[gmx-users] System Blowing up when more than one MPI thread is used

[Mayank Vats]

Hi,
I am trying to do a simple simulation in GROMCAS 2018.6, of a protein in
tip3p water with the amber99 forcefield. Its a 14nm cubic box with two
protein chains, and 87651 water molecules, 269525 atoms total. I am able to
energy minimise to an Fmax < 500, and then perform nvt and npt
equilibriation for 100ps each at 300K and 1 bar. I am facing issues in the
production run (dt=2fs, for 5ns).
A little bit about the hardware i'm using: My local workstation has 8 cpu
cores and 1 gpu. I'm also connecting to a Power9 system, where i have
access to 1 node with 160 cpu cores and 4 gpus. I have built the
gromacs version for the P9 system with GMX_OPENMP_MAX_THREADS=192, so it
can run using more than the default 64 threads.
I do not have a clear understanding of the way mpi, ranks etc work, which
is why I'm here.
Now the issue, with information from the log files:
On my *local workstation*, i run *gmx mdrun* and it uses 1 mpi thread, 8
openMP threads, and the one gpu available is assigned two gpu tasks:

Using 1 MPI thread
Using 8 OpenMP threads

1 GPU auto-selected for this run.
Mapping of GPU IDs to the 2 GPU tasks in the 1 rank on this node:
   PP:0,PME:0

This runs and completes successfully.
On the *P9 system*, where i have one node with the configuration mentioned
above, i have run *gmx_mpi mdrun* which uses 1 mpi thread, 160 openMP
threads and 1 gpu as follows:

Using 1 MPI thread
Using 160 OpenMP threads

1 GPU auto-selected for this run.
Mapping of GPU IDs to the 2 GPU tasks in the 1 rank on this node:
   PP:0,PME:0

This two completes successfully.
However, i wanted to be able to use all the available gpus for the
simulation on the *P9 system*, and tried *gmx mdrun* which gave this in the
log file:

Using 32 MPI threads
Using 5 OpenMP threads per tMPI thread

On host bgrs02 4 GPUs auto-selected for this run.
Mapping of GPU IDs to the 32 GPU tasks in the 32 ranks on this node:

PP:0,PP:0,PP:0,PP:0,PP:0,PP:0,PP:0,PP:0,PP:1,PP:1,PP:1,PP:1,PP:1,PP:1,PP:1,PP:1,PP:2,PP:2,PP:2,PP:2,PP:2,PP:2,PP:2,PP:2,PP:3,PP:3,PP:3,PP:3,PP:3,PP:3,PP:3,PP:3

This gives me warnings saying:
"One or more water molecules cannot be settled.
Check for bad contacts and/or reduce the timestep if appropriate."
"LINCS warnings.."
and finally exits with this:

Program: gmx mdrun, version 2018.6
Source file: src/gromacs/ewald/pme-redistribute.cpp (line 282)
MPI rank:12 (out of 32)

Fatal error:
891 particles communicated to PME rank 12 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.

I looked up the error on the documentation as suggested, and it says that
this an indication of the system blowing up. I don't understand how the
same input configuration completes production successfully when using one
MPI thread, but fails and gives a 'blowing up' message when using more MPI
threads.
Are there arguments that i should be using? Or should i build the P9
Gromacs in a different way? Or is it an artifact of my system itself, and
if so, any suggestions on what to change?
I can provide more information if needed. Any help will be appreciated.
Thanks,
Mayank
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Re: [gmx-users] system blowing up

[Justin Lemkul]

On 12/1/16 1:23 PM, abhisek Mondal wrote:

Hi,

I'm constantly getting a strange error of system blow up during
equilibration procedure. I'm relatively new to gromacs, please help me to
get my things straight.

I have a ligand bound protein structure in solvated condition.
So, I was using:
gmx mdrun -v -deffnm em #for minimization

Upon successful completion, I try to equilibrate using:
gmx mdrun -deffnm npt

But this command is failing with a lot of LINCS errors.
Surprising thing is that, I'm running the same code in 2 clusters
simultaneously. In one cluster it is running fine but in other cluster it
is giving me LINCS error.

Can you please suggest what actually is going wrong.



http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System

-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] system blowing up

[abhisek Mondal]

Hi,

I'm constantly getting a strange error of system blow up during
equilibration procedure. I'm relatively new to gromacs, please help me to
get my things straight.

I have a ligand bound protein structure in solvated condition.
So, I was using:
gmx mdrun -v -deffnm em #for minimization

Upon successful completion, I try to equilibrate using:
gmx mdrun -deffnm npt

But this command is failing with a lot of LINCS errors.
Surprising thing is that, I'm running the same code in 2 clusters
simultaneously. In one cluster it is running fine but in other cluster it
is giving me LINCS error.

Can you please suggest what actually is going wrong.





-- 
Abhisek Mondal

*Research Fellow*

*Structural Biology and Bioinformatics Division*
*CSIR-Indian Institute of Chemical Biology*

*Kolkata 700032*

*INDIA*
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Re: [gmx-users] System blowing up in final MD run

[Deep Bhattacharya]

Thank you Justin.

Sent from my iPhone

> On Jul 13, 2016, at 8:13 AM, Justin Lemkul  wrote:
> 
> 
> 
>> On 7/13/16 9:12 AM, Deep Bhattacharya wrote:
>> Sure. I will use the PME henceforth. Are the other parameters okay in the 
>> .mdp file?
> 
> I made several comments, embedded within the .mdp text.  Correct all of them 
> carefully.
> 
> -Justin
> 
>> 
>> 
>> Sent from my iPhone
>> 
>>> On Jul 13, 2016, at 8:09 AM, Justin Lemkul  wrote:
>>> 
>>> 
>>> 
 On 7/13/16 9:07 AM, Deep Bhattacharya wrote:
 Hello Justin,
 Is it appropriate to use Nose-Hoover thermostat with Parrinello rahman 
 thermostat in the .mdp file? In the previous mail I have reduced the time 
 step , will all there changes be appropriate for the simulation ?
>>> 
>>> It's fine as long as you have done a previous equilibration and are 
>>> appropriately continuing the run.  But you have big fundamental problems 
>>> with the .mdp file that I indicated below.  Be sure your settings are 
>>> logical, otherwise your thermostat and barostat choices are basically 
>>> irrelevant because the underlying physics computing the forces is junk.
>>> 
>>> -Justin
>>> 
 Sincerely,
 Deep
 Sent from my iPhone
 
> On Jul 13, 2016, at 8:01 AM, Justin Lemkul  wrote:
> 
> 
> 
>> On 7/13/16 8:56 AM, Deep Bhattacharya wrote:
>> Hello Tsjerk,
>> 
>> These are the notes that I got before running the NPT equilibration
>> 
>> 
>> NOTE 1 [file npt.mdp]:
>> leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 
>> 1
>> 
>> Generated 165 of the 1596 non-bonded parameter combinations
>> Excluding 3 bonded neighbours molecule type 'Protein_chain_A'
>> Excluding 3 bonded neighbours molecule type 'UNK'
>> Excluding 2 bonded neighbours molecule type 'SOL'
>> Excluding 1 bonded neighbours molecule type 'NA'
>> The center of mass of the position restraint coord's is  3.516  4.410  
>> 3.815
>> 
>> NOTE 2 [file topol.top]:
>> 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.
>> 
>> 
>> NOTE 3 [file topol.top]:
>> The bond in molecule-type Protein_chain_A between atoms 1 N and 2 H1 has
>> an estimated oscillational period of 1.0e-02 ps, which is less than 10
>> times the time step of 1.0e-03 ps.
>> Maybe you forgot to change the constraints mdp option.
>> 
>> Number of degrees of freedom in T-Coupling group Protein_UNK is 5339.83
>> Number of degrees of freedom in T-Coupling group Water_and_ions is 
>> 89787.17
>> 
>> NOTE 4 [file npt.mdp]:
>> You are using a plain Coulomb cut-off, which might produce artifacts.
>> You might want to consider using PME electrostatics.
> 
> Here's your biggest problem.  Plain cutoffs are wildly inaccurate and 
> haven't generally been used in about two decades.  Use something more 
> accurate like PME.
> 
>> I am using GROMOS53a6 forcefield. The system is a protein carbohydrate
>> solvent system. While observing the trajectory during the MD run, I found
>> that the system was blowing up.
>> Please help.
>> 
>> Sincerely,
>> Deep Bhattacharya
>> 
>> On Wed, Jul 13, 2016 at 12:37 PM, Tsjerk Wassenaar 
>> wrote:
>> 
>>> Hi Deep,
>>> 
>>> What force field? What system? How many cores? Did you try running on 
>>> one?
>>> What error? Did pdb2gmx or grompp give any warnings?
>>> 
>>> Cheers,
>>> 
>>> Tsjerk
>>> 
>>> On Wed, Jul 13, 2016 at 5:44 AM, Deep Bhattacharya <
>>> hypergenet...@gmail.com>
>>> wrote:
>>> 
 Hello,
 My system is blowing up for the protein carbohydrate solvent complex. I
 have attached the mdp file below. The NPT and NVT were in good 
 accordance
 to tutorial listed by Justin. 'Please help me solve the issue.
 title   = CD44  complex MD simulation
 ; Run parameters
 integrator  = md; leap-frog integrator
 nsteps  = 1000; 0.001 * 100 = 1 ps (10 ns)
 dt  = 0.001 ; 1 fs
 ; Output control
 nstxout = 5 ; suppress .trr output
 nstvout = 5 ; suppress .trr output
 nstenergy   = 5; save energies every 1000.0 ps
 nstlog  = 5  ; update log file every 1000.0 ps
 nstxtcout = 5
 xtc_precision = 1000
 energygrps  = Protein LIG SOL
 ; Bond parameters
 continua

Re: [gmx-users] System blowing up in final MD run

[Justin Lemkul]

On 7/13/16 9:12 AM, Deep Bhattacharya wrote:

Sure. I will use the PME henceforth. Are the other parameters okay in the .mdp 
file?



I made several comments, embedded within the .mdp text.  Correct all of them 
carefully.


-Justin




Sent from my iPhone


On Jul 13, 2016, at 8:09 AM, Justin Lemkul  wrote:




On 7/13/16 9:07 AM, Deep Bhattacharya wrote:
Hello Justin,
Is it appropriate to use Nose-Hoover thermostat with Parrinello rahman 
thermostat in the .mdp file? In the previous mail I have reduced the time step 
, will all there changes be appropriate for the simulation ?


It's fine as long as you have done a previous equilibration and are 
appropriately continuing the run.  But you have big fundamental problems with 
the .mdp file that I indicated below.  Be sure your settings are logical, 
otherwise your thermostat and barostat choices are basically irrelevant because 
the underlying physics computing the forces is junk.

