Re: [gmx-users] NVT error

2017-08-14 Thread Justin Lemkul 


Please don't reply to the entire digest, and be sure to change the 
subject line.


On 8/14/17 9:51 AM, Faez Iqbal Khan wrote:

Dear Justin,

I talk to administrator
They said:

"Dear Faez,

I picked this up in your error file:

There is no domain decomposition for 105 ranks that is compatible with the
given box and a minimum cell size of 1.025 nm
Change the number of ranks or mdrun option -rcon or -dds or your LINCS
settings
Look in the log file for details on the domain decomposition"

Have you tried Googling this error?  People ask about it all the time.

The short answer is that you have to determine an appropriate number of 
ranks over which to parallelize your system.  You can't just arbitrarily 
parallelize over any number of ranks/cores.  Your system is much too 
small to use so many ranks.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

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Re: [gmx-users] NVT error

2017-08-13 Thread Justin Lemkul 



On 8/13/17 12:45 PM, Faez Iqbal Khan wrote:

Hi
I am running MD simulation of Pro-Lig complex using protocol provided by Justin 
Lemkul. 
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/06_equil.html 



I am getting error at NVT stage.

I am attaching my log files. Please suggest. Many many Thanks


I don't see any error message, it just looks like your run hung.  Talk to your 
system administrator about proper usage and/or compilation.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

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Re: [gmx-users] NVT error

2017-02-16 Thread Sotirios Dionysios I. Papadatos 
Sorry for being late and I hope you already found it yourself, but in any case 
here goes, in tc-grps you use one system HEM, while right below you enter 
params for two tau-t = 0.1(1) 0.2(2). Although I don't know what you want to 
simulate but in general you use: Protein(protein + ligands) non-Protein(SOL + 
ions)


From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
<gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Mehreen Jan 
<mehreen_jan1...@yahoo.com>
Sent: Friday, February 10, 2017 1:37:09 PM
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: [gmx-users] NVT error

VNT error:
5.0.7
ff 43A1
error:
Invalid T coupling input: 1 groups, 2 ref-t values and 2 tau-t values


 read from gromacs mail list "Precisely what it says. You specify one group to 
be coupled (System), but then
provide coupling information for two groups." i have no idea to correct my own 
NVT and NPT

title   = OPLS Lysozyme NVT equilibration
define  = -DPOSRES  ; position restrain the protein
; Run parameters
integrator  = md; leap-frog integrator
nsteps  = 5 ; 2 * 5 = 100 ps
dt  = 0.002 ;
; Output control
nstxout = 5000  ; save coordinates every 0.2 ps
nstvout = 5000  ; save velocities every 0.2 ps
nstenergy   = 5000  ; save energies every 0.2 ps
nstlog  = 1000  ; update log file every 0.2 ps
; Bond parameters
continuation= no; first dynamics run
constraint_algorithm = lincs; holonomic constraints
constraints = H-bonds   ; all bonds (even heavy atom-H bonds) 
constrained
lincs_iter  = 1 ; accuracy of LINCS
lincs_order = 4 ; also related to accuracy
; Neighborsearching
ns_type = grid  ; search neighboring grid cells
nstlist = 5 ; 10 fs
rlist   = 1.0   ; short-range neighborlist cutoff (in nm)
rcoulomb= 1.0   ; short-range electrostatic cutoff (in nm)
rvdw= 1.0   ; short-range van der Waals cutoff (in nm)
; Electrostatics
coulombtype = PME   ; Particle Mesh Ewald for long-range 
electrostatics
pme_order   = 4 ; cubic interpolation
fourierspacing  = 0.16  ; grid spacing for FFT
; Temperature coupling is on
tcoupl  = V-rescale ; modified Berendsen thermostat
tc-grps = HEM; two coupling groups - more accurate
tau_t   = 0.1   0.1 ; time constant, in ps
ref_t   = 300300 ; reference temperature, one for each group, 
in K
; Pressure coupling is off
pcoupl  = no ; no pressure coupling in NVT
; Periodic boundary conditions
pbc = xyz   ; 3-D PBC
; Dispersion correction
DispCorr= EnerPres  ; account for cut-off vdW scheme
; Velocity generation
gen_vel = yes   ; assign velocities from Maxwell distribution
gen_temp= 300   ; temperature for Maxwell distribution
gen_seed= -1; generate a random seed
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[gmx-users] NVT error

