r_199 r_200 r_201 r_202 r_203
>> r_222 r_223 r_224 r_225 r_226 r_227 r_228 r_231 r_232 r_233 r_234
>> r_243 r_246 r_247 r_249 r_250 r_251 r_275 r_277 r_278 r_279 r_280
>> r_281 r_282 r_283 r_284 r_285 r_286 r_287 r_288 r_289 r_290 r_291
>> r_292 r_293 r_294 r_295 r_296 r_297 r_325 r_326 r_327 r_328 r_329
>> r_330 r_331 r_332 r_333 r_334 r_335 r_336 r_337 r_338 r_339 r_340
>> r_341 r_342 r_343 r_344 r_345 r_346 r_354 r_355 r_356 r_357 r_358
>> r_359 r_360 r_361 r_362 r_363 r_364 r_365 r_367 r_368 r_369 r_370
>> r_371 r_378 r_395 r_396 r_397 r_398 r_399 r_401 r_402 r_403 r_424
>> r_426 r_430 r_432 r_433 r_434 r_435 r_438 r_439 r_440 r_441 r_442
>> r_443 r_444 r_445 r_446 r_447 r_448 r_449 r_450 r_451 r_452 r_453
>> r_456 r_458 r_459 r_460 r_461 r_476 r_521 r_536 r_537 r_538 r_539
>>
>> I would like some advice on the matter.
>> Thank you in advance
>> Fabrício Bracht
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Re: [gmx-users] mdp file for monitoring pair groups

[XAvier Periole]

what is not working exactly?

This should give you as output all the pair interacts and you can
select the ones you want ... ?!

On Jul 17, 2009, at 4:23 PM, Ragnarok sdf wrote:


I have created an mdp file with 202 groups for monitoring in the
energygrps string. Being 201 of these aminoacids which interact with
the 202nd which is the ligand. The problem is that I found out that
this does not work properly, and also does not work the way I thought
it would work. Well, the deal is that I want to monitor each of the
pair interactions, i.e., aminoacid1-ligand, aminoacid2-ligand,
aminoacid3-ligand etc. Is there a way I can do this with a single mdp
file, or should I create 202 different mdp files and -rerun 202 times
the same simulation (which sounds just as crazy as the idea i had
before)?
Here is what I have written for the energygrps:
energygrps  =  _S r_29 r_30 r_61 r_63 r_64 r_65 r_66 r_67 r_68
r_69 r_70 r_71 r_72 r_73 r_74 r_75 r_76 r_77 r_78 r_79 r_80 r_81 r_82
r_83 r_84 r_85 r_86 r_87 r_88 r_92 r_94 r_95 r_96 r_98 r_111 r_112
r_113 r_114 r_115 r_116 r_117 r_118 r_119 r_120 r_121 r_122 r_123
r_124 r_125 r_126 r_127 r_128 r_129 r_130 r_131 r_132 r_133 r_134
r_142 r_143 r_144 r_145 r_146 r_147 r_148 r_149 r_150 r_151 r_152
r_154 r_172 r_195 r_196 r_197 r_198 r_199 r_200 r_201 r_202 r_203
r_222 r_223 r_224 r_225 r_226 r_227 r_228 r_231 r_232 r_233 r_234
r_243 r_246 r_247 r_249 r_250 r_251 r_275 r_277 r_278 r_279 r_280
r_281 r_282 r_283 r_284 r_285 r_286 r_287 r_288 r_289 r_290 r_291
r_292 r_293 r_294 r_295 r_296 r_297 r_325 r_326 r_327 r_328 r_329
r_330 r_331 r_332 r_333 r_334 r_335 r_336 r_337 r_338 r_339 r_340
r_341 r_342 r_343 r_344 r_345 r_346 r_354 r_355 r_356 r_357 r_358
r_359 r_360 r_361 r_362 r_363 r_364 r_365 r_367 r_368 r_369 r_370
r_371 r_378 r_395 r_396 r_397 r_398 r_399 r_401 r_402 r_403 r_424
r_426 r_430 r_432 r_433 r_434 r_435 r_438 r_439 r_440 r_441 r_442
r_443 r_444 r_445 r_446 r_447 r_448 r_449 r_450 r_451 r_452 r_453
r_456 r_458 r_459 r_460 r_461 r_476 r_521 r_536 r_537 r_538 r_539