-Justin


Sincerely,
Deep
Sent from my iPhone


On Jul 13, 2016, at 8:01 AM, Justin Lemkul  wrote:




On 7/13/16 8:56 AM, Deep Bhattacharya wrote:
Hello Tsjerk,

These are the notes that I got before running the NPT equilibration


NOTE 1 [file npt.mdp]:
leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1

Generated 165 of the 1596 non-bonded parameter combinations
Excluding 3 bonded neighbours molecule type 'Protein_chain_A'
Excluding 3 bonded neighbours molecule type 'UNK'
Excluding 2 bonded neighbours molecule type 'SOL'
Excluding 1 bonded neighbours molecule type 'NA'
The center of mass of the position restraint coord's is  3.516  4.410  3.815

NOTE 2 [file topol.top]:
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.


NOTE 3 [file topol.top]:
The bond in molecule-type Protein_chain_A between atoms 1 N and 2 H1 has
an estimated oscillational period of 1.0e-02 ps, which is less than 10
times the time step of 1.0e-03 ps.
Maybe you forgot to change the constraints mdp option.

Number of degrees of freedom in T-Coupling group Protein_UNK is 5339.83
Number of degrees of freedom in T-Coupling group Water_and_ions is 89787.17

NOTE 4 [file npt.mdp]:
You are using a plain Coulomb cut-off, which might produce artifacts.
You might want to consider using PME electrostatics.


Here's your biggest problem.  Plain cutoffs are wildly inaccurate and haven't 
generally been used in about two decades.  Use something more accurate like PME.


I am using GROMOS53a6 forcefield. The system is a protein carbohydrate
solvent system. While observing the trajectory during the MD run, I found
that the system was blowing up.
Please help.

Sincerely,
Deep Bhattacharya

On Wed, Jul 13, 2016 at 12:37 PM, Tsjerk Wassenaar 
wrote:


Hi Deep,

What force field? What system? How many cores? Did you try running on one?
What error? Did pdb2gmx or grompp give any warnings?

Cheers,

Tsjerk

On Wed, Jul 13, 2016 at 5:44 AM, Deep Bhattacharya <
hypergenet...@gmail.com>
wrote:


Hello,
My system is blowing up for the protein carbohydrate solvent complex. I
have attached the mdp file below. The NPT and NVT were in good accordance
to tutorial listed by Justin. 'Please help me solve the issue.
title   = CD44  complex MD simulation
; Run parameters
integrator  = md; leap-frog integrator
nsteps  = 1000; 0.001 * 100 = 1 ps (10 ns)
dt  = 0.001 ; 1 fs
; Output control
nstxout = 5 ; suppress .trr output
nstvout = 5 ; suppress .trr output
nstenergy   = 5; save energies every 1000.0 ps
nstlog  = 5  ; update log file every 1000.0 ps
nstxtcout = 5
xtc_precision = 1000
energygrps  = Protein LIG SOL
; Bond parameters
continuation= yes   ; first dynamics run
constraint_algorithm = lincs; holonomic constraints
constraints = all-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 = 1;


nstlist should not be set to 1.  That is only for energy minimization and you 
will be losing a huge amount of performance if you do this during MD.


rcoulomb= 0.81
rvdw= 0.81


These values are incorrect.  rvdw should be 1.4 for GROMOS force fields, and 
rcoulomb should be 0.8 (used in the original parametrized, with RF for 
electrostatics) or 0.9 (I've seen this more recently).  With PME, rcoulomb 
becomes a bit more flexible.


coulombtype = Cut-off   ; Particle Mesh Ewald for long-
vdwtyp

Re: [gmx-users] System blowing up in final MD run

[Deep Bhattacharya]

Sure. I will use the PME henceforth. Are the other parameters okay in the .mdp 
file?



Sent from my iPhone

> On Jul 13, 2016, at 8:09 AM, Justin Lemkul  wrote:
> 
> 
> 
>> On 7/13/16 9:07 AM, Deep Bhattacharya wrote:
>> Hello Justin,
>> Is it appropriate to use Nose-Hoover thermostat with Parrinello rahman 
>> thermostat in the .mdp file? In the previous mail I have reduced the time 
>> step , will all there changes be appropriate for the simulation ?
> 
> It's fine as long as you have done a previous equilibration and are 
> appropriately continuing the run.  But you have big fundamental problems with 
> the .mdp file that I indicated below.  Be sure your settings are logical, 
> otherwise your thermostat and barostat choices are basically irrelevant 
> because the underlying physics computing the forces is junk.
> 
> -Justin
> 
>> Sincerely,
>> Deep
>> Sent from my iPhone
>> 
>>> On Jul 13, 2016, at 8:01 AM, Justin Lemkul  wrote:
>>> 
>>> 
>>> 
 On 7/13/16 8:56 AM, Deep Bhattacharya wrote:
 Hello Tsjerk,
 
 These are the notes that I got before running the NPT equilibration
 
 
 NOTE 1 [file npt.mdp]:
 leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
 
 Generated 165 of the 1596 non-bonded parameter combinations
 Excluding 3 bonded neighbours molecule type 'Protein_chain_A'
 Excluding 3 bonded neighbours molecule type 'UNK'
 Excluding 2 bonded neighbours molecule type 'SOL'
 Excluding 1 bonded neighbours molecule type 'NA'
 The center of mass of the position restraint coord's is  3.516  4.410  
 3.815
 
 NOTE 2 [file topol.top]:
 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.
 
 
 NOTE 3 [file topol.top]:
 The bond in molecule-type Protein_chain_A between atoms 1 N and 2 H1 has
 an estimated oscillational period of 1.0e-02 ps, which is less than 10
 times the time step of 1.0e-03 ps.
 Maybe you forgot to change the constraints mdp option.
 
 Number of degrees of freedom in T-Coupling group Protein_UNK is 5339.83
 Number of degrees of freedom in T-Coupling group Water_and_ions is 89787.17
 
 NOTE 4 [file npt.mdp]:
 You are using a plain Coulomb cut-off, which might produce artifacts.
 You might want to consider using PME electrostatics.
>>> 
>>> Here's your biggest problem.  Plain cutoffs are wildly inaccurate and 
>>> haven't generally been used in about two decades.  Use something more 
>>> accurate like PME.
>>> 
 I am using GROMOS53a6 forcefield. The system is a protein carbohydrate
 solvent system. While observing the trajectory during the MD run, I found
 that the system was blowing up.
 Please help.
 
 Sincerely,
 Deep Bhattacharya
 
 On Wed, Jul 13, 2016 at 12:37 PM, Tsjerk Wassenaar 
 wrote:
 
> Hi Deep,
> 
> What force field? What system? How many cores? Did you try running on one?
> What error? Did pdb2gmx or grompp give any warnings?
> 
> Cheers,
> 
> Tsjerk
> 
> On Wed, Jul 13, 2016 at 5:44 AM, Deep Bhattacharya <
> hypergenet...@gmail.com>
> wrote:
> 
>> Hello,
>> My system is blowing up for the protein carbohydrate solvent complex. I
>> have attached the mdp file below. The NPT and NVT were in good accordance
>> to tutorial listed by Justin. 'Please help me solve the issue.
>> title   = CD44  complex MD simulation
>> ; Run parameters
>> integrator  = md; leap-frog integrator
>> nsteps  = 1000; 0.001 * 100 = 1 ps (10 ns)
>> dt  = 0.001 ; 1 fs
>> ; Output control
>> nstxout = 5 ; suppress .trr output
>> nstvout = 5 ; suppress .trr output
>> nstenergy   = 5; save energies every 1000.0 ps
>> nstlog  = 5  ; update log file every 1000.0 ps
>> nstxtcout = 5
>> xtc_precision = 1000
>> energygrps  = Protein LIG SOL
>> ; Bond parameters
>> continuation= yes   ; first dynamics run
>> constraint_algorithm = lincs; holonomic constraints
>> constraints = all-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 = 1;
>>> 
>>> nstlist should not be set to 1.  That is only for energy minimization and 
>>>

Re: [gmx-users] System blowing up in final MD run

[Justin Lemkul]

On 7/13/16 9:07 AM, Deep Bhattacharya wrote:

Hello Justin,
Is it appropriate to use Nose-Hoover thermostat with Parrinello rahman 
thermostat in the .mdp file? In the previous mail I have reduced the time step 
, will all there changes be appropriate for the simulation ?



It's fine as long as you have done a previous equilibration and are 
appropriately continuing the run.  But you have big fundamental problems with 
the .mdp file that I indicated below.  Be sure your settings are logical, 
otherwise your thermostat and barostat choices are basically irrelevant because 
the underlying physics computing the forces is junk.


-Justin


Sincerely,
Deep
Sent from my iPhone


On Jul 13, 2016, at 8:01 AM, Justin Lemkul  wrote:




On 7/13/16 8:56 AM, Deep Bhattacharya wrote:
Hello Tsjerk,

These are the notes that I got before running the NPT equilibration


NOTE 1 [file npt.mdp]:
 leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1

Generated 165 of the 1596 non-bonded parameter combinations
Excluding 3 bonded neighbours molecule type 'Protein_chain_A'
Excluding 3 bonded neighbours molecule type 'UNK'
Excluding 2 bonded neighbours molecule type 'SOL'
Excluding 1 bonded neighbours molecule type 'NA'
The center of mass of the position restraint coord's is  3.516  4.410  3.815

NOTE 2 [file topol.top]:
 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.


NOTE 3 [file topol.top]:
 The bond in molecule-type Protein_chain_A between atoms 1 N and 2 H1 has
 an estimated oscillational period of 1.0e-02 ps, which is less than 10
 times the time step of 1.0e-03 ps.
 Maybe you forgot to change the constraints mdp option.

Number of degrees of freedom in T-Coupling group Protein_UNK is 5339.83
Number of degrees of freedom in T-Coupling group Water_and_ions is 89787.17

NOTE 4 [file npt.mdp]:
 You are using a plain Coulomb cut-off, which might produce artifacts.
 You might want to consider using PME electrostatics.


Here's your biggest problem.  Plain cutoffs are wildly inaccurate and haven't 
generally been used in about two decades.  Use something more accurate like PME.


I am using GROMOS53a6 forcefield. The system is a protein carbohydrate
solvent system. While observing the trajectory during the MD run, I found
that the system was blowing up.
Please help.

Sincerely,
Deep Bhattacharya

On Wed, Jul 13, 2016 at 12:37 PM, Tsjerk Wassenaar 
wrote:


Hi Deep,

What force field? What system? How many cores? Did you try running on one?
What error? Did pdb2gmx or grompp give any warnings?

Cheers,

Tsjerk

On Wed, Jul 13, 2016 at 5:44 AM, Deep Bhattacharya <
hypergenet...@gmail.com>
wrote:


Hello,
My system is blowing up for the protein carbohydrate solvent complex. I
have attached the mdp file below. The NPT and NVT were in good accordance
to tutorial listed by Justin. 'Please help me solve the issue.
title   = CD44  complex MD simulation
; Run parameters
integrator  = md; leap-frog integrator
nsteps  = 1000; 0.001 * 100 = 1 ps (10 ns)
dt  = 0.001 ; 1 fs
; Output control
nstxout = 5 ; suppress .trr output
nstvout = 5 ; suppress .trr output
nstenergy   = 5; save energies every 1000.0 ps
nstlog  = 5  ; update log file every 1000.0 ps
nstxtcout = 5
xtc_precision = 1000
energygrps  = Protein LIG SOL
; Bond parameters
continuation= yes   ; first dynamics run
constraint_algorithm = lincs; holonomic constraints
constraints = all-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 = 1;


nstlist should not be set to 1.  That is only for energy minimization and you 
will be losing a huge amount of performance if you do this during MD.


rcoulomb= 0.81
rvdw= 0.81


These values are incorrect.  rvdw should be 1.4 for GROMOS force fields, and 
rcoulomb should be 0.8 (used in the original parametrized, with RF for 
electrostatics) or 0.9 (I've seen this more recently).  With PME, rcoulomb 
becomes a bit more flexible.


coulombtype = Cut-off   ; Particle Mesh Ewald for long-
vdwtype= cut-off
rlistlong  = 1.4
epsilon-rf = 61
rlist  = 0.8


As with rvdw, rlist should be 1.4.

