Re: [gmx-users] Umbrella_pull_simulation

[shahid nayeem]

Thanks. But Does that mean that I should look in pullf.xvg of each window
and see whether the value is converged or not. If not then I should extend
the simulation.
Shahid Nayeem

On Sat, Feb 25, 2012 at 12:05 AM, Justin A. Lemkul  wrote:

>
>
> shahid nayeem wrote:
>
>> My protein complex interface has a hydrophobic core and on each side of
>> this core at the edge are two hydrogen bonds. The Hydrogen bond on one side
>> is between Arg and Asp and another side it is between Arg and Glu. Its
>> experimental Kd is in nanomolar regions. How should I decide the length of
>> the simulation required in each window with this information.
>>
>
> As you would any other system.  Look for convergence of observables of
> interest.  Your PMF alone suggests insufficient sampling for these
> simulations, so as I've said several times, you probably need longer
> simulations to do so, but you can start by examining the physical
> properties of each window.  What you're looking for is up to you, based on
> your knowledge of the system at hand.
>
>
> -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] query reg.

[Mark Abraham]

On 28/02/2012 3:36 PM, Vishwambhar Bhandare wrote:

Hello,
Is it possible to analyse structure during running simulation?
Hw we can do that



Make a copy of the trajectory file and then do whatever you want.

Mark
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Re: [gmx-users] mdrun extension and concatenation

[Mark Abraham]

On 28/02/2012 3:50 PM, priya thiyagarajan wrote:

hello sir,

while performing simulation for 30ns, because of queue time limit my 
run terminated at 11.6ns.. then i extended my simulation using mdrun 
as you suggest..


while doing so i got error as

Fatal error:
Failed to lock: md20.log. Function not implemented.
For more information and tips for troubleshooting, please check the 
GROMACS

website at http://www.gromacs.org/Documentation/Errors


when i searched in mailing list i got one solution to this as

as a workaround you could run with -noappend and later
concatenate the output files. Then you should have no
problems with locking.


now when i tried using -noappend my simulation is working,.


is it correct??


Maybe. We can't know.



Also because my simulation is terminated because of queue limit i didnt get my 
gro file..

did i get my gro file at the end of simulation without any error?


I don't understand what you are asking. See 
http://www.gromacs.org/Documentation/How-tos/Extending_Simulation for 
general discussion of this topic.


Mark
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[gmx-users] mdrun extension and concatenation

[priya thiyagarajan]

hello sir,

while performing simulation for 30ns, because of queue time limit my run
terminated at 11.6ns.. then i extended my simulation using mdrun as you
suggest..

while doing so i got error as

Fatal error:
Failed to lock: md20.log. Function not implemented.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors


when i searched in mailing list i got one solution to this as

as a workaround you could run with -noappend and later
concatenate the output files. Then you should have no
problems with locking.

now when i tried using -noappend my simulation is working,.

is it correct??

Also because my simulation is terminated because of queue limit i
didnt get my gro file..

did i get my gro file at the end of simulation without any error?


please help me with your answer..

thanking you,
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[gmx-users] query reg.

[Vishwambhar Bhandare]

Hello,
Is it possible to analyse structure during running simulation?
Hw we can do that
Thanks and Regards,
--
Vishwambhar
Centre for Bioinformatics
Pondicherry University
Pondicherry
--

Note: Strictly confidential to Vishwayogi
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Re: [gmx-users] cutting a cylinder from simulation box

[Jianguo Li]

Maybe you can try "trjorder" to order the water molecules around your protein 
and make a group of those nearest water molecules and output them using trjconv
Jianguo




 From: Sanku M 
To: Discussion list for GROMACS users  
Sent: Tuesday, 28 February 2012, 7:49
Subject: [gmx-users] cutting a cylinder from simulation box
 

Hi,
  I have run a simulation of a fixed object in water using gromacs. Now, I want 
to analyze only water molecules which are present within a cylinder of certain 
radius (smaller than simulation box dimension in XY plane).
I wonder whether gromacs has any particular tool which can identify the 
particles within a cylindrical volume of a simulation box.
Thanks
Sanku
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Re: [gmx-users] cutting a cylinder from simulation box

[Mark Abraham]

On 28/02/2012 10:49 AM, Sanku M wrote:

Hi,
  I have run a simulation of a fixed object in water using gromacs. 
Now, I want to analyze only water molecules which are present within a 
cylinder of certain radius (smaller than simulation box dimension in 
XY plane).
I wonder whether gromacs has any particular tool which can identify 
the particles within a cylindrical volume of a simulation box.




g_select can make such a selection from a trajectory frame and write it 
to an index file, but the diffusion of the water over time will be a 
problem for a static selection. The kind of dynamic selection you would 
want is not yet available. You could make do by scripting g_select and 
some subsequent analysis tool inside a shell loop.