I would like some advice on the matter.
Thank you in advance
Fabrício Bracht
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Re: [gmx-users] mdp file to calculate local pressure

[Justin A. Lemkul]

anirban polley wrote:

Dear Sir,
 I am looking for local pressure where I am using 
gromacs-4.0.2_localpressure.tar 
 
package. I have download it from

   ftp://ftp.gromacs.org/pub/tmp
The error which it gives during running to make tpr file, is given below
---
Program grompp_mpi, VERSION 4.0.2_localpressure
Source code file: gmx_fatal.c, line: 481

Fatal error:
Too many warnings (1), 
/home/anirban/gromacs402localpressure/bin/grompp_mpi terminated.

If you are sure all warnings are harmless, use the -maxwarn option.
---
The warning which it gives during running to make tpr file, is given below

WARNING 1 [file popc-sm-chol-assymmetric-bilayer.top, line unknown]:
 The largest charge group contains 11 atoms. 
Since atoms only see each other when the centers of geometry of the charge

groups they belong to are within the cut-off distance, too large charge
 groups can lead to serious cut-off artifacts.
 For efficiency and accuracy, charge group should consist of a few atoms.
 For all-atom force fields use: CH3, CH2, CH, NH2, NH, OH, CO2, CO, etc.


Sir, now, could you please tell me where I have done mistake? In the 
README file, it is written that it will give localpressure.dat file 
automatically. But I could not do it.


The error message is clear.  You have a charge group containing 11 atoms, which 
is far larger than charge groups normally are.  Revise your parameters to give 
something more reasonable.  If you are comfortable with the 11-atom charge 
group, then increase the -maxwarn option, as grompp has told you.


-Justin


Thank you very much for you kind help,
Anirban Polley





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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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] mdp file to calculate local pressure

[Justin A. Lemkul]

anirban polley wrote:

Dear Justin,
 I am using gromacs-localp of version 4.0.2. for the calculation of 
local pressure. But I could not understand what I should put in the mdp 
file. Because when I tried by the following below mdp file, it does not 
even create tpr file. I have tried by different options as for example 
by using Wall but failed to get local pressure profile. I thought that I 
have write some thing so that it can be ok for giving local pressure. 
Could you please correct my mdp file and write what extra term I should 
write in my mdp file to get local pressure.

Thank you very much for your kind help.


Where did you get gromacs-localp version 4.0.2?  The software by that name in 
the Users Contributions is much older.  If you have made modifications to the 
code yourself, you may have broken something.


As I understand it, the .mdp file is probably going to be the same as any other 
run, you'll just get additional output for local pressure.  That information is 
likely in whatever README or help files that come with the localp code.


Also, if grompp is failing to produce your .tpr, it is better to post the error 
message you got instead of saying "it does not even create tpr file."  For 
diagnostic purposes, a real error message is infinitely more useful.


-Justin


Anirban

title=  lipid bilayer in water
cpp  =  /lib/cpp

integrator   =  sd  ; stochastic dynamics -> Langevin!
ld_seed  =  -1  ; random seed for sd
dt   =  0.002   ; ps !
nsteps   =  25  ; total 500 ps
nstcomm  =  1   ; freq. for cm-motion removal
tinit=  0   ; starting time (ps)

constraints  =  all-bonds   ; constraint for all bond lengths
constraint_algorithm =  lincs   ; default
lincs_order  =  4   ; default

nstxout  =  5000; T(x_out) 10 ps
nstvout  =  5000; T(v_out) 10 ps
nstfout  =  0   ; T(f_out)
nstlog   =  250 ; energies to log (0.5 ps)
nstenergy=  250 ; energies to energy file

ns_type  =  grid; nl type
nstlist  =  10  ; Freq. to update neighbour list
rlist=  1.0 ; nm (cutoff for short-range nl)

coulombtype  =  Reaction-Field  ; Coulomb interactions
rcoulomb =  2.0 ; nm (Coulomb cut-off!!)
epsilon_r=  80.0; dielectric constant for 
reaction field

vdwtype  =  Cut-off ; Wan der Waals interactions
rvdw =  1.0 ; nm (LJ cut-off)
optimize_fft =  yes