-Justin


; Temperature coupling is on
tcoupl = nose-hoover; modified Berendsen thermostat
tc-grps   =Protein_LIG Water_and_ions   ; two coupling groups - more
accu

Re: [gmx-users] System blowing up in final MD run

[Deep Bhattacharya]

Hello Justin,
Is it appropriate to use Nose-Hoover thermostat with Parrinello rahman 
thermostat in the .mdp file? In the previous mail I have reduced the time step 
, will all there changes be appropriate for the simulation ?

Sincerely,
Deep
Sent from my iPhone

> On Jul 13, 2016, at 8:01 AM, Justin Lemkul  wrote:
> 
> 
> 
>> On 7/13/16 8:56 AM, Deep Bhattacharya wrote:
>> Hello Tsjerk,
>> 
>> These are the notes that I got before running the NPT equilibration
>> 
>> 
>> NOTE 1 [file npt.mdp]:
>>  leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
>> 
>> Generated 165 of the 1596 non-bonded parameter combinations
>> Excluding 3 bonded neighbours molecule type 'Protein_chain_A'
>> Excluding 3 bonded neighbours molecule type 'UNK'
>> Excluding 2 bonded neighbours molecule type 'SOL'
>> Excluding 1 bonded neighbours molecule type 'NA'
>> The center of mass of the position restraint coord's is  3.516  4.410  3.815
>> 
>> NOTE 2 [file topol.top]:
>>  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.
>> 
>> 
>> NOTE 3 [file topol.top]:
>>  The bond in molecule-type Protein_chain_A between atoms 1 N and 2 H1 has
>>  an estimated oscillational period of 1.0e-02 ps, which is less than 10
>>  times the time step of 1.0e-03 ps.
>>  Maybe you forgot to change the constraints mdp option.
>> 
>> Number of degrees of freedom in T-Coupling group Protein_UNK is 5339.83
>> Number of degrees of freedom in T-Coupling group Water_and_ions is 89787.17
>> 
>> NOTE 4 [file npt.mdp]:
>>  You are using a plain Coulomb cut-off, which might produce artifacts.
>>  You might want to consider using PME electrostatics.
> 
> Here's your biggest problem.  Plain cutoffs are wildly inaccurate and haven't 
> generally been used in about two decades.  Use something more accurate like 
> PME.
> 
>> I am using GROMOS53a6 forcefield. The system is a protein carbohydrate
>> solvent system. While observing the trajectory during the MD run, I found
>> that the system was blowing up.
>> Please help.
>> 
>> Sincerely,
>> Deep Bhattacharya
>> 
>> On Wed, Jul 13, 2016 at 12:37 PM, Tsjerk Wassenaar 
>> wrote:
>> 
>>> Hi Deep,
>>> 
>>> What force field? What system? How many cores? Did you try running on one?
>>> What error? Did pdb2gmx or grompp give any warnings?
>>> 
>>> Cheers,
>>> 
>>> Tsjerk
>>> 
>>> On Wed, Jul 13, 2016 at 5:44 AM, Deep Bhattacharya <
>>> hypergenet...@gmail.com>
>>> wrote:
>>> 
 Hello,
 My system is blowing up for the protein carbohydrate solvent complex. I
 have attached the mdp file below. The NPT and NVT were in good accordance
 to tutorial listed by Justin. 'Please help me solve the issue.
 title   = CD44  complex MD simulation
 ; Run parameters
 integrator  = md; leap-frog integrator
 nsteps  = 1000; 0.001 * 100 = 1 ps (10 ns)
 dt  = 0.001 ; 1 fs
 ; Output control
 nstxout = 5 ; suppress .trr output
 nstvout = 5 ; suppress .trr output
 nstenergy   = 5; save energies every 1000.0 ps
 nstlog  = 5  ; update log file every 1000.0 ps
 nstxtcout = 5
 xtc_precision = 1000
 energygrps  = Protein LIG SOL
 ; Bond parameters
 continuation= yes   ; first dynamics run
 constraint_algorithm = lincs; holonomic constraints
 constraints = all-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 = 1;
> 
> nstlist should not be set to 1.  That is only for energy minimization and you 
> will be losing a huge amount of performance if you do this during MD.
> 
 rcoulomb= 0.81
 rvdw= 0.81
> 
> These values are incorrect.  rvdw should be 1.4 for GROMOS force fields, and 
> rcoulomb should be 0.8 (used in the original parametrized, with RF for 
> electrostatics) or 0.9 (I've seen this more recently).  With PME, rcoulomb 
> becomes a bit more flexible.
> 
 coulombtype = Cut-off   ; Particle Mesh Ewald for long-
 vdwtype= cut-off
 rlistlong  = 1.4
 epsilon-rf = 61
 rlist  = 0.8
> 
> As with rvdw, rlist should be 1.4.
> 
> -Justin
> 
 ; Temperature coupling is on
 tcoupl = nose-hoover; modified Berendsen thermostat
 tc-grps   =Protein_LIG Water_and_ions   ; two coupling groups - more
 a

Re: [gmx-users] System blowing up in final MD run

[Deep Bhattacharya]

Sent from my iPhone

> On Jul 13, 2016, at 8:01 AM, Justin Lemkul  wrote:
> 
> 
> 
>> On 7/13/16 8:56 AM, Deep Bhattacharya wrote:
>> Hello Tsjerk,
>> 
>> These are the notes that I got before running the NPT equilibration
>> 
>> 
>> NOTE 1 [file npt.mdp]:
>>  leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
>> 
>> Generated 165 of the 1596 non-bonded parameter combinations
>> Excluding 3 bonded neighbours molecule type 'Protein_chain_A'
>> Excluding 3 bonded neighbours molecule type 'UNK'
>> Excluding 2 bonded neighbours molecule type 'SOL'
>> Excluding 1 bonded neighbours molecule type 'NA'
>> The center of mass of the position restraint coord's is  3.516  4.410  3.815
>> 
>> NOTE 2 [file topol.top]:
>>  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.
>> 
>> 
>> NOTE 3 [file topol.top]:
>>  The bond in molecule-type Protein_chain_A between atoms 1 N and 2 H1 has
>>  an estimated oscillational period of 1.0e-02 ps, which is less than 10
>>  times the time step of 1.0e-03 ps.
>>  Maybe you forgot to change the constraints mdp option.
>> 
>> Number of degrees of freedom in T-Coupling group Protein_UNK is 5339.83
>> Number of degrees of freedom in T-Coupling group Water_and_ions is 89787.17
>> 
>> NOTE 4 [file npt.mdp]:
>>  You are using a plain Coulomb cut-off, which might produce artifacts.
>>  You might want to consider using PME electrostatics.
> 
> Here's your biggest problem.  Plain cutoffs are wildly inaccurate and haven't 
> generally been used in about two decades.  Use something more accurate like 
> PME.
> 
>> I am using GROMOS53a6 forcefield. The system is a protein carbohydrate
>> solvent system. While observing the trajectory during the MD run, I found
>> that the system was blowing up.
>> Please help.
>> 
>> Sincerely,
>> Deep Bhattacharya
>> 
>> On Wed, Jul 13, 2016 at 12:37 PM, Tsjerk Wassenaar 
>> wrote:
>> 
>>> Hi Deep,
>>> 
>>> What force field? What system? How many cores? Did you try running on one?
>>> What error? Did pdb2gmx or grompp give any warnings?
>>> 
>>> Cheers,
>>> 
>>> Tsjerk
>>> 
>>> On Wed, Jul 13, 2016 at 5:44 AM, Deep Bhattacharya <
>>> hypergenet...@gmail.com>
>>> wrote:
>>> 
 Hello,
 My system is blowing up for the protein carbohydrate solvent complex. I
 have attached the mdp file below. The NPT and NVT were in good accordance
 to tutorial listed by Justin. 'Please help me solve the issue.
 title   = CD44  complex MD simulation
 ; Run parameters
 integrator  = md; leap-frog integrator
 nsteps  = 1000; 0.001 * 100 = 1 ps (10 ns)
 dt  = 0.001 ; 1 fs
 ; Output control
 nstxout = 5 ; suppress .trr output
 nstvout = 5 ; suppress .trr output
 nstenergy   = 5; save energies every 1000.0 ps
 nstlog  = 5  ; update log file every 1000.0 ps
 nstxtcout = 5
 xtc_precision = 1000
 energygrps  = Protein LIG SOL
 ; Bond parameters
 continuation= yes   ; first dynamics run
 constraint_algorithm = lincs; holonomic constraints
 constraints = all-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 = 1;
> 
> nstlist should not be set to 1.  That is only for energy minimization and you 
> will be losing a huge amount of performance if you do this during MD.
> 
 rcoulomb= 0.81
 rvdw= 0.81
> 
> These values are incorrect.  rvdw should be 1.4 for GROMOS force fields, and 
> rcoulomb should be 0.8 (used in the original parametrized, with RF for 
> electrostatics) or 0.9 (I've seen this more recently).  With PME, rcoulomb 
> becomes a bit more flexible.
> 
 coulombtype = Cut-off   ; Particle Mesh Ewald for long-
 vdwtype= cut-off
 rlistlong  = 1.4
 epsilon-rf = 61
 rlist  = 0.8
> 
> As with rvdw, rlist should be 1.4.
> 
> -Justin
> 
 ; Temperature coupling is on
 tcoupl = nose-hoover; modified Berendsen thermostat
 tc-grps   =Protein_LIG Water_and_ions   ; two coupling groups - more
 accurate
 tau_t = 2.0  2.0; time constant, in ps
 ref_t = 300  300; reference temperature, one for each group, in K
 ; Pressure coupling is on
 pcoupl= Parrinello-Rahman; Pressure coupling on

Re: [gmx-users] System blowing up in final MD run

[Justin Lemkul]

On 7/13/16 8:56 AM, Deep Bhattacharya wrote:

Hello Tsjerk,

These are the notes that I got before running the NPT equilibration


NOTE 1 [file npt.mdp]:
  leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1

Generated 165 of the 1596 non-bonded parameter combinations
Excluding 3 bonded neighbours molecule type 'Protein_chain_A'
Excluding 3 bonded neighbours molecule type 'UNK'
Excluding 2 bonded neighbours molecule type 'SOL'
Excluding 1 bonded neighbours molecule type 'NA'
The center of mass of the position restraint coord's is  3.516  4.410  3.815

NOTE 2 [file topol.top]:
  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.