Mark
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[gmx-users] cutting a cylinder from simulation box

[Sanku M]

Hi,
  I have run a simulation of a fixed object in water using gromacs. Now, I want 
to analyze only water molecules which are present within a cylinder of certain 
radius (smaller than simulation box dimension in XY plane).
I wonder whether gromacs has any particular tool which can identify the 
particles within a cylindrical volume of a simulation box.
Thanks
Sanku-- 
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RE: [gmx-users] analysis pdb file

[Dallas Warren]

The trajectory file contains that information (.xtc or .trr).

You can do a couple of things here:
# load the trajectory using your viewer (be careful if the trajectory is large, 
you may want to change the number of frames it contains using trjconv)
# extract the coordination files (.gro or .pdb) from the trajectory file using 
trjconv for the appropriate times interested in.

Catch ya,

Dr. Dallas Warren
Medicinal Chemistry and Drug Action
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.war...@monash.edu
+61 3 9903 9304
-
When the only tool you own is a hammer, every problem begins to resemble a nail.

From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On 
Behalf Of Nathalia Garces
Sent: Tuesday, 28 February 2012 9:24 AM
To: gmx-users
Subject: [gmx-users] analysis pdb file

Good Day,
I ran a molecular dynamic simulation for over a month and I gathered the ".pdb" 
file containing the molecular structure at the end of the simulation. I can see 
the final configuration using a pdb viewer but I would like to know if it is 
possible (without redoing the simulation) to obtain previous configurations of 
the atoms.

Thank you for your help,

Nathalia
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[gmx-users] analysis pdb file

[Nathalia Garces]

Good Day,
I ran a molecular dynamic simulation for over a month and I gathered the
".pdb" file containing the molecular structure at the end of the
simulation. I can see the final configuration using a pdb viewer but I
would like to know if it is possible (without redoing the simulation) to
obtain previous configurations of the atoms.

Thank you for your help,

Nathalia
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Re: [gmx-users] Re: gmx-users Digest, Vol 94, Issue 159

[Justin A. Lemkul]

priya thiyagarajan wrote:


hello sir,

Thanks for your kind reply..

i tried like what you suggest..
i used the command

mdrun -s md60.tpr -cpi state.cpt -o md60.trr -x traj.xtc -e md60.edr -c 
md60.gro -g md60.log


to extend my simulation..
 
but again  i got error as follows



Reading file md60.tpr, VERSION 4.5.5 (single precision)
Starting 8 threads

Reading checkpoint file state.cpt generated: Fri Feb 17 19:46:58 2012



---
Program mdrun, VERSION 4.5.5
Source code file: checkpoint.c, line: 1757

Fatal error:
Failed to lock: md60.log. Function not implemented.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---



please help me with your answer...

i dono how to resolve this problem..



Use -noappend and just concatenate your output later.  Something in the 
filesystem thinks your .log file is still in use.


-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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[gmx-users] add new residue in OPLS-aa ff

[nana gomez]

  Dear Justin and All

 Right now, I am trying to add new residue in OPLS-aa ff

 when I make the following grompp -f file.mdp -c file.gro -p file.top -o file

 I have the following error
> 
> Program grompp, VERSION 4.5.2
> Source code file: toppush.c, line: 1071
> 
> Fatal error:
> Atoms in the .top are not numbered consecutively from 1 (rather,
> atomnr = -89390831, while at->nr = 0)
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors-
> 
 These are my files


 0- file forcefiel.itp
 [ defaults ]
 ; nbfunccomb-rule   gen-pairs   fudgeLJ fudgeQQ
 1   3   yes 0.5 0.5
 
 1- file.rtp

 ; Ion thiocyanate adiciionado
 [ SCN ]
 [ atoms ]
 SQ   opls_966-0.7501
 CQ   opls_967 0.4901
 NQ   opls_968-0.7401
 [ bonds ]