; Temperature coupling
Tcoupl   =  no  ; no effect when integrator = sd
tc-grps  =  POPC  SMCHOL  SOL
tau_t=  0.1   0.1   0.1   0.1
ref_t=  296   296   296   296

; Pressure coupling
;Pcoupl = no
Pcoupl   =  berendsen
Pcoupltype   =  semiisotropic
tau_p=  1.01.0   ; ps
compressibility  =  4.5e-5 4.5e-5; 1/bar (water: 1 atm, 300 K)
ref_p=  1.01.0   ; bar

; Generate velocites in the beginning
gen_vel  =  yes
gen_temp =  296.0
gen_seed =  173529




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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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] mdp file to calculate local pressure

[Justin A. Lemkul]

anirban polley wrote:

Dear Sir,
 I want to calculate local pressure of the membrane 
(pressure variation with z -axis). I am using gromacs-localp packages. 
As I see that all types of errors coming from saying specifically the 
option of WALL in .mdp file.

Actually I did not understand clearly what to do in the following options.


The simple answer to me is - why are you using walls?  The gromacs-localp 
package is based on version 3.0.2, and IIRC walls were introduced much later in 
development, probably version 4.0.  At least, there is no mention of walls in 
any documentation prior to the 4.0 manual.


-Justin


WALLS
; Number of walls, type, atom types, densities and box-z scale factor 
for Ewald

nwall= 2
wall_type= 9-3
wall_r_linpot= -1
wall_atomtype=
wall_density =
wall_ewald_zfac  = 3

Could you please write clearly what to write on above options ??

I am writing here the mdp file what I am using in gromacs-localp package 
to calculate local pressure.

integrator   =  sd  ; stochastic dynamics -> Langevin!
ld_seed  =  -1  ; random seed for sd
dt   =  0.002   ; ps !
nsteps   =  5   ; total 500/5=100 ps
nstcomm  =  1   ; freq. for cm-motion removal
tinit=  0   ; starting time (ps)

constraints  =  all-bonds   ; constraint for all bond lengths
constraint_algorithm =  lincs   ; default
lincs_order  =  4   ; default

nstxout  =  1000; T(x_out) 10 ps
nstvout  =  1000; T(v_out) 10 ps
nstfout  =  0   ; T(f_out)
nstlog   =  250 ; energies to log (0.5 ps)
nstenergy=  250 ; energies to energy file

ns_type  =  grid; nl type
nstlist  =  10  ; Freq. to update neighbour list
rlist=  1.0 ; nm (cutoff for short-range nl)
 
; Periodic boundary conditions: xyz (default), no (vacuum)

; or full (infinite systems only)
pbc  = xy

coulombtype  =  PME ;Reaction-Field  ; Coulomb 
interactions
rcoulomb =  1.0 ;2.0 ; nm (Coulomb 
cut-off!!)
epsilon_r=  80.0; dielectric constant for 
reaction field

vdwtype  =  Cut-off ; Wan der Waals interactions
rvdw =  1.0 ; nm (LJ cut-off)
optimize_fft =  yes

; Temperature coupling
Tcoupl   =  no  ; no effect when integrator = sd
tc-grps  =  POPC   SM   CHOL   SOL
tau_t=  0.1   0.1   0.1   0.1
ref_t=  296   296   296   296

; Pressure coupling
;Pcoupl = no
Pcoupl   =  berendsen
Pcoupltype   =  semiisotropic
tau_p=  1.01.0   ; ps
compressibility  =  4.5e-5 4.5e-5; 1/bar (water: 1 atm, 300 K)
ref_p=  1.01.0   ; bar

; Generate velocites in the beginning
gen_vel  =  yes
gen_temp =  296.0
gen_seed =  173529

;WALLS
; Number of walls, type, atom types, densities and box-z scale factor 
for Ewald

nwall= 2
wall_type= 9-3
wall_r_linpot= -1
wall_atomtype=
wall_density =
wall_ewald_zfac  = 3

Thanks a lot in advance.
Regards,
Anirban




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--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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] mdp file for local pressure

[Cheong Wee Loong, Daniel]

Is there a local pressure version of Gromacs 4?  I can only find Gromacs 
version 3.02 with local pressure.  If there is, could you tell me where to get 
it?  Thanks.