NOTE 3 [file topol.top]:
  The bond in molecule-type Protein_chain_A between atoms 1 N and 2 H1 has
  an estimated oscillational period of 1.0e-02 ps, which is less than 10
  times the time step of 1.0e-03 ps.
  Maybe you forgot to change the constraints mdp option.

Number of degrees of freedom in T-Coupling group Protein_UNK is 5339.83
Number of degrees of freedom in T-Coupling group Water_and_ions is 89787.17

NOTE 4 [file npt.mdp]:
  You are using a plain Coulomb cut-off, which might produce artifacts.
  You might want to consider using PME electrostatics.



Here's your biggest problem.  Plain cutoffs are wildly inaccurate and haven't 
generally been used in about two decades.  Use something more accurate like PME.



I am using GROMOS53a6 forcefield. The system is a protein carbohydrate
solvent system. While observing the trajectory during the MD run, I found
that the system was blowing up.
Please help.

Sincerely,
Deep Bhattacharya

On Wed, Jul 13, 2016 at 12:37 PM, Tsjerk Wassenaar 
wrote:


Hi Deep,

What force field? What system? How many cores? Did you try running on one?
What error? Did pdb2gmx or grompp give any warnings?

Cheers,

Tsjerk

On Wed, Jul 13, 2016 at 5:44 AM, Deep Bhattacharya <
hypergenet...@gmail.com>
wrote:


Hello,
My system is blowing up for the protein carbohydrate solvent complex. I
have attached the mdp file below. The NPT and NVT were in good accordance
to tutorial listed by Justin. 'Please help me solve the issue.
title   = CD44  complex MD simulation
; Run parameters
integrator  = md; leap-frog integrator
nsteps  = 1000; 0.001 * 100 = 1 ps (10 ns)
dt  = 0.001 ; 1 fs
; Output control
nstxout = 5 ; suppress .trr output
nstvout = 5 ; suppress .trr output
nstenergy   = 5; save energies every 1000.0 ps
nstlog  = 5  ; update log file every 1000.0 ps
nstxtcout = 5
xtc_precision = 1000
energygrps  = Protein LIG SOL
; Bond parameters
continuation= yes   ; first dynamics run
constraint_algorithm = lincs; holonomic constraints
constraints = all-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 = 1;


nstlist should not be set to 1.  That is only for energy minimization and you 
will be losing a huge amount of performance if you do this during MD.



rcoulomb= 0.81
rvdw= 0.81


These values are incorrect.  rvdw should be 1.4 for GROMOS force fields, and 
rcoulomb should be 0.8 (used in the original parametrized, with RF for 
electrostatics) or 0.9 (I've seen this more recently).  With PME, rcoulomb 
becomes a bit more flexible.



coulombtype = Cut-off   ; Particle Mesh Ewald for long-
vdwtype= cut-off
rlistlong  = 1.4
epsilon-rf = 61
rlist  = 0.8


As with rvdw, rlist should be 1.4.

-Justin


; Temperature coupling is on
tcoupl = nose-hoover; modified Berendsen thermostat
tc-grps   =Protein_LIG Water_and_ions   ; two coupling groups - more
accurate
tau_t = 2.0  2.0; time constant, in ps
ref_t = 300  300; reference temperature, one for each group, in K
; Pressure coupling is on
pcoupl= Parrinello-Rahman; Pressure coupling on in

NPT

pcoupltype= isotropic; uniform scaling of box vectors
tau_p= 6.0; time constant, in ps
ref_p= 1.0; reference pressure, in bar
compressibility = 4.5e-5; isothermal compressibility of
water, bar^-1
refcoord_scaling= com
; Periodic boundary conditions
pbc = xyz   ; 3-D PBC
; Dispersion correction
DispCorr= EnerPres  ; account for cut-off vdW scheme
; Velocity generation
gen_vel = no;

Re: [gmx-users] System blowing up in final MD run

[Deep Bhattacharya]

Hello Tsjerk,

These are the notes that I got before running the NPT equilibration


NOTE 1 [file npt.mdp]:
  leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1

Generated 165 of the 1596 non-bonded parameter combinations
Excluding 3 bonded neighbours molecule type 'Protein_chain_A'
Excluding 3 bonded neighbours molecule type 'UNK'
Excluding 2 bonded neighbours molecule type 'SOL'
Excluding 1 bonded neighbours molecule type 'NA'
The center of mass of the position restraint coord's is  3.516  4.410  3.815

NOTE 2 [file topol.top]:
  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.


NOTE 3 [file topol.top]:
  The bond in molecule-type Protein_chain_A between atoms 1 N and 2 H1 has
  an estimated oscillational period of 1.0e-02 ps, which is less than 10
  times the time step of 1.0e-03 ps.
  Maybe you forgot to change the constraints mdp option.

Number of degrees of freedom in T-Coupling group Protein_UNK is 5339.83
Number of degrees of freedom in T-Coupling group Water_and_ions is 89787.17

NOTE 4 [file npt.mdp]:
  You are using a plain Coulomb cut-off, which might produce artifacts.
  You might want to consider using PME electrostatics.

I am using GROMOS53a6 forcefield. The system is a protein carbohydrate
solvent system. While observing the trajectory during the MD run, I found
that the system was blowing up.
Please help.

Sincerely,
Deep Bhattacharya

On Wed, Jul 13, 2016 at 12:37 PM, Tsjerk Wassenaar 
wrote:

> Hi Deep,
>
> What force field? What system? How many cores? Did you try running on one?
> What error? Did pdb2gmx or grompp give any warnings?
>
> Cheers,
>
> Tsjerk
>
> On Wed, Jul 13, 2016 at 5:44 AM, Deep Bhattacharya <
> hypergenet...@gmail.com>
> wrote:
>
> > Hello,
> > My system is blowing up for the protein carbohydrate solvent complex. I
> > have attached the mdp file below. The NPT and NVT were in good accordance
> > to tutorial listed by Justin. 'Please help me solve the issue.
> > title   = CD44  complex MD simulation
> > ; Run parameters
> > integrator  = md; leap-frog integrator
> > nsteps  = 1000; 0.001 * 100 = 1 ps (10 ns)
> > dt  = 0.001 ; 1 fs
> > ; Output control
> > nstxout = 5 ; suppress .trr output
> > nstvout = 5 ; suppress .trr output
> > nstenergy   = 5; save energies every 1000.0 ps
> > nstlog  = 5  ; update log file every 1000.0 ps
> > nstxtcout = 5
> > xtc_precision = 1000
> > energygrps  = Protein LIG SOL
> > ; Bond parameters
> > continuation= yes   ; first dynamics run
> > constraint_algorithm = lincs; holonomic constraints
> > constraints = all-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 = 1;
> > rcoulomb= 0.81
> > rvdw= 0.81
> > coulombtype = Cut-off   ; Particle Mesh Ewald for long-
> > vdwtype= cut-off
> > rlistlong  = 1.4
> > epsilon-rf = 61
> > rlist  = 0.8
> > ; Temperature coupling is on
> > tcoupl = nose-hoover; modified Berendsen thermostat
> > tc-grps   =Protein_LIG Water_and_ions   ; two coupling groups - more
> > accurate
> > tau_t = 2.0  2.0; time constant, in ps
> > ref_t = 300  300; reference temperature, one for each group, in K
> > ; Pressure coupling is on
> > pcoupl= Parrinello-Rahman; Pressure coupling on in
> NPT
> > pcoupltype= isotropic; uniform scaling of box vectors
> > tau_p= 6.0; time constant, in ps
> > ref_p= 1.0; reference pressure, in bar
> > compressibility = 4.5e-5; isothermal compressibility of
> > water, bar^-1
> > refcoord_scaling= com
> > ; Periodic boundary conditions
> > pbc = xyz   ; 3-D PBC
> > ; Dispersion correction
> > DispCorr= EnerPres  ; account for cut-off vdW scheme
> > ; Velocity generation
> > gen_vel = no; assign velocities from Maxwell distribution
> >
> >
> > Steepest Descents converged to Fmax < 1000 in 573 steps
> > Potential Energy  = -7.58370311664555e+05
> > Maximum force =  9.53896348096555e+02 on atom 1163
> > Norm of force =  2.44608995242254e+01
> >
> >
> > *Deep S Bhattacharya*
> >
> > *Graduate Research Assistant*
> >
> > Mohs Biomedical Imaging & Nanotechnology Group
> >
> > Pharmaceutical Sciences
> >
> > *Universit

Re: [gmx-users] System blowing up in final MD run

[Tsjerk Wassenaar]

Hi Deep,

What force field? What system? How many cores? Did you try running on one?
What error? Did pdb2gmx or grompp give any warnings?

Cheers,

Tsjerk

On Wed, Jul 13, 2016 at 5:44 AM, Deep Bhattacharya 
wrote:

> Hello,
> My system is blowing up for the protein carbohydrate solvent complex. I
> have attached the mdp file below. The NPT and NVT were in good accordance
> to tutorial listed by Justin. 'Please help me solve the issue.
> title   = CD44  complex MD simulation
> ; Run parameters
> integrator  = md; leap-frog integrator
> nsteps  = 1000; 0.001 * 100 = 1 ps (10 ns)
> dt  = 0.001 ; 1 fs
> ; Output control
> nstxout = 5 ; suppress .trr output
> nstvout = 5 ; suppress .trr output
> nstenergy   = 5; save energies every 1000.0 ps
> nstlog  = 5  ; update log file every 1000.0 ps
> nstxtcout = 5
> xtc_precision = 1000
> energygrps  = Protein LIG SOL
> ; Bond parameters
> continuation= yes   ; first dynamics run
> constraint_algorithm = lincs; holonomic constraints
> constraints = all-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 = 1;
> rcoulomb= 0.81
> rvdw= 0.81
> coulombtype = Cut-off   ; Particle Mesh Ewald for long-
> vdwtype= cut-off
> rlistlong  = 1.4
> epsilon-rf = 61
> rlist  = 0.8
> ; Temperature coupling is on
> tcoupl = nose-hoover; modified Berendsen thermostat
> tc-grps   =Protein_LIG Water_and_ions   ; two coupling groups - more
> accurate
> tau_t = 2.0  2.0; time constant, in ps
> ref_t = 300  300; reference temperature, one for each group, in K
> ; Pressure coupling is on
> pcoupl= Parrinello-Rahman; Pressure coupling on in NPT
> pcoupltype= isotropic; uniform scaling of box vectors
> tau_p= 6.0; time constant, in ps
> ref_p= 1.0; reference pressure, in bar
> compressibility = 4.5e-5; isothermal compressibility of
> water, bar^-1
> refcoord_scaling= com
> ; Periodic boundary conditions
> pbc = xyz   ; 3-D PBC
> ; Dispersion correction
> DispCorr= EnerPres  ; account for cut-off vdW scheme
> ; Velocity generation
> gen_vel = no; assign velocities from Maxwell distribution
>
>
> Steepest Descents converged to Fmax < 1000 in 573 steps
> Potential Energy  = -7.58370311664555e+05
> Maximum force =  9.53896348096555e+02 on atom 1163
> Norm of force =  2.44608995242254e+01
>
>
> *Deep S Bhattacharya*
>
> *Graduate Research Assistant*
>
> Mohs Biomedical Imaging & Nanotechnology Group
>
> Pharmaceutical Sciences
>
> *University of Nebraska Medical Center*
>
> 4018 Eppley Science Hall  |  Omaha, NE 68198-6805
>
> office 402.559.4349  | cell 402.906.1640
>
> deep.bhattacha...@unmc.edu.deep.bhattacharya...@gmail.com
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>