 CQ   SQ
 CQ   NQ


 2- file.atp

 opls_966   32.06000  ; SQ (SCN-)
 opls_967   12.01100  ; CQ (SCN-)
 opls_968   14.00670  ; NQ (SCN-)


 3- file ffbonded.itp

 [ bondtypes ]
 ; ij  func   b0  kb
 CQ SQ   10.16700   284082.0; JChemPhys_2008_118_154504
 CQ NQ   10.11900   122389e1   ; JChemPhys_2008_118_154504

 [ angletypes ]
 ;  ijk  func   th0   cth

 SQ   CQNQ   1180.000   652.802  ;JChemPhys_2008_118_154504

 4- file ffnonbonded.itp
 [ atomtypes ]
 ; full atom descriptions are available in ffoplsaa.atp
 ; name  bond_typemasscharge   ptype  sigma  epsilon
 opls_966   SQ1632.06000-0.750   A3.55000e-01  1.04600e+00
 opls_967   CQ 612.01100 0.490   A3.75000e-01  4.39320e-01
 opls_968   NQ 714.00670-0.740   A3.25000e-01  7.11280e-01


5. file minimization.mdp

 ; Minimization
 integrator  = steep
 emtol   = 1000.0
 emstep  = 0.01
 nsteps  = 5
 dt  = 0.01
 ns_type = grid
 pbc = xyz
 ;Electrostatic
 coulombtype = PME pme_order   = 4
 fourierspacing  = 0.12
 rcoulomb= 0.9
 rvdw= 0.9
 
 6. file .gro
 SCN THIOCYANATE ION
 3
 1SCN SQ1   1.720   1.647   1.785
 1SCN CQ2   1.640   1.651   1.631
 1SCN NQ3   1.590   1.653   1.534
 3.3   3.3   3.3

 7 file.top

 [ moleculetype ] ; Namenrexcl
 Ion 3

 [ atoms ]
 ;   nr   type  resnr residue  atom   cgnr charge   mass  typeB
ch
 argeB  massB
 ; residue   1 SCN rtp SCN  q -1.0
 1   opls_966  1SCN SQ  1  -0.75  32.06   ; qtot -0.
 75
 2   opls_967  1SCN CQ  1   0.49 12.011   ; qtot -0.
 26
 3   opls_968  1SCN NQ  1  -0.7414.0067   ; qtot -1

 [ bonds ]
 ;  aiaj functc0c1c2c3
 1 2 1
 2 3 1

 [ angles ]
 ;  aiajak functc0c1c2c3
 1 2 3 1
 ; Include topology for ions
 #include "./modif.ff/ions.itp"

 [ system ]
 ; Name
 SCN THIOCYANATE ION

 [ molecules ]
 ; Compound#mols
 Ion 1


 Thanks,

Ana GomezStudent
  
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[gmx-users] RE: add new residue in OPLS-aa ff

[nana gomez]

  Dear Justin and All

 Right now, I am trying to add new residue in OPLS-aa ff

 when I make the following grompp -f file.mdp -c file.gro -p file.top -o file

 I have the following error
> 
> Program grompp, VERSION 4.5.2
> Source code file: toppush.c, line: 1071
> 
> Fatal error:
> Atoms in the .top are not numbered consecutively from 1 (rather,
> atomnr = -89390831, while at->nr = 0)
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors-
> 
 These are my files


 0- file forcefiel.itp
 [ defaults ]
 ; nbfunccomb-rule   gen-pairs   fudgeLJ fudgeQQ
 1   3   yes 0.5 0.5
 
 1- file.rtp

 ; Ion thiocyanate adiciionado
 [ SCN ]
 [ atoms ]
 SQ   opls_966-0.7501
 CQ   opls_967 0.4901
 NQ   opls_968-0.7401
 [ bonds ]

 CQ   SQ
 CQ   NQ


 2- file.atp

 opls_966   32.06000  ; SQ (SCN-)
 opls_967   12.01100  ; CQ (SCN-)
 opls_968   14.00670  ; NQ (SCN-)


 3- file ffbonded.itp

 [ bondtypes ]
 ; ij  func   b0  kb
 CQ SQ   10.16700   284082.0; JChemPhys_2008_118_154504
 CQ NQ   10.11900   122389e1   ; JChemPhys_2008_118_154504