Daniel



From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On 
Behalf Of anirban polley
Sent: Monday, May 18, 2009 7:39 PM
To: gmx-users@gromacs.org
Subject: [gmx-users] mdp file for local pressure


---
Program grompp_mpi, VERSION 4.0.2_localpressure
Source code file: readir.c, line: 454

Fatal error:
Expected 2 elements for wall_atomtype, found 0
---

Could you please tell me where my fault is?
Thanks a lot in advance.
Anirban


This email is confidential and may be privileged. If you are not the intended 
recipient, please delete it and notify us immediately. Please do not copy or 
use it for any purpose, or disclose its contents to any other person. Thank you.
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RE: [gmx-users] mdp file for local pressure

[Dallas B. Warren]

The error message explicitly tells you what is wrong:

"Expected 2 elements for wall_atomtype, found 0"

And looking in your .mdp file ...

;WALLS
; Number of walls, type, atom types, densities and box-z scale factor
for Ewald
nwall= 2
wall_type= 9-3
wall_r_linpot= -1
wall_atomtype=
wall_density =
wall_ewald_zfac  = 3

On the wall_atomtype line, you have defined zero elements and you should
have two.

Catch ya,

Dr. Dallas Warren
Department of Pharmaceutical Biology and Pharmacology
Pharmacy and Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.war...@pharm.monash.edu.au
+61 3 9903 9167
-
When the only tool you own is a hammer, every problem begins to resemble
a nail.
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RE: [gmx-users] .mdp file for polymer

[Berk Hess]

Hi,

You should be much more precise in describing your problems.
gmxdump does not seem to give a segv at all.
Also you did not mail me your Gromacs version.

mdrun immediately gives a warning:
Warning: 1-4 interaction between 1 and 28 at distance 0.982 which is larger 
than the 1-4 table size 0.500 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

You seem to have reduced the table size from the default 1.0 to 0.5.
But if interactions are beyond the table size, you need to increase the table.

Also your cut-off's are 0.1 nm, which is much smaller than the size of your 
atoms.
This simulation setup is complete nonsens.
You can never expect a system to run propely with these kind of settings.

Berk

Date: Mon, 16 Feb 2009 12:57:50 +0400
From: varsha.gautha...@gmail.com
To: gmx-users@gromacs.org
Subject: [gmx-users] .mdp file for polymer

Hello sir,

On giving gmxdump its giving me an error saying "segmentation fault.My box size 
 is 6x6X6.Am trying to run it it vaccum for 250 ps wit 5 timesteps and with 
columb type=PME. I read from mailing list that PME calculations requires large 
amount of memory space.Is this an issue with dimension of box or with the 
system memory allocation ?Here's my log file.


T-Coupling  : 106  (total 106 atoms)
Energy Mon. : 106  (total 106 atoms)
Acceleration: 106  (total 106 atoms)
Freeze  : 106  (total 106 atoms)
User1   : 106  (total 106 atoms)

User2   : 106  (total 106 atoms)
VCM : 106  (total 106 atoms)
XTC : 106  (total 106 atoms)
Or. Res. Fit: 106  (total 106 atoms)
QMMM: 106  (total 106 atoms)
ben-nch0.xtc frame 0:

   natoms= 1  step= 0  time=-2.9120485e-05  prec=2.8026e-45
   box (3x3):
  box[0]={-2.89059e-05,  3.98821e-34, -2.39380e-05}
  box[1]={ 3.98770e-34,  1.40130e-45, -2.91168e-05}

  box[2]={-1.96789e+00, -2.91207e-05, -1.96789e+00}
   x (1x3):
Segmentation fault
  



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RE: [gmx-users] .mdp file for polymer

[Berk Hess]

Hi,

Independent of any other problems you might have, gmxdump should never give a 
segmentation fault.

Could you mail me the tpr file?
Which version of Gromacs are you using?