-- 
Tsjerk A. Wassenaar, Ph.D.
-- 
Gromacs Users mailing list

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[gmx-users] System blowing up in final MD run

[Deep Bhattacharya]

Hello,
My system is blowing up for the protein carbohydrate solvent complex. I
have attached the mdp file below. The NPT and NVT were in good accordance
to tutorial listed by Justin. 'Please help me solve the issue.
title   = CD44  complex MD simulation
; Run parameters
integrator  = md; leap-frog integrator
nsteps  = 1000; 0.001 * 100 = 1 ps (10 ns)
dt  = 0.001 ; 1 fs
; Output control
nstxout = 5 ; suppress .trr output
nstvout = 5 ; suppress .trr output
nstenergy   = 5; save energies every 1000.0 ps
nstlog  = 5  ; update log file every 1000.0 ps
nstxtcout = 5
xtc_precision = 1000
energygrps  = Protein LIG SOL
; Bond parameters
continuation= yes   ; first dynamics run
constraint_algorithm = lincs; holonomic constraints
constraints = all-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 = 1;
rcoulomb= 0.81
rvdw= 0.81
coulombtype = Cut-off   ; Particle Mesh Ewald for long-
vdwtype= cut-off
rlistlong  = 1.4
epsilon-rf = 61
rlist  = 0.8
; Temperature coupling is on
tcoupl = nose-hoover; modified Berendsen thermostat
tc-grps   =Protein_LIG Water_and_ions   ; two coupling groups - more
accurate
tau_t = 2.0  2.0; time constant, in ps
ref_t = 300  300; reference temperature, one for each group, in K
; Pressure coupling is on
pcoupl= Parrinello-Rahman; Pressure coupling on in NPT
pcoupltype= isotropic; uniform scaling of box vectors
tau_p= 6.0; time constant, in ps
ref_p= 1.0; reference pressure, in bar
compressibility = 4.5e-5; isothermal compressibility of
water, bar^-1
refcoord_scaling= com
; Periodic boundary conditions
pbc = xyz   ; 3-D PBC
; Dispersion correction
DispCorr= EnerPres  ; account for cut-off vdW scheme
; Velocity generation
gen_vel = no; assign velocities from Maxwell distribution


Steepest Descents converged to Fmax < 1000 in 573 steps
Potential Energy  = -7.58370311664555e+05
Maximum force =  9.53896348096555e+02 on atom 1163
Norm of force =  2.44608995242254e+01


*Deep S Bhattacharya*

*Graduate Research Assistant*

Mohs Biomedical Imaging & Nanotechnology Group

Pharmaceutical Sciences

*University of Nebraska Medical Center*

4018 Eppley Science Hall  |  Omaha, NE 68198-6805

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Re: [gmx-users] System blowing up in Gromacsv5.0.5 but not in v4.5.4

[Justin Lemkul]

On 12/16/15 12:54 PM, NISHA Prakash wrote:

Dear Justin,

You are right and I totally agree with you. But, the point that I was
trying to make was that "the same input coordinates and input .mdp files
run in 4.5.4 and fail in 5.0.5".  Also, if this situation persists, does
that mean the results that have been obtained from the version 4.5.4 are
not reliable?

The second query was that - the topology and co-ordinates should be fine
because I have obtained these files from the simulation of protein alone in
version-5.0.5. Yet, I get LINCS warning for the protein atoms alone when I
simulate it as a complex with the ligand.
Kindly help me identify the problem.



You would have to actually do debugging on the code level to find out which 
function is failing, or at least follow 
http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System. 
 Simply saying the system fails provides exactly zero useful diagnostic 
information.


-Justin


Thanking you,
Nisha

On Wed, Dec 16, 2015 at 7:05 PM, Justin Lemkul  wrote:




On 12/16/15 12:08 AM, NISHA Prakash wrote:


Dear Justin,

I am simulating a protein ligand complex. The protein co-ordinate file
that
I have taken is an output of the simulation of the protein alone in
Gromacs-v5.0.5. The topology and the co-ordinates are fine. I am still
facing this problem wherein I get the LINCS warning for only the protein
atoms. The ligand also is fine.



If the protein fails, you have a problem somewhere.  That's either
topology (unlikely), coordinates (probable), or .mdp (most probable).  You
said in your earlier message that energy minimization failed, which points
to coordinates being the problem.

Like I mentioned before, I do not have this problem when I use the

Gromacs-4.5.4 where I have used the same co-ordinate file with different
ligands and same parameter file.



If you're comparing a protein-ligand complex in 5.0.5 against different
complexes in 4.5.4, that is a meaningless comparison.  It's apples and
oranges.  If the same input coordinates and input .mdp files run in 4.5.4
and fail in 5.0.5, that might be something to look into.  But the general
advice applies here - either way you're using outdated software, so if
something is failing, upgrade to the latest version and try again.

-Justin


Kindly let me know how to resolve the issue.


Thanking you in anticipation.

Nisha




On Wed, Dec 16, 2015 at 12:26 AM, Justin Lemkul  wrote:




On 12/15/15 8:42 AM, NISHA Prakash wrote:

Hi all,


I am trying to simulate a protein using similar parameters as in the
tutorial - Protein ligand by Justin Lemkul.

I am facing a problem wherein the protein simulation is exploding only
in
this version - Gromacs-v5.0.5 but not in the older version
Gromacs-v4.5.4.

The warning message is as follows

---
There were 4 inconsistent shifts. Check your topology

Steepest Descents:
  Tolerance (Fmax)   =  1.0e+03
  Number of steps=5

WARNING: Listed nonbonded interaction between particles 1312 and 1315
at distance 4.728 which is larger than the table limit 2.000 nm.

This is likely either a 1,4 interaction, or a listed interaction inside
a smaller molecule you are decoupling during a free energy calculation.
Since interactions at distances beyond the table cannot be computed,
they are skipped until they are inside the table limit again. You will
only see this message once, even if it occurs for several interactions.

IMPORTANT: This should not happen in a stable simulation, so there is
probably something wrong with your system. Only change the
table-extension
distance in the mdp file if you are really sure that is the reason.

ATOM   1312  O   TYR A 207
ATOM   1315  CD1 TYR A 207
-



---
em_real.mdp file

; LINES STARTING WITH ';' ARE COMMENTS
title = Minimization ; Title of run

; Parameters describing what to do, when to stop and what to save
integrator = steep ; Algorithm (steep = steepest descent minimization)
emtol = 1000.0   ; Stop minimization when the maximum force < 10.0
kJ/mol
emstep  = 0.01  ; Energy step size
nsteps = 5   ; Maximum number of (minimization) steps to perform
energygrps = Protein ; Which energy group(s) to write to disk

; Parameters describing how to find the neighbors of each atom and how
to
calculate the interactions
nstlist= 1; Frequency to update the neighbor list and long range
forces
cutoff-scheme   = Verlet
ns_type= grid ; Method to determine neighbor list (simple, grid)
rlist= 1.0 ; Cut-off for making neighbor list (short range forces)
coulombtype= PME ; Treatment of long range electrostatic
interactions
rcoulomb= 1.0 ; long range electrostatic cut-off
rvdw= 1.0 ; long range Van der Waals cut-off
pbc= xyz ; Periodic Bo

Re: [gmx-users] System blowing up in Gromacsv5.0.5 but not in v4.5.4

[NISHA Prakash]

Dear Justin,

You are right and I totally agree with you. But, the point that I was
trying to make was that "the same input coordinates and input .mdp files
run in 4.5.4 and fail in 5.0.5".  Also, if this situation persists, does
that mean the results that have been obtained from the version 4.5.4 are
not reliable?

The second query was that - the topology and co-ordinates should be fine
because I have obtained these files from the simulation of protein alone in
version-5.0.5. Yet, I get LINCS warning for the protein atoms alone when I
simulate it as a complex with the ligand.
Kindly help me identify the problem.

Thanking you,
Nisha

On Wed, Dec 16, 2015 at 7:05 PM, Justin Lemkul  wrote:

>
>
> On 12/16/15 12:08 AM, NISHA Prakash wrote:
>
>> Dear Justin,
>>
>> I am simulating a protein ligand complex. The protein co-ordinate file
>> that
>> I have taken is an output of the simulation of the protein alone in
>> Gromacs-v5.0.5. The topology and the co-ordinates are fine. I am still
>> facing this problem wherein I get the LINCS warning for only the protein
>> atoms. The ligand also is fine.
>>
>
> If the protein fails, you have a problem somewhere.  That's either
> topology (unlikely), coordinates (probable), or .mdp (most probable).  You
> said in your earlier message that energy minimization failed, which points
> to coordinates being the problem.
>
> Like I mentioned before, I do not have this problem when I use the
>> Gromacs-4.5.4 where I have used the same co-ordinate file with different
>> ligands and same parameter file.
>>
>>
> If you're comparing a protein-ligand complex in 5.0.5 against different
> complexes in 4.5.4, that is a meaningless comparison.  It's apples and
> oranges.  If the same input coordinates and input .mdp files run in 4.5.4
> and fail in 5.0.5, that might be something to look into.  But the general
> advice applies here - either way you're using outdated software, so if
> something is failing, upgrade to the latest version and try again.
>
> -Justin
>
>
> Kindly let me know how to resolve the issue.
>>
>> Thanking you in anticipation.
>>
>> Nisha
>>
>>
>>
>>
>> On Wed, Dec 16, 2015 at 12:26 AM, Justin Lemkul  wrote:
>>
>>
>>>
>>> On 12/15/15 8:42 AM, NISHA Prakash wrote:
>>>
>>> Hi all,

 I am trying to simulate a protein using similar parameters as in the
 tutorial - Protein ligand by Justin Lemkul.

 I am facing a problem wherein the protein simulation is exploding only
 in
 this version - Gromacs-v5.0.5 but not in the older version
 Gromacs-v4.5.4.

 The warning message is as follows

 ---
 There were 4 inconsistent shifts. Check your topology

 Steepest Descents:
  Tolerance (Fmax)   =  1.0e+03
  Number of steps=5

 WARNING: Listed nonbonded interaction between particles 1312 and 1315
 at distance 4.728 which is larger than the table limit 2.000 nm.

 This is likely either a 1,4 interaction, or a listed interaction inside
 a smaller molecule you are decoupling during a free energy calculation.
 Since interactions at distances beyond the table cannot be computed,
 they are skipped until they are inside the table limit again. You will
 only see this message once, even if it occurs for several interactions.