 [ angletypes ]
 ;  ijk  func   th0   cth

 SQ   CQNQ   1180.000   652.802  ;JChemPhys_2008_118_154504

 4- file ffnonbonded.itp
 [ atomtypes ]
 ; full atom descriptions are available in ffoplsaa.atp
 ; name  bond_typemasscharge   ptype  sigma  epsilon
 opls_966   SQ1632.06000-0.750   A3.55000e-01  1.04600e+00
 opls_967   CQ 612.01100 0.490   A3.75000e-01  4.39320e-01
 opls_968   NQ 714.00670-0.740   A3.25000e-01  7.11280e-01


5. file minimization.mdp

 ; Minimization
 integrator  = steep
 emtol   = 1000.0
 emstep  = 0.01
 nsteps  = 5
 dt  = 0.01
 ns_type = grid
 pbc = xyz
 ;Electrostatic
 coulombtype = PME pme_order   = 4
 fourierspacing  = 0.12
 rcoulomb= 0.9
 rvdw= 0.9
 
 6. file .gro
 SCN THIOCYANATE ION
 3
 1SCN SQ1   1.720   1.647   1.785
 1SCN CQ2   1.640   1.651   1.631
 1SCN NQ3   1.590   1.653   1.534
 3.3   3.3   3.3

 7 file.top

 [ moleculetype ] ; Namenrexcl
 Ion 3

 [ atoms ]
 ;   nr   type  resnr residue  atom   cgnr charge   mass  typeB
ch
 argeB  massB
 ; residue   1 SCN rtp SCN  q -1.0
 1   opls_966  1SCN SQ  1  -0.75  32.06   ; qtot -0.
 75
 2   opls_967  1SCN CQ  1   0.49 12.011   ; qtot -0.
 26
 3   opls_968  1SCN NQ  1  -0.7414.0067   ; qtot -1

 [ bonds ]
 ;  aiaj functc0c1c2c3
 1 2 1
 2 3 1

 [ angles ]
 ;  aiajak functc0c1c2c3
 1 2 3 1
 ; Include topology for ions
 #include "./modif.ff/ions.itp"

 [ system ]
 ; Name
 SCN THIOCYANATE ION

 [ molecules ]
 ; Compound#mols
 Ion 1


 Thanks,

Ana GomezStudent
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Re: [gmx-users] Positive Coul. recip. term

[Denny Frost]

The ionic liquid is bistriflate N-methyl-N-propyl pyrrolidinium and the
force field is from Lopes (CLaP).  I tried deleting all of the cation
dihedrals from the itp file and found that the run did not crash, although
it still had a positive coul recip term.  Upon examination of the cation
dihedrals I noticed that there was a typo in which a set of unbonded
carbons were put together in a dihedral term.  Perhaps this is what made
the previous runs crash.
Even with this correction, the coul. recip. term is still positive.  I have
tried smaller time steps and changing ewald_tol to 1e-3, but these have not
resolved this issue.  How can I calculate the error in the electrostatic
force?
Denny

On Sat, Feb 25, 2012 at 4:43 AM, Dommert Florian <
domm...@icp.uni-stuttgart.de> wrote:

> On Fri, 2012-02-24 at 11:03 -0700, Denny Frost wrote:
> > Thank you both for your replies.  I currently have another ionic
> > liquid running just fine on the same gromacs build (compiled the tpr
> > file yesterday), so I am reluctant to conclude that the problem is
> > with the linking.  Please let me know if you disagree.
> > The force field I am using was published in 2004 and has been
> > validated by another group.  I have double and triple checked my itp
> > files to make sure they match the force field, but it's possible there
> > are still some errors there.
>
> Is it the force field of Lopes (CLaP) et al. or Liu et al. (LHW) and who
> validated it, I am just curious, and what is the ionic liquid ?
>
> Though you are constraining the hbonds, I would be cautious with the
> time step of 2fs, because it might be, that the eigenfrequency of the
> anionic bonds requires a shorter time step, but this should not be the
> problem of a positive Coulomb energy. Have you calculated the error in
> the electrostatic force ? I would suggest to tune it to a limit of 1e-3,
> perhaps this resolves the problem of the positive Coulomb term.
>
> Perhaps some 1--4 and dihedral interactions are missing in the itp file,
> so assure if all of them are provided correctly.
>
> /Flo
>
> > I agree that this is very strange and feel that there must be
> > something fundamentally wrong in the mdp file or deeper.  I have
> > included my mdp file below.
> >
> >
> > title   =  PMP+TFN
> > cpp =  /lib/cpp
> > constraints =  hbonds
> > integrator  =  md
> > dt  =  0.002   ; ps !
> > nsteps  =  1000   ; total 20 ns
> > nstcomm =  10
> > nstxout =  5
> > nstvout =  5
> > nstfout =  0
> > nstlog  =  5000
> > nstenergy   =  5000
> > nstxtcout   =  25000
> > nstlist =  10
> > ns_type =  grid
> > pbc =  xyz
> > coulombtype =  PME
> > vdwtype =  Cut-off
> > rlist   =  1.2
> > rcoulomb=  1.2
> > rvdw=  1.2
> > fourierspacing  =  0.12
> > pme_order   =  4
> > ewald_rtol  =  1e-5
> > ; Berendsen temperature coupling is on in two groups
> > Tcoupl  =  v-rescale
> > tc_grps =  PMP   TFN
> > tau_t   =  0.2  0.2
> > ref_t   =  300  300
> > nsttcouple  =  1
> > ; Energy monitoring
> > energygrps  =  PMP   TFN
> > ; Isotropic pressure coupling is now on
> > Pcoupl  =  berendsen
> > pcoupltype  =  isotropic
> > tau_p   =  2.0
> > ref_p   =  1.0
> > compressibility =  4.5e-5
> >
> >
> > ; Generate velocites is on at 300 K.
> > gen_vel =  yes
> > gen_temp=  300.0
> > gen_seed=  -1
> >
> >
> >
> > On Fri, Feb 24, 2012 at 12:17 AM, Dommert Florian
> >  wrote:
> > On Thu, 2012-02-23 at 13:35 -0700, Denny Frost wrote:
> > > Dear all,
> > > I am trying to equilibrate a solvent of pure ionic liquid.
> >  The system
> > > keeps exploding (after 2-5 ns) and I am not sure why, though
> > I believe
> > > coulombic interactions are to blame.  This is because the
> > Coul-SR term
> > > is negative, but the Coul. recip term is very positive
> > throughout the
> > > entire run (giving the entire system a positive potential
> > energy).  I
> > > think this means that the short-range electrostatics are
> > okay, but the
> > > long range electrostatics (calculated with PME) are not.
> >  Does anybody
> > > have any suggestions as to why this would happen?  I have
> > used the
> > > exact same PME input parameters for another ionic liquid
> > that works
> > > just fine.  They are listed below.
> > >
> > >
> > > rcoulomb = 1.2
> > > fourierspacing = 0.12
> > > pme_order = 4
> > > ewald_rtol = 1e-5
> > >
> >
> >
> > Depends on the force field you are u

Re: [gmx-users] Re: Internal water in the membrane receptor

[Mark Abraham]

On 27/02/2012 8:35 PM, James Starlight wrote:

Mark,

I've found a possible sollution to restrict oxygens of my X-ray water 
by possible plasing the below string in the TOPOLOGY.top of my system


; Include X-ray water topology
#include "XW.itp"

; Include Position restraint file
#ifdef POSRES_XW
[ position_restraints ]
;  i funct   fcxfcyfcz
   11   1000   1000   1000
#endif

I havent recieved any errors from gromp. Does this aproach correct in 
general ?


Yes. There's only one heavy atom in a water, so that's all you need to 
restrain. You want it to have rotational freedom for EM, of course.




I dont know why but after minimisation constrained mollecules were 
diffused from the protein interious so POSRES have not worked :(


That's sterically impossible with or without position restraints. Either 
you're looking at the wrong before-and-after files, or the after file 
has some periodicity artefact in your viewing program. If you set 
nstxout = 1 then you can watch the EM process step by step.




My minim.mdp consist of two separate posres for water as well as for 
ligand groups ( there are no posre for protein).



define= -DPOSRES_LIG -DPOSRES_XW; position restrain the 
protein
integrator= steep; Algorithm (steep = steepest descent 
minimization)
emtol= 1000.0  ; Stop minimization when the maximum force 
< 1000.0 kJ/mol/nm

emstep  = 0.01  ; Energy step size
nsteps= 5  ; Maximum number of (minimization) 
steps to perform

energygrps = Protein CAR

What should I add to that file to activate posres?
Finally are the constraints algorithm needed here ?