Berk

Date: Mon, 16 Feb 2009 12:57:50 +0400
From: varsha.gautha...@gmail.com
To: gmx-users@gromacs.org
Subject: [gmx-users] .mdp file for polymer

Hello sir,

On giving gmxdump its giving me an error saying "segmentation fault.My box size 
 is 6x6X6.Am trying to run it it vaccum for 250 ps wit 5 timesteps and with 
columb type=PME. I read from mailing list that PME calculations requires large 
amount of memory space.Is this an issue with dimension of box or with the 
system memory allocation ?Here's my log file.


T-Coupling  : 106  (total 106 atoms)
Energy Mon. : 106  (total 106 atoms)
Acceleration: 106  (total 106 atoms)
Freeze  : 106  (total 106 atoms)
User1   : 106  (total 106 atoms)

User2   : 106  (total 106 atoms)
VCM : 106  (total 106 atoms)
XTC : 106  (total 106 atoms)
Or. Res. Fit: 106  (total 106 atoms)
QMMM: 106  (total 106 atoms)
ben-nch0.xtc frame 0:

   natoms= 1  step= 0  time=-2.9120485e-05  prec=2.8026e-45
   box (3x3):
  box[0]={-2.89059e-05,  3.98821e-34, -2.39380e-05}
  box[1]={ 3.98770e-34,  1.40130e-45, -2.91168e-05}

  box[2]={-1.96789e+00, -2.91207e-05, -1.96789e+00}
   x (1x3):
Segmentation fault
  



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Re: [gmx-users] .mdp file for polymer

[Mark Abraham]

varsha gautham wrote:

Hello sir,

On giving gmxdump its giving me an error saying "segmentation fault.


99.9% of the time there is more information available. Check your 
stdout, stderr and the .log file.


My 
box size is 6x6X6.Am trying to run it it vaccum for 250 ps wit 5 
timesteps and with columb type=PME. I read from mailing list that PME 
calculations requires large amount of memory space.Is this an issue with 
dimension of box or with the system memory allocation ?Here's my log file.


You don't need/want PME for a system with only 106 atoms. A vacuum 
simulation also isn't likely to tell you anything useful.



T-Coupling  : 106  (total 106 atoms)
Energy Mon. : 106  (total 106 atoms)
Acceleration: 106  (total 106 atoms)
Freeze  : 106  (total 106 atoms)
User1   : 106  (total 106 atoms)
User2   : 106  (total 106 atoms)
VCM : 106  (total 106 atoms)
XTC : 106  (total 106 atoms)
Or. Res. Fit: 106  (total 106 atoms)
QMMM: 106  (total 106 atoms)
ben-nch0.xtc frame 0:
   natoms= 1  step= 0  time=-2.9120485e-05  prec=2.8026e-45
   box (3x3):
  box[0]={-2.89059e-05,  3.98821e-34, -2.39380e-05}
  box[1]={ 3.98770e-34,  1.40130e-45, -2.91168e-05}
  box[2]={-1.96789e+00, -2.91207e-05, -1.96789e+00}
   x (1x3):
Segmentation fault
 






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Re: [gmx-users] .mdp file for polymer

[Mark Abraham]

varsha gautham wrote:

hello sir,

I made nstvout  and nstfout   parameters to zero and frequency to update 
position coordinates alone (nstxout) to 1000.But still am getting only 
one frame when viewed the trajectory in VMD.


Just like some other trajectory formats, you do have to open a structure 
file and then import the trajectory...


It is an NVT ensemble.How 
can i get more than one frame?I  think the timestep and nsteps i have 
given is right only.Please help me out in this issue.


So what does gmxcheck or gmxdump tell you about your trajectories?

Mark
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RE: [gmx-users] .mdp file

[Kukol, Andreas]

You have to modify the input .mdp and run grompp again. The mdout.mdp is for 
information only.