2017-02-10 Thread Mehreen Jan 
VNT error:
5.0.7
ff 43A1
error:
Invalid T coupling input: 1 groups, 2 ref-t values and 2 tau-t values


 read from gromacs mail list "Precisely what it says. You specify one group to 
be coupled (System), but then
provide coupling information for two groups." i have no idea to correct my own 
NVT and NPT

title   = OPLS Lysozyme NVT equilibration 
define  = -DPOSRES  ; position restrain the protein
; Run parameters
integrator  = md; leap-frog integrator
nsteps  = 5 ; 2 * 5 = 100 ps
dt  = 0.002 ;
; Output control
nstxout = 5000  ; save coordinates every 0.2 ps
nstvout = 5000  ; save velocities every 0.2 ps
nstenergy   = 5000  ; save energies every 0.2 ps
nstlog  = 1000  ; update log file every 0.2 ps
; Bond parameters
continuation= no; first dynamics run
constraint_algorithm = lincs; holonomic constraints 
constraints = H-bonds   ; all bonds (even heavy atom-H bonds) 
constrained
lincs_iter  = 1 ; accuracy of LINCS
lincs_order = 4 ; also related to accuracy
; Neighborsearching
ns_type = grid  ; search neighboring grid cells
nstlist = 5 ; 10 fs
rlist   = 1.0   ; short-range neighborlist cutoff (in nm)
rcoulomb= 1.0   ; short-range electrostatic cutoff (in nm)
rvdw= 1.0   ; short-range van der Waals cutoff (in nm)
; Electrostatics
coulombtype = PME   ; Particle Mesh Ewald for long-range 
electrostatics
pme_order   = 4 ; cubic interpolation
fourierspacing  = 0.16  ; grid spacing for FFT
; Temperature coupling is on
tcoupl  = V-rescale ; modified Berendsen thermostat
tc-grps = HEM   ; two coupling groups - more accurate
tau_t   = 0.1   0.1 ; time constant, in ps
ref_t   = 300   300 ; reference temperature, one for each group, in 
K
; Pressure coupling is off
pcoupl  = no; no pressure coupling in NVT
; Periodic boundary conditions
pbc = xyz   ; 3-D PBC
; Dispersion correction
DispCorr= EnerPres  ; account for cut-off vdW scheme
; Velocity generation
gen_vel = yes   ; assign velocities from Maxwell distribution
gen_temp= 300   ; temperature for Maxwell distribution
gen_seed= -1; generate a random seed
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Re: [gmx-users] nvt error

2015-11-02 Thread Justin Lemkul 



On 11/2/15 9:13 AM, Urszula Uciechowska wrote:



Hi,

During nvt simulations I obtained an error message:

---
Program mdrun_mpi, VERSION 5.0.6
Source code file:
/scratch/60488192.batch.grid.cyf-kr.edu.pl/gromacs-5.0.6/src/gromacs/mdlib/pme.c,
line: 754

Fatal error:
11 particles communicated to PME rank 3 are more than 2/3 times the
cut-off out of the domain decomposition cell of their charge
  group in dimension x.
This usually means that your system is not well equilibrated.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---

Error on rank 15, will try to stop all ranks
Halting parallel program mdrun_mpi on CPU 15 out of 32


---
Program mdrun_mpi, VERSION 5.0.6
Source code file:
/scratch/60488192.batch.grid.cyf-kr.edu.pl/gromacs-5.0.6/src/gromacs/mdlib/pme.c,
line: 754

Fatal error:
1 particles communicated to PME rank 4 are more than 2/3 times the cut-off
out of the domain decomposition cell of their charge
group in dimension x.
This usually means that your system is not well equilibrated.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---

Error on rank 19, will try to stop all ranks
Halting parallel program mdrun_mpi on CPU 19 out of 32



My nvt input file is:

; 7.3.2 Preprocessing
define  = -DPOSRES

; 7.3.3 Run Control
integrator  = md
tinit   = 0
dt  = 0.002
nsteps  = 10
comm_mode   = Linear
nstcalcenergy   = 1
comm_grps   = Protein Non-Protein

; 7.3.8 Output Control
nstxout = 25000
nstvout = 25000
nstfout = 25000
nstlog  = 100
nstenergy   = 100
nstxtcout   = 100
xtc_precision   = 1000
xtc_grps= System
energygrps  = System
cutoff-scheme   = verlet
; 7.3.9 Neighbor Searching
nstlist = 10
ns_type = grid
pbc = xyz
rlist   = 0.9

; 7.3.10 Electrostatics
coulombtype = PME
rcoulomb= 0.9

; 7.3.11 VdW
vdwtype = cut-off
rvdw= 0.9
DispCorr= EnerPres

; 7.3.13 Ewald
fourierspacing  = 0.12
pme_order   = 4
ewald_rtol  = 1e-5

; 7.3.14 Temperature Coupling
tcoupl  = V-rescale
tc_grps = ProteinNon-Protein
tau_t   = 0.10.1
ref_t   = 300300

; 7.3.17 Velocity Generation
gen_vel = yes
gen_temp= 310
gen_seed= -1

; 7.3.18 Bonds
constraints = all-bonds
constraint_algorithm= LINCS
continuation= no
lincs_order = 4
lincs_iter  = 1
lincs_warnangle = 30

What is wrong in the input file?