 IMPORTANT: This should not happen in a stable simulation, so there is
 probably something wrong with your system. Only change the
 table-extension
 distance in the mdp file if you are really sure that is the reason.
 
 ATOM   1312  O   TYR A 207
 ATOM   1315  CD1 TYR A 207
 -



 ---
 em_real.mdp file

 ; LINES STARTING WITH ';' ARE COMMENTS
 title = Minimization ; Title of run

 ; Parameters describing what to do, when to stop and what to save
 integrator = steep ; Algorithm (steep = steepest descent minimization)
 emtol = 1000.0   ; Stop minimization when the maximum force < 10.0
 kJ/mol
 emstep  = 0.01  ; Energy step size
 nsteps = 5   ; Maximum number of (minimization) steps to perform
 energygrps = Protein ; Which energy group(s) to write to disk

 ; Parameters describing how to find the neighbors of each atom and how
 to
 calculate the interactions
 nstlist= 1; Frequency to update the neighbor list and long range
 forces
 cutoff-scheme   = Verlet
 ns_type= grid ; Method to determine neighbor list (simple, grid)
 rlist= 1.0 ; Cut-off for making neighbor list (short range forces)
 coulombtype= PME ; Treatment of long range electrostatic
 interactions
 rcoulomb= 1.0 ; long range electrostatic cut-off
 rvdw= 1.0 ; long range Van

Re: [gmx-users] System blowing up in Gromacsv5.0.5 but not in v4.5.4

[Justin Lemkul]

On 12/16/15 12:08 AM, NISHA Prakash wrote:

Dear Justin,

I am simulating a protein ligand complex. The protein co-ordinate file that
I have taken is an output of the simulation of the protein alone in
Gromacs-v5.0.5. The topology and the co-ordinates are fine. I am still
facing this problem wherein I get the LINCS warning for only the protein
atoms. The ligand also is fine.


If the protein fails, you have a problem somewhere.  That's either topology 
(unlikely), coordinates (probable), or .mdp (most probable).  You said in your 
earlier message that energy minimization failed, which points to coordinates 
being the problem.



Like I mentioned before, I do not have this problem when I use the
Gromacs-4.5.4 where I have used the same co-ordinate file with different
ligands and same parameter file.



If you're comparing a protein-ligand complex in 5.0.5 against different 
complexes in 4.5.4, that is a meaningless comparison.  It's apples and oranges. 
 If the same input coordinates and input .mdp files run in 4.5.4 and fail in 
5.0.5, that might be something to look into.  But the general advice applies 
here - either way you're using outdated software, so if something is failing, 
upgrade to the latest version and try again.


-Justin


Kindly let me know how to resolve the issue.

Thanking you in anticipation.

Nisha




On Wed, Dec 16, 2015 at 12:26 AM, Justin Lemkul  wrote:




On 12/15/15 8:42 AM, NISHA Prakash wrote:


Hi all,

I am trying to simulate a protein using similar parameters as in the
tutorial - Protein ligand by Justin Lemkul.

I am facing a problem wherein the protein simulation is exploding only in
this version - Gromacs-v5.0.5 but not in the older version Gromacs-v4.5.4.

The warning message is as follows

---
There were 4 inconsistent shifts. Check your topology

Steepest Descents:
 Tolerance (Fmax)   =  1.0e+03
 Number of steps=5

WARNING: Listed nonbonded interaction between particles 1312 and 1315
at distance 4.728 which is larger than the table limit 2.000 nm.

This is likely either a 1,4 interaction, or a listed interaction inside
a smaller molecule you are decoupling during a free energy calculation.
Since interactions at distances beyond the table cannot be computed,
they are skipped until they are inside the table limit again. You will
only see this message once, even if it occurs for several interactions.

IMPORTANT: This should not happen in a stable simulation, so there is
probably something wrong with your system. Only change the table-extension
distance in the mdp file if you are really sure that is the reason.

ATOM   1312  O   TYR A 207
ATOM   1315  CD1 TYR A 207
-



---
em_real.mdp file

; LINES STARTING WITH ';' ARE COMMENTS
title = Minimization ; Title of run

; Parameters describing what to do, when to stop and what to save
integrator = steep ; Algorithm (steep = steepest descent minimization)
emtol = 1000.0   ; Stop minimization when the maximum force < 10.0 kJ/mol
emstep  = 0.01  ; Energy step size
nsteps = 5   ; Maximum number of (minimization) steps to perform
energygrps = Protein ; Which energy group(s) to write to disk

; Parameters describing how to find the neighbors of each atom and how to
calculate the interactions
nstlist= 1; Frequency to update the neighbor list and long range
forces
cutoff-scheme   = Verlet
ns_type= grid ; Method to determine neighbor list (simple, grid)
rlist= 1.0 ; Cut-off for making neighbor list (short range forces)
coulombtype= PME ; Treatment of long range electrostatic interactions
rcoulomb= 1.0 ; long range electrostatic cut-off
rvdw= 1.0 ; long range Van der Waals cut-off
pbc= xyz ; Periodic Boundary Conditions




The initial minimization step itself fails.



If minimization fails, you have a problem with the topology or
coordinates. Perhaps you got a bit lucky with some quirk of an algorithmic
difference in the old version that is failing here.

-Justin

I have tried to simulate a minimized structure as well, I still encounter

the same problem.

I would appreciate any help in this regard.
I would also like to know if this means, that the results from the older
version of gromacs reliable?

Thanking you in anticipation

Nisha



--
==

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

==

Re: [gmx-users] System blowing up in Gromacsv5.0.5 but not in v4.5.4

[NISHA Prakash]

Dear Justin,

I am simulating a protein ligand complex. The protein co-ordinate file that
I have taken is an output of the simulation of the protein alone in
Gromacs-v5.0.5. The topology and the co-ordinates are fine. I am still
facing this problem wherein I get the LINCS warning for only the protein
atoms. The ligand also is fine.
Like I mentioned before, I do not have this problem when I use the
Gromacs-4.5.4 where I have used the same co-ordinate file with different
ligands and same parameter file.

Kindly let me know how to resolve the issue.

Thanking you in anticipation.

Nisha




On Wed, Dec 16, 2015 at 12:26 AM, Justin Lemkul  wrote:

>
>
> On 12/15/15 8:42 AM, NISHA Prakash wrote:
>
>> Hi all,
>>
>> I am trying to simulate a protein using similar parameters as in the
>> tutorial - Protein ligand by Justin Lemkul.
>>
>> I am facing a problem wherein the protein simulation is exploding only in
>> this version - Gromacs-v5.0.5 but not in the older version Gromacs-v4.5.4.
>>
>> The warning message is as follows
>>
>> ---
>> There were 4 inconsistent shifts. Check your topology
>>
>> Steepest Descents:
>> Tolerance (Fmax)   =  1.0e+03
>> Number of steps=5
>>
>> WARNING: Listed nonbonded interaction between particles 1312 and 1315
>> at distance 4.728 which is larger than the table limit 2.000 nm.
>>
>> This is likely either a 1,4 interaction, or a listed interaction inside
>> a smaller molecule you are decoupling during a free energy calculation.
>> Since interactions at distances beyond the table cannot be computed,
>> they are skipped until they are inside the table limit again. You will
>> only see this message once, even if it occurs for several interactions.
>>
>> IMPORTANT: This should not happen in a stable simulation, so there is
>> probably something wrong with your system. Only change the table-extension
>> distance in the mdp file if you are really sure that is the reason.
>> 
>> ATOM   1312  O   TYR A 207
>> ATOM   1315  CD1 TYR A 207
>> -
>>
>>
>>
>> ---
>> em_real.mdp file
>>
>> ; LINES STARTING WITH ';' ARE COMMENTS
>> title = Minimization ; Title of run
>>
>> ; Parameters describing what to do, when to stop and what to save
>> integrator = steep ; Algorithm (steep = steepest descent minimization)
>> emtol = 1000.0   ; Stop minimization when the maximum force < 10.0 kJ/mol
>> emstep  = 0.01  ; Energy step size
>> nsteps = 5   ; Maximum number of (minimization) steps to perform
>> energygrps = Protein ; Which energy group(s) to write to disk
>>
>> ; Parameters describing how to find the neighbors of each atom and how to
>> calculate the interactions
>> nstlist= 1; Frequency to update the neighbor list and long range
>> forces
>> cutoff-scheme   = Verlet
>> ns_type= grid ; Method to determine neighbor list (simple, grid)
>> rlist= 1.0 ; Cut-off for making neighbor list (short range forces)
>> coulombtype= PME ; Treatment of long range electrostatic interactions
>> rcoulomb= 1.0 ; long range electrostatic cut-off
>> rvdw= 1.0 ; long range Van der Waals cut-off
>> pbc= xyz ; Periodic Boundary Conditions
>>
>>
>> 
>>
>> The initial minimization step itself fails.
>>
>
> If minimization fails, you have a problem with the topology or
> coordinates. Perhaps you got a bit lucky with some quirk of an algorithmic
> difference in the old version that is failing here.
>
> -Justin
>
> I have tried to simulate a minimized structure as well, I still encounter
>> the same problem.
>>
>> I would appreciate any help in this regard.
>> I would also like to know if this means, that the results from the older
>> version of gromacs reliable?
>>
>> Thanking you in anticipation
>>
>> Nisha
>>
>>
> --
> ==
>
> 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
>
> ==
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
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Re: [gmx-users] System blowing up in Gromacsv5.0.5 but not in v4.5.4

[Justin Lemkul]

On 12/15/15 8:42 AM, NISHA Prakash wrote:

Hi all,

I am trying to simulate a protein using similar parameters as in the
tutorial - Protein ligand by Justin Lemkul.

I am facing a problem wherein the protein simulation is exploding only in
this version - Gromacs-v5.0.5 but not in the older version Gromacs-v4.5.4.

The warning message is as follows

---
There were 4 inconsistent shifts. Check your topology

Steepest Descents:
Tolerance (Fmax)   =  1.0e+03
Number of steps=5

WARNING: Listed nonbonded interaction between particles 1312 and 1315
at distance 4.728 which is larger than the table limit 2.000 nm.

This is likely either a 1,4 interaction, or a listed interaction inside
a smaller molecule you are decoupling during a free energy calculation.
Since interactions at distances beyond the table cannot be computed,
they are skipped until they are inside the table limit again. You will
only see this message once, even if it occurs for several interactions.

IMPORTANT: This should not happen in a stable simulation, so there is
probably something wrong with your system. Only change the table-extension
distance in the mdp file if you are really sure that is the reason.