Andreas

> -Original Message-
> From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED]
> On Behalf Of Andrea Muntean
> Sent: 10 November 2008 12:42
> To: Gromacs Users' List
> Subject: [gmx-users] .mdp file
>
> Hello there,
>
> I have a practical question regarding the mdp file, regardless the
> system to simulate. Before I would run a md simulation, usually we
> have to run grompp in order to preprocess the system. So I obtain,
> among other files, the mdout.mdp, based on the input mdp file. My
> question:
>
> If I want to run another simulation, with the same input, only with
> small changes in the mdp file (like number of steps or so), do I have
> to each time modify the input .mdp and run grompp, or is it enough if
> I modify mdout.mdp?
>
> Best regards,
> Andrea
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Re: [gmx-users] .mdp file

[Andrea Muntean]

I thought so. Thank you very much!

Cheers
Andrea

2008/11/10 Justin A. Lemkul <[EMAIL PROTECTED]>:
>
>
> Andrea Muntean wrote:
>>
>> Hello there,
>>
>> I have a practical question regarding the mdp file, regardless the
>> system to simulate. Before I would run a md simulation, usually we
>> have to run grompp in order to preprocess the system. So I obtain,
>> among other files, the mdout.mdp, based on the input mdp file. My
>> question:
>>
>> If I want to run another simulation, with the same input, only with
>> small changes in the mdp file (like number of steps or so), do I have
>> to each time modify the input .mdp and run grompp, or is it enough if
>> I modify mdout.mdp?
>
> No.  The mdout.mdp file is output, a record of all the simulation
> parameters, including the ones you accepted as defaults by not explicitly
> entering into your grompp.mdp file (the input).  If you want to run
> different simulations, you need  to modify your input, or else these new
> parameters will never reach the .tpr file and you will be running the same
> thing over and over again.
>
> -Justin
>
>>
>> Best regards,
>> Andrea
>> ___
>> gmx-users mailing listgmx-users@gromacs.org
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>>
>
> --
> 
>
> Justin A. Lemkul
> Graduate Research Assistant
> 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] .mdp file

[Justin A. Lemkul]

Andrea Muntean wrote:

Hello there,

I have a practical question regarding the mdp file, regardless the
system to simulate. Before I would run a md simulation, usually we
have to run grompp in order to preprocess the system. So I obtain,
among other files, the mdout.mdp, based on the input mdp file. My
question:

If I want to run another simulation, with the same input, only with
small changes in the mdp file (like number of steps or so), do I have
to each time modify the input .mdp and run grompp, or is it enough if
I modify mdout.mdp?


No.  The mdout.mdp file is output, a record of all the simulation parameters, 
including the ones you accepted as defaults by not explicitly entering into your 
grompp.mdp file (the input).  If you want to run different simulations, you need 
 to modify your input, or else these new parameters will never reach the .tpr 
file and you will be running the same thing over and over again.


-Justin



Best regards,
Andrea
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--


Justin A. Lemkul
Graduate Research Assistant
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] mdp file

[Mark Abraham]

He, Yang wrote:

Hi Mark,

This is what I got when I use the command gmxcheck:

Checking file traj.trr
trn version: GMX_trn_file (single precision)
Reading frame   0 time0.000
# Atoms  34
Last frame  1 time0.100


Item#frames Timestep (ps)
Step 20.1
Time 20.1
Lambda   20.1
Coords   20.1
Velocities   20.1
Forces   0
Box  20.1

Also, I have tried to increase  the value of nsteps to 1, but no change 
happened still just the static figure.

I really got stuck about that.

Hope to get your further suggestions,


I think what I said last time covers it pretty well. You're crashing and 
I gave you a link to somewhere with some explanations and ideas. Fix that.


Mark
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RE: [gmx-users] mdp file

[He, Yang]

Hi Mark,

This is what I got when I use the command gmxcheck:

Checking file traj.trr
trn version: GMX_trn_file (single precision)
Reading frame   0 time0.000
# Atoms  34
Last frame  1 time0.100


Item#frames Timestep (ps)
Step 20.1
Time 20.1
Lambda   20.1
Coords   20.1
Velocities   20.1
Forces   0
Box  20.1

Also, I have tried to increase  the value of nsteps to 1, but no change 
happened still just the static figure.

I really got stuck about that.

Hope to get your further suggestions,

Thank you .