James




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Re: [gmx-users] Re: Internal water in the membrane receptor

[James Starlight]

Mark,

I've found a possible sollution to restrict oxygens of my X-ray water by
possible plasing the below string in the TOPOLOGY.top of my system

; Include X-ray water topology
#include "XW.itp"

; Include Position restraint file
#ifdef POSRES_XW
[ position_restraints ]
;  i funct   fcxfcyfcz
   11   1000   1000   1000
#endif

I havent recieved any errors from gromp. Does this aproach correct in
general ?

I dont know why but after minimisation constrained mollecules were diffused
from the protein interious so POSRES have not worked :(

My minim.mdp consist of two separate posres for water as well as for ligand
groups ( there are no posre for protein).


define= -DPOSRES_LIG -DPOSRES_XW; position restrain the protein
integrator= steep; Algorithm (steep = steepest descent
minimization)
emtol= 1000.0  ; Stop minimization when the maximum force <
1000.0 kJ/mol/nm
emstep  = 0.01  ; Energy step size
nsteps= 5  ; Maximum number of (minimization) steps to
perform
energygrps = Protein CAR

What should I add to that file to activate posres?
Finally are the constraints algorithm needed here ?


James
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Re: [gmx-users] tau-p value

[Mark Abraham]

On 27/02/2012 6:35 PM, zhongjin wrote:

Dear GMX users,
 I find that tau_p value is very important to NTP simulation, when I 
use tau_p  = 1ps, the default value, the box change a lot, only when I 
use tau_p = 10 ps, it is OK.

; Pressure coupling
Pcoupl   = Parrinello-Rahman
Pcoupltype   = semiisotropic
nstpcouple   = -1
; Time constant (ps), compressibility (1/bar) and reference P (bar)
tau-p= 10
compressibility  = 0  4.5e-5
ref-p= 1.0 1.0
; Scaling of reference coordinates, No, All or COM
refcoord_scaling = No
; Random seed for Andersen thermostat
andersen_seed= 815131
So How to set up tau_p value, is 10 ps acceptable? My system cotain a 
CNT membrance in it.




Such values during equilibration are often different for those for 
production runs. You should not be using P-R during equilibration, as 
you will see in the relevant manual section.


Mark
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Re: [gmx-users] Re: Internal water in the membrane receptor

[Mark Abraham]

On 27/02/2012 5:03 PM, James Starlight wrote:

Justin,

2012/2/25 Justin A. Lemkul mailto:jalem...@vt.edu>>




You likely have a [settles] directive applied the the XW molecules
(crystal waters, yes?) and SOL.  You can't do that.  The block of
molecules to which [settles] are applied must be continuous.
 You'll have to replace the [settles] directive in XW with normal
constraints.


Yes, this works! Thanks alot.
I only wounder to know should I delete
[ exclusions ] from the itp of my X-ray water or not ? This directive 
is linked with the [settles] by the if expression so I've replaced it too.



Your numbering is wrong.  Numbering within a [position_restraints]
directive has nothing to do with the .gro file, and is based on
the numbering of the atoms in a [moleculetype].


It's clear now. As I understtod the  [moleculetype] of the restricted 
molecule must be in FIRST place in my topol.top


No. There's a numbering *within* a [moleculetype]. Your 
[position_restraints] must be numbers in that range. The contents of the 
.gro file are irrelevant to the correct interpretation of 
[position_restraints]. The contents of the .gro file matters only 
inasmuch as the ordering in your [molecules] section (and the [atoms] 
sections it references) must match it.


file but in that file the PROTEIN at first place instead. How I could 
make this changing in my multi-topology file ? I've tried to place


; Include X-ray water topology
#include "XW.itp"

; Include Position restraint for XW
#ifdef POSRES_XW
#include "posre_XW.itp"
#endif

at the begining of the topol.top file. But the error during grompt was 
the same about wrong atom order :(


You've shuffled the chapters in the book, but this doesn't help you find 
the 10th word in the chapter about the X-ray waters. (Yes, I realise my 
analogy is not perfect...)


Mark
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