ATOM   1312  O   TYR A 207
ATOM   1315  CD1 TYR A 207
-



---
em_real.mdp file

; LINES STARTING WITH ';' ARE COMMENTS
title = Minimization ; Title of run

; Parameters describing what to do, when to stop and what to save
integrator = steep ; Algorithm (steep = steepest descent minimization)
emtol = 1000.0   ; Stop minimization when the maximum force < 10.0 kJ/mol
emstep  = 0.01  ; Energy step size
nsteps = 5   ; Maximum number of (minimization) steps to perform
energygrps = Protein ; Which energy group(s) to write to disk

; Parameters describing how to find the neighbors of each atom and how to
calculate the interactions
nstlist= 1; Frequency to update the neighbor list and long range
forces
cutoff-scheme   = Verlet
ns_type= grid ; Method to determine neighbor list (simple, grid)
rlist= 1.0 ; Cut-off for making neighbor list (short range forces)
coulombtype= PME ; Treatment of long range electrostatic interactions
rcoulomb= 1.0 ; long range electrostatic cut-off
rvdw= 1.0 ; long range Van der Waals cut-off
pbc= xyz ; Periodic Boundary Conditions




The initial minimization step itself fails.


If minimization fails, you have a problem with the topology or coordinates. 
Perhaps you got a bit lucky with some quirk of an algorithmic difference in the 
old version that is failing here.


-Justin


I have tried to simulate a minimized structure as well, I still encounter
the same problem.

I would appreciate any help in this regard.
I would also like to know if this means, that the results from the older
version of gromacs reliable?

Thanking you in anticipation

Nisha



--
==

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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* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

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

* For (un)subscribe requests visit
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mail to gmx-users-requ...@gromacs.org.

[gmx-users] System blowing up in Gromacsv5.0.5 but not in v4.5.4

[NISHA Prakash]

Hi all,

I am trying to simulate a protein using similar parameters as in the
tutorial - Protein ligand by Justin Lemkul.

I am facing a problem wherein the protein simulation is exploding only in
this version - Gromacs-v5.0.5 but not in the older version Gromacs-v4.5.4.

The warning message is as follows

---
There were 4 inconsistent shifts. Check your topology

Steepest Descents:
   Tolerance (Fmax)   =  1.0e+03
   Number of steps=5

WARNING: Listed nonbonded interaction between particles 1312 and 1315
at distance 4.728 which is larger than the table limit 2.000 nm.

This is likely either a 1,4 interaction, or a listed interaction inside
a smaller molecule you are decoupling during a free energy calculation.
Since interactions at distances beyond the table cannot be computed,
they are skipped until they are inside the table limit again. You will
only see this message once, even if it occurs for several interactions.

IMPORTANT: This should not happen in a stable simulation, so there is
probably something wrong with your system. Only change the table-extension
distance in the mdp file if you are really sure that is the reason.

ATOM   1312  O   TYR A 207
ATOM   1315  CD1 TYR A 207
-



---
em_real.mdp file

; LINES STARTING WITH ';' ARE COMMENTS
title = Minimization ; Title of run

; Parameters describing what to do, when to stop and what to save
integrator = steep ; Algorithm (steep = steepest descent minimization)
emtol = 1000.0   ; Stop minimization when the maximum force < 10.0 kJ/mol
emstep  = 0.01  ; Energy step size
nsteps = 5   ; Maximum number of (minimization) steps to perform
energygrps = Protein ; Which energy group(s) to write to disk

; Parameters describing how to find the neighbors of each atom and how to
calculate the interactions
nstlist= 1; Frequency to update the neighbor list and long range
forces
cutoff-scheme   = Verlet
ns_type= grid ; Method to determine neighbor list (simple, grid)
rlist= 1.0 ; Cut-off for making neighbor list (short range forces)
coulombtype= PME ; Treatment of long range electrostatic interactions
rcoulomb= 1.0 ; long range electrostatic cut-off
rvdw= 1.0 ; long range Van der Waals cut-off
pbc= xyz ; Periodic Boundary Conditions




The initial minimization step itself fails.
I have tried to simulate a minimized structure as well, I still encounter
the same problem.

I would appreciate any help in this regard.
I would also like to know if this means, that the results from the older
version of gromacs reliable?

Thanking you in anticipation

Nisha
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

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

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mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] System blowing up at restart

[Mark Abraham]

Hi,

That's indeed curious. Please open an issue at http://redmine.gromacs.org and
attach your .tpr and .cpt files so we can see if we can reproduce it.

Mark

On Wed, Dec 2, 2015 at 9:22 PM Marlon Sidore 
wrote:

> It actually went on a few steps before blowing up, it didn't blow up
> directly at restart.
> Does that mean it simply blew up because of the system ? It always blows up
> a little time after restarting though, and that's strange given the time it
> ran the first time.
>
> gmx dump doesn't say anything special, should I include its output in a
> file here ?
>
> The restarted log file says:
> "Restarting from checkpoint, appending to previous log file.
>
> Log file opened on Tue Dec  1 14:26:27 2015
> Host: occigen1318  pid: 36303  rank ID: 0  number of ranks:  96
> :-) GROMACS - mdrun_mpi, VERSION 5.1 (-:
>
> Executable:   /opt/software/applications/gromacs/5.1/bullxmpi/bin/mdrun_mpi
> Data prefix:  /opt/software/applications/gromacs/5.1/bullxmpi
> Command line:
>   mdrun_mpi -deffnm vict -cpi vict.cpt -maxh 22 -append
> "
> ...
> "Started mdrun on rank 0 Tue Dec  1 14:26:27 2015
>Step   Time Lambda
>   155718960   3114379.20.0
>
>Energies (kJ/mol)
>Bond  Harmonic Pot.   G96AngleProper Dih.  Improper Dih.
> 2.66021e+042.78094e+031.40622e+047.50553e+021.72141e+02
> LJ (SR)   Coulomb (SR)  PotentialKinetic En.   Total Energy
>-8.26979e+05   -1.38652e+04   -7.96476e+051.43116e+05   -6.53360e+05
> Temperature Pressure (bar)   Constr. rmsd
> 3.22749e+02   -1.62340e+010.0e+00
>
> DD  step 155718979 load imb.: force 79.6%
>
> At step 155718980 the performance loss due to force load imbalance is 6.2 %
>
> NOTE: Turning on dynamic load balancing
>
> DD  step 15571  vol min/aver 0.516  load imb.: force  3.2%
> "
> it then continued for a few steps before blowing up. It's basically the
> same as the beginning of the log file (for the first run).
> --
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>
> * Please search the archive at
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Re: [gmx-users] System blowing up at restart

[Marlon Sidore]

It actually went on a few steps before blowing up, it didn't blow up
directly at restart.
Does that mean it simply blew up because of the system ? It always blows up
a little time after restarting though, and that's strange given the time it
ran the first time.

gmx dump doesn't say anything special, should I include its output in a
file here ?

The restarted log file says:
"Restarting from checkpoint, appending to previous log file.

Log file opened on Tue Dec  1 14:26:27 2015
Host: occigen1318  pid: 36303  rank ID: 0  number of ranks:  96
:-) GROMACS - mdrun_mpi, VERSION 5.1 (-:

Executable:   /opt/software/applications/gromacs/5.1/bullxmpi/bin/mdrun_mpi
Data prefix:  /opt/software/applications/gromacs/5.1/bullxmpi
Command line:
  mdrun_mpi -deffnm vict -cpi vict.cpt -maxh 22 -append
"
...
"Started mdrun on rank 0 Tue Dec  1 14:26:27 2015
   Step   Time Lambda
  155718960   3114379.20.0

   Energies (kJ/mol)
   Bond  Harmonic Pot.   G96AngleProper Dih.  Improper Dih.
2.66021e+042.78094e+031.40622e+047.50553e+021.72141e+02
LJ (SR)   Coulomb (SR)  PotentialKinetic En.   Total Energy
   -8.26979e+05   -1.38652e+04   -7.96476e+051.43116e+05   -6.53360e+05
Temperature Pressure (bar)   Constr. rmsd
3.22749e+02   -1.62340e+010.0e+00

DD  step 155718979 load imb.: force 79.6%

At step 155718980 the performance loss due to force load imbalance is 6.2 %

NOTE: Turning on dynamic load balancing

DD  step 15571  vol min/aver 0.516  load imb.: force  3.2%
"
it then continued for a few steps before blowing up. It's basically the
same as the beginning of the log file (for the first run).
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Re: [gmx-users] System blowing up at restart

[Mark Abraham]

Hi,

That should work, and I can't see why it should ever blow up. What does gmx
dump have to say about vict.cpt? Does the restarted .log file say after the
restart?

Mark

On Wed, Dec 2, 2015 at 8:20 PM Marlon  wrote:

> Hello,
>
> I have a problem continuing my simulation after the queue system stops
> the job (as I can't get -maxh to work). I would like to append the files
> to the old ones.
>
> The first production run, which ran one full day and 155 million steps,
> had the mdrun options:
> mdrun_mpi -deffnm vict -cpi equil.cpt -maxh 22
> (equil.cpt being the restart from the equilibration, and the file
> vict.tpr was made with equil.gro using grompp)
>
> The second production run blows up almost immediately with these
> options:
> mdrun_mpi -deffnm vict -cpi vict.cpt -maxh 22 -append
> (I didn't modify the .tpr here)
>
> I tried a few times with different options and it always blows up after
> the restart. Is it because I put equil.gro in the .tpr using grompp ? Do
> you have any idea why it blows up ?
>
> Best regards,
> Marlon
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
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[gmx-users] System blowing up at restart

[Marlon]

Hello,

I have a problem continuing my simulation after the queue system stops
the job (as I can't get -maxh to work). I would like to append the files
to the old ones.

The first production run, which ran one full day and 155 million steps,
had the mdrun options:
mdrun_mpi -deffnm vict -cpi equil.cpt -maxh 22
(equil.cpt being the restart from the equilibration, and the file
vict.tpr was made with equil.gro using grompp)

The second production run blows up almost immediately with these
options:
mdrun_mpi -deffnm vict -cpi vict.cpt -maxh 22 -append
(I didn't modify the .tpr here)

I tried a few times with different options and it always blows up after
the restart. Is it because I put equil.gro in the .tpr using grompp ? Do
you have any idea why it blows up ?

Best regards,
Marlon 

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Re: [gmx-users] System blowing up - equilibration step - CG simulation

[Tsjerk Wassenaar]

Hi Carlos,

You can try to contact Floris about the MGDG model.