Yang



From: [EMAIL PROTECTED] [EMAIL PROTECTED] On Behalf Of Mark Abraham [EMAIL 
PROTECTED]
Sent: Thursday, November 06, 2008 3:52 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] mdp file

He, Yang wrote:
> Hi all users,
>
> When I use the command "mdrun -tablep table.xvg " to run my model in gromacs, 
>  it always shows that:
>
> starting mdrun 'DNA in water'
> 1 steps, 20.0 ps.

This is orders of magnitude too short to expect a large conformational
change to happen. Think nanoseconds at least. Depending on the number of
base pairs, think much more than that. You should be aware of how long
this might take, since you've read some literature about MD on DNA, right?

> Warning: 1-4 interaction between 11 and 19 at distance 1.437 which is larger 
> than the 1-4 table size 1.000 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

Don't ignore warnings unless you know what they mean and it's OK. See
http://wiki.gromacs.org/index.php/Errors#1-4_interaction_not_within_cut-off

> And no more information . Furthermore, I use the command ngmx to look at the 
> trajectory , I found that  only when I set the value of nsteps by 10,  will 
> there be little animation about my DNA two strands' disassociation . While I 
> try to reduce the value of dt , nstdisreout , nstorireout and nstdihreout , 
> it also did not work and I can not see any disassociation of DNA strands  
> using the command "ngmx".

Probably, you only wrote one frame before it crashed. Does the log file
look like it terminated normally after 1 steps? Use gmxcheck to see
how many frames you have in the trajectory file.

> Also, what I got confused is that when I set the value of nsteps larger than 
> 10, there is just static figure about DNA model.  This is my part of mdp file

1) You need the simulation not to crash
2) You need to simulate for long enough (nsteps) to see a change
3) You need to write output (nstxout or nstxtcout) sufficiently often to
keep yourself happy.

Mark
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Re: [gmx-users] mdp file

[Mark Abraham]

He, Yang wrote:

Hi all users,

When I use the command "mdrun -tablep table.xvg " to run my model in gromacs,  
it always shows that:

starting mdrun 'DNA in water'
1 steps, 20.0 ps.


This is orders of magnitude too short to expect a large conformational 
change to happen. Think nanoseconds at least. Depending on the number of 
base pairs, think much more than that. You should be aware of how long 
this might take, since you've read some literature about MD on DNA, right?



Warning: 1-4 interaction between 11 and 19 at distance 1.437 which is larger 
than the 1-4 table size 1.000 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


Don't ignore warnings unless you know what they mean and it's OK. See 
http://wiki.gromacs.org/index.php/Errors#1-4_interaction_not_within_cut-off



And no more information . Furthermore, I use the command ngmx to look at the trajectory , 
I found that  only when I set the value of nsteps by 10,  will there be little animation 
about my DNA two strands' disassociation . While I try to reduce the value of dt , 
nstdisreout , nstorireout and nstdihreout , it also did not work and I can not see any 
disassociation of DNA strands  using the command "ngmx".


Probably, you only wrote one frame before it crashed. Does the log file 
look like it terminated normally after 1 steps? Use gmxcheck to see 
how many frames you have in the trajectory file.



Also, what I got confused is that when I set the value of nsteps larger than 
10, there is just static figure about DNA model.  This is my part of mdp file


1) You need the simulation not to crash
2) You need to simulate for long enough (nsteps) to see a change
3) You need to write output (nstxout or nstxtcout) sufficiently often to 
keep yourself happy.


Mark
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Re: [gmx-users] mdp file help

[Mark Abraham]

Probably, you've broken your line endings transferring to/from a Windows 
machine.


Mark
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Re: [gmx-users] mdp file help

[james zhang]

You can get a typical mdp file from some tutorials.
By the way, I think the topology is wrong.
Thanks.


On 7/18/07, Christopher Stiles <[EMAIL PROTECTED]> wrote:


 I am trying to simulate a single wall CNT in a box filled with water for
about 500 ps and 300K just to start and I am having trouble with the mdp
file, basicly what should and should not be in it. I just want it generic to
start and tune it up later. Here is what I have done so far along with links
to copys of the files I have used:




*



Must have the following files in the working directory to start:

SWNT_6_6_144.pdb

Can find a copy at: http://cs86.com/CNSE/SWNT_6_6_144.pdb



ffgmx.n2t

 must change this files name to ffG43b1.n2t and add the following 2
lines:

C   C   1   C   ; CNT Carbon with
one bond

C   C   2   C   C   ; CNT double
bonded Carbon



ffgmxbon.itp

add the following line to it:

CC1   0.14210 478900.