There is no reason for separate comm-grps for a simple protein system. 
Otherwise, 
http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System 
and the million or so other threads in the archive about dealing with instability.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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[gmx-users] nvt error

2014-08-10 Thread Prajisha Sujaya 
*im running protein-ligand complex using GROMOS96 43a1 force field*

*while performing nvt step im getting this error, i have used
protein-ligand tutorial nvt file to run the complex*

Ignoring obsolete mdp entry 'title'

Back Off! I just backed up mdout.mdp to ./#mdout.mdp.5#

WARNING 1 [file nvt.mdp, line 44]:
  Unknown left-hand 'cutoff-scheme' in parameter file



ERROR 1 [file nvt.mdp]:
  With coulombtype = PME, rcoulomb must be equal to rlist
  If you want optimal energy conservation or exact integration use
PME-Switch

Generated 279 of the 1225 non-bonded parameter combinations
Excluding 3 bonded neighbours molecule type 'Protein'
turning all bonds into constraints...
Excluding 3 bonded neighbours molecule type 'UNK'
turning all bonds into constraints...
Excluding 2 bonded neighbours molecule type 'SOL'
turning all bonds into constraints...
Excluding 1 bonded neighbours molecule type 'CL'
turning all bonds into constraints...

NOTE 1 [file topol.top, line 22744]:
  System has non-zero total charge: -9.98
  Total charge should normally be an integer. See
  http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
  for discussion on how close it should be to an integer.



Setting gen_seed to 13237
Velocities were taken from a Maxwell distribution at 300 K

There was 1 note

There was 1 warning

---
Program grompp, VERSION 4.5.5
Source code file: grompp.c, line: 1372

Fatal error:
There was 1 error in input file(s)
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---

Every Sperm is Sacred (Monty Python)

 Please help me to rectify this error
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Re: [gmx-users] nvt error

2014-08-10 Thread rama david 
Dear Prajisha,
 It seems that u dont have neutralized system.
paste your nvt.mdp file , as ur nvt file may have some problem  and
add -neutral command at the time of addition of ion ( genion ).
 And it will be better more if you paste your command so we can discuss
more.


With Best Wishes,
 Rama


On Sun, Aug 10, 2014 at 3:08 PM, Prajisha Sujaya prajishasuj...@gmail.com
wrote:

 *im running protein-ligand complex using GROMOS96 43a1 force field*

 *while performing nvt step im getting this error, i have used
 protein-ligand tutorial nvt file to run the complex*

 Ignoring obsolete mdp entry 'title'

 Back Off! I just backed up mdout.mdp to ./#mdout.mdp.5#

 WARNING 1 [file nvt.mdp, line 44]:
   Unknown left-hand 'cutoff-scheme' in parameter file



 ERROR 1 [file nvt.mdp]:
   With coulombtype = PME, rcoulomb must be equal to rlist
   If you want optimal energy conservation or exact integration use
 PME-Switch

 Generated 279 of the 1225 non-bonded parameter combinations
 Excluding 3 bonded neighbours molecule type 'Protein'
 turning all bonds into constraints...
 Excluding 3 bonded neighbours molecule type 'UNK'
 turning all bonds into constraints...
 Excluding 2 bonded neighbours molecule type 'SOL'
 turning all bonds into constraints...
 Excluding 1 bonded neighbours molecule type 'CL'
 turning all bonds into constraints...

 NOTE 1 [file topol.top, line 22744]:
   System has non-zero total charge: -9.98
   Total charge should normally be an integer. See
   http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
   for discussion on how close it should be to an integer.



 Setting gen_seed to 13237
 Velocities were taken from a Maxwell distribution at 300 K

 There was 1 note

 There was 1 warning

 ---
 Program grompp, VERSION 4.5.5
 Source code file: grompp.c, line: 1372

 Fatal error:
 There was 1 error in input file(s)
 For more information and tips for troubleshooting, please check the GROMACS
 website at http://www.gromacs.org/Documentation/Errors
 ---

 Every Sperm is Sacred (Monty Python)

  Please help me to rectify this error
 --
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Re: [gmx-users] nvt error

2014-08-10 Thread Justin Lemkul 



On 8/10/14, 5:38 AM, Prajisha Sujaya wrote:

*im running protein-ligand complex using GROMOS96 43a1 force field*

*while performing nvt step im getting this error, i have used
protein-ligand tutorial nvt file to run the complex*

Ignoring obsolete mdp entry 'title'

Back Off! I just backed up mdout.mdp to ./#mdout.mdp.5#

WARNING 1 [file nvt.mdp, line 44]:
   Unknown left-hand 'cutoff-scheme' in parameter file



This warning implies that your input settings are designed for version 4.6 or 
5.0, but you are using an older (pre-4.6) version.





ERROR 1 [file nvt.mdp]:
   With coulombtype = PME, rcoulomb must be equal to rlist
   If you want optimal energy conservation or exact integration use
PME-Switch



Self-explanatory.  Your input file is not sensible, and grompp is telling you 
what the problem is.



Generated 279 of the 1225 non-bonded parameter combinations
Excluding 3 bonded neighbours molecule type 'Protein'
turning all bonds into constraints...
Excluding 3 bonded neighbours molecule type 'UNK'
turning all bonds into constraints...
Excluding 2 bonded neighbours molecule type 'SOL'
turning all bonds into constraints...
Excluding 1 bonded neighbours molecule type 'CL'
turning all bonds into constraints...

NOTE 1 [file topol.top, line 22744]:
   System has non-zero total charge: -9.98
   Total charge should normally be an integer. See
   http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
   for discussion on how close it should be to an integer.



Typically systems are neutralized with counterions in this case.

-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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