*** you can find copies of both of these files at the following location:

/usr/local/gromacs/share/gromacs/top/



x2top -f SWNT_6_6_144.pdb -o SWNT_6_6_144.top -r SWNT_6_6_144.rtp

Note: for some reason it does not generate SWNT_6_6_144.rtp*



editconf -f SWNT_6_6_144.gro -o SWNT_6_6_144.gro  -d 0.5



genbox -cp SWNT_6_6_144.gro  -cs -o SWNT_6_6_144_b4em.gro -p
SWNT_6_6_144.top -maxsol 300

* *

grompp -f em3.mdp -r SWNT_6_6_144_b4em.gro -p SWNT_6_6_144.top -o -maxwarn
310




***



 em3.mdp###  Can find a copy at: http://cs86.com/CNSE/em3.mdp



title= SWNT_6_6_144

cpp  = cpp

include  = /usr/local/gromacs/share/gromacs/top/

define   = -DFLEX_SPC

integrator   = md

dt   = 0.002

nsteps   = 50

nstxout  = 5000

nstvout  = 5000

nstlog   = 5000

nstenergy= 250

nstxtcout= 250

xtc_grps = Protein

energygrps   = Protein  SOL

nstlist  = 10

ns_type  = grid

rlist= 0.8

coulombtype  = cut-off

rcoulomb = 1.4

rvdw = 0.8

tcoupl   = Berendsen

tc-grps  = Protein  SOL

tau_t= 0.1  0.1

ref_t= 300  300

Pcoupl   = Berendsen

tau_p= 1.0

compressibility  = 4.5e-5

ref_p= 1.0

gen_vel  = yes

gen_temp = 300

gen_seed = 173529

constraints  = all-bonds



**



This is what I get after running grommp:







-bash-3.00$ grompp -f em3.mdp -r SWNT_6_6_144_b4em.gro -p SWNT_6_6_144.top
-o -maxwarn 310

 :-)  G  R  O  M  A  C  S  (-:

.

.

.



  -[no]renum   boolyes  Renumber atomtypes and minimize number of

atomtypes



creating statusfile for 1 node...

' for variable integrator, using 'md'

Next time use one of: 'md' 'steep' 'cg' 'bd' 'sd' 'nm' 'l-bfgs' 'tpi'

' for variable ns-type, using 'Grid'

Next time use one of: 'Grid' 'Simple'

' for variable coulombtype, using 'Cut-off'

Next time use one of: 'Cut-off' 'Reaction-Field'
'Generalized-Reaction-Field' 'PME' 'Ewald' 'PPPM' 'Poisson' 'Switch' 'Shift'
'User' 'Generalized-Born' 'Reaction-Field-nec' 'Encad-shift' 'PME-User'

' for variable tcoupl, using 'No'

Next time use one of: 'No' 'Berendsen' 'Nose-Hoover' 'yes' 'Andersen'
'Andersen-interval'

' for variable Pcoupl, using 'No'

Next time use one of: 'No' 'Berendsen' 'Parrinello-Rahman' 'Isotropic'

' for variable gen-vel, using 'no'

Next time use one of: 'no' 'yes'

' for variable constraints, using 'none'

Next time use one of: 'none' 'h-bonds' 'all-bonds' 'h-angles' 'all-angles'



Back Off! I just backed up mdout.mdp to ./#mdout.mdp.15#

checking input for internal consistency...

...ling cpp

: command not found

cpp exit code: 32512

 SWNT_6_6_144.top > gromppOpff2m'cs/top -DFLEX_SPC

' command is defined in the .mdp file

processing topology...

processing coordinates...

---

Program grompp, VERSION 3.3.1

Source code file: futil.c, line: 340



File input/output error:

conf.gro

---



"This May Come As a Shock" (F. Black)






***





Any help or advice is greatly appreciated!



~Christopher Stiles

College of Nanoscale Science and Engineering (CNSE)

State University of New York, Albany, New Y