Cheers,

Tsjerk

On Fri, Mar 6, 2015 at 9:56 PM, Carlos Navarro Retamal 
wrote:

> Hi Tsjerk,
> I tried to follow as closer as i could the parameters you used, but again
> without luck:
> .mdp file:
> dt   =  0.01
> nsteps   =  500
> nstxout  =  0
> nstvout  =  0
> nstlog   =  1
> nstxtcout=  1000
> xtc-precision=  10
> rlist=  1.4
> coulombtype  =  shift
> rcoulomb =  1.2
> epsilon_r=  15
> vdw-type =  shift
> rvdw-switch  =  0.9
> rvdw =  1.2
> cutoff-scheme= verlet
> tcoupl   =  Berendsen
> tc-grps  =  Protein MGDG W_ION
> tau-t=  2.0 2.0 2.0
> ref-t=  323 323 323
> Pcoupl   =  Berendsen
> Pcoupltype   =  isotropic
> tau-p=  12.0
> compressibility  =  3e-4
> ref-p=  1.0
> refcoord_scaling =  com
> (using also -rdd 1.6 and 1.8)
> When i used a timestep of 5fs i was able to run 50ns, but i don’t want to
> cut in half the speed of my simulation since i’m not able to use my GPU's
> (coulomb type and vdw_type = shift).
> What do you suggest me to do?
> Thanks in advance,
>
> --
> Carlos Navarro Retamal
> Bioinformatics Engineering
> Ph. D (c) Applied Sciences.
> Center of Bioinformatics and Molecular Simulations. CBSM
> University of Talca
> Av. Lircay S/N, Talca, Chile
> T: (+56) 712201 798
> E: carlos.navarr...@gmail.com or cnava...@utalca.cl
>
>
>
> On March 6, 2015 at 5:37:06 PM, Tsjerk Wassenaar (tsje...@gmail.com
> ) wrote:
>
> Hi Carlos,
>
> Most of that work (and the tutorials) was started some time ago. You can
> use Gromacs 5. At some point, the tutorials will get updated, but usually
> if there's pressure from a course or workshop. Otherwise the science comes
> first :)
>
> Cheers,
>
> Tsjerk
> On Mar 6, 2015 8:38 PM, "Carlos Navarro Retamal" 
> wrote:
>
> > Hi Tsjerk,
> > Thanks for your kind reply. I just start to reading your manuscript and
> > notice that you used GROMACS version 4.5.5 instead of the latest one
> (5.X)
> > Is there an specific reason to do these? (maybe martini works in a better
> > way with older version of gromacs? )
> > I’m asking you these, because in Martini forums all the tutorial are
> still
> > using gromacs version 4.6.X as the standard.
> > Kind regards,
> > Carlos
> >
> > --
> > Carlos Navarro Retamal
> > Bioinformatics Engineering
> > Ph. D (c) Applied Sciences.
> > Center of Bioinformatics and Molecular Simulations. CBSM
> > University of Talca
> > Av. Lircay S/N, Talca, Chile
> > T: (+56) 712201 798
> > E: carlos.navarr...@gmail.com or cnava...@utalca.cl
> >
> >
> >
> > On March 6, 2015 at 4:08:21 PM, Tsjerk Wassenaar (tsje...@gmail.com
> > ) wrote:
> >
> > Hi Carlos,
> >
> > Other things to consider are doing a first short equilibration on a
> single
> > processor and increasing the dom.dec. radius to 1.6 or 1.8 (mdrun -rdd
> > 1.6). Maybe you might want to check the just accepted manuscript on
> > thylakoid membranes from the Martini group (
> > http://dx.doi.org/10.1016/j.bbamem.2015.02.025), which also includes
> MGDG.
> > Those simulations were run with a 10 fs time step.
> >
> > Hope it helps,
> >
> > Tsjerk
> >
> > On Fri, Mar 6, 2015 at 7:07 PM, Carlos Navarro Retamal <
> cnava...@utalca.cl
> > >
> > wrote:
> >
> > > Dear Justin,
> > > I was looking into the paper where the ‘martini’ group described the
> > > parameters for glycolipids, and the mention that in order to
> equilibrate
> > > some glycolipids the had to used a timestep of 5fs. Sadly they not
> > mention
> > > which glycolipid were, so i reduced the timestep from 20fs to 10fs.
> > > I was able to perform performed the equilibration (NPT) with the
> changes
> > > you suggest me (a short one of 5ns).
> > > But later, when i ran the production step of 100ns, at about 60ns the
> > > simulation crashed again (using a timestep of 10fs again).
> > > This is the production .mdp file:
> > >
> > > integrator = md
> > > dt = 0.01
> > > nsteps = 1000
> > > nstcomm = 10
> > > comm-grps =
> > >
> > > nstxout = 0
> > > nstvout = 0
> > > nstfout = 0
> > > nstlog = 1000
> > > nstenergy = 100
> > > nstxtcout = 1000
> > > xtc_precision = 100
> > > xtc-grps =
> > > energygrps = Protein MGDG W_ION
> > >
> > > nstlist = 10
> > > ns_type = grid
> > > pbc = xyz
> > > rlist = 1.4
> > >
> > > cutoff-scheme = verlet
> > > coulomb-modifier = Potential-shift
> > > vdw-modifier = Potential-shift
> > > epsilon_rf = 0 ; epsilon_rf = 0 really means epsilon_rf =
> > > infinity
> > > verlet-buffer-drift = 0.005
> > >
> > > tcoupl = v-rescale
> > > tc-grps = Protein MGDG W_ION
> > > tau_t = 1.0 1.0 1.0
> > > ref_t = 320 320 320
> > > Pcoupl = parrinello-rahman
> > > Pcoupltype = semiisotropic
> > > tau_p = 12.0 12.0 ;parrinello-rahman is more stable
> > > with larger tau-p, DdJ, 20130422
> > > compressibility = 3e

Re: [gmx-users] System blowing up - equilibration step - CG simulation

[Carlos Navarro Retamal]

Hi Tsjerk,
I tried to follow as closer as i could the parameters you used, but again 
without luck:
.mdp file:
dt   =  0.01
nsteps   =  500
nstxout  =  0
nstvout  =  0
nstlog   =  1
nstxtcout=  1000
xtc-precision=  10
rlist=  1.4
coulombtype  =  shift
rcoulomb =  1.2
epsilon_r=  15
vdw-type =  shift
rvdw-switch  =  0.9
rvdw =  1.2
cutoff-scheme= verlet
tcoupl   =  Berendsen
tc-grps  =  Protein MGDG W_ION
tau-t=  2.0 2.0 2.0
ref-t=  323 323 323
Pcoupl   =  Berendsen
Pcoupltype   =  isotropic
tau-p=  12.0
compressibility  =  3e-4
ref-p=  1.0
refcoord_scaling =  com
(using also -rdd 1.6 and 1.8)
When i used a timestep of 5fs i was able to run 50ns, but i don’t want to cut 
in half the speed of my simulation since i’m not able to use my GPU's (coulomb 
type and vdw_type = shift).
What do you suggest me to do?
Thanks in advance,

--
Carlos Navarro Retamal
Bioinformatics Engineering
Ph. D (c) Applied Sciences.
Center of Bioinformatics and Molecular Simulations. CBSM
University of Talca
Av. Lircay S/N, Talca, Chile
T: (+56) 712201 798
E: carlos.navarr...@gmail.com or cnava...@utalca.cl



On March 6, 2015 at 5:37:06 PM, Tsjerk Wassenaar 
(tsje...@gmail.com) wrote:

Hi Carlos,

Most of that work (and the tutorials) was started some time ago. You can
use Gromacs 5. At some point, the tutorials will get updated, but usually
if there's pressure from a course or workshop. Otherwise the science comes
first :)

Cheers,

Tsjerk
On Mar 6, 2015 8:38 PM, "Carlos Navarro Retamal"  wrote:

> Hi Tsjerk,
> Thanks for your kind reply. I just start to reading your manuscript and
> notice that you used GROMACS version 4.5.5 instead of the latest one (5.X)
> Is there an specific reason to do these? (maybe martini works in a better
> way with older version of gromacs? )
> I’m asking you these, because in Martini forums all the tutorial are still
> using gromacs version 4.6.X as the standard.
> Kind regards,
> Carlos
>
> --
> Carlos Navarro Retamal
> Bioinformatics Engineering
> Ph. D (c) Applied Sciences.
> Center of Bioinformatics and Molecular Simulations. CBSM
> University of Talca
> Av. Lircay S/N, Talca, Chile
> T: (+56) 712201 798
> E: carlos.navarr...@gmail.com or cnava...@utalca.cl
>
>
>
> On March 6, 2015 at 4:08:21 PM, Tsjerk Wassenaar (tsje...@gmail.com
> ) wrote:
>
> Hi Carlos,
>
> Other things to consider are doing a first short equilibration on a single
> processor and increasing the dom.dec. radius to 1.6 or 1.8 (mdrun -rdd
> 1.6). Maybe you might want to check the just accepted manuscript on
> thylakoid membranes from the Martini group (
> http://dx.doi.org/10.1016/j.bbamem.2015.02.025), which also includes MGDG.
> Those simulations were run with a 10 fs time step.
>
> Hope it helps,
>
> Tsjerk
>
> On Fri, Mar 6, 2015 at 7:07 PM, Carlos Navarro Retamal  >
> wrote:
>
> > Dear Justin,
> > I was looking into the paper where the ‘martini’ group described the
> > parameters for glycolipids, and the mention that in order to equilibrate
> > some glycolipids the had to used a timestep of 5fs. Sadly they not
> mention
> > which glycolipid were, so i reduced the timestep from 20fs to 10fs.
> > I was able to perform performed the equilibration (NPT) with the changes
> > you suggest me (a short one of 5ns).
> > But later, when i ran the production step of 100ns, at about 60ns the
> > simulation crashed again (using a timestep of 10fs again).
> > This is the production .mdp file:
> >
> > integrator = md
> > dt = 0.01
> > nsteps = 1000
> > nstcomm = 10
> > comm-grps =
> >
> > nstxout = 0
> > nstvout = 0
> > nstfout = 0
> > nstlog = 1000
> > nstenergy = 100
> > nstxtcout = 1000
> > xtc_precision = 100
> > xtc-grps =
> > energygrps = Protein MGDG W_ION
> >
> > nstlist = 10
> > ns_type = grid
> > pbc = xyz
> > rlist = 1.4
> >
> > cutoff-scheme = verlet
> > coulomb-modifier = Potential-shift
> > vdw-modifier = Potential-shift
> > epsilon_rf = 0 ; epsilon_rf = 0 really means epsilon_rf =
> > infinity
> > verlet-buffer-drift = 0.005
> >
> > tcoupl = v-rescale
> > tc-grps = Protein MGDG W_ION
> > tau_t = 1.0 1.0 1.0
> > ref_t = 320 320 320
> > Pcoupl = parrinello-rahman
> > Pcoupltype = semiisotropic
> > tau_p = 12.0 12.0 ;parrinello-rahman is more stable
> > with larger tau-p, DdJ, 20130422
> > compressibility = 3e-4 3e-4
> > ref_p = 1.0 1.0
> >
> > gen_vel = no
> > gen_temp = 320
> > gen_seed = 473529
> >
> > constraints = none
> > constraint_algorithm = Lincs
> > unconstrained_start = no
> > lincs_order = 4
> > lincs_warnangle = 30
> > I’m currently increasing the time of equilibration step to 50ns.
> > What else do you suggest me?
> > Best regards,
> > Carlos
> > --
> > Carlos Navarro Retamal
> > Bioinformatics Engineering
> > Ph. D (c) Applied Sciences.
> > Center of Bioinformatics

Re: [gmx-users] System blowing up - equilibration step - CG simulation

[Tsjerk Wassenaar]

Hi Carlos,

Most of that work (and the tutorials) was started some time ago. You can
use Gromacs 5. At some point, the tutorials will get updated, but usually
if there's pressure from a course or workshop. Otherwise the science comes
first :)

Cheers,

Tsjerk
On Mar 6, 2015 8:38 PM, "Carlos Navarro Retamal"  wrote:

> Hi Tsjerk,
> Thanks for your kind reply. I just start to reading your manuscript and
> notice that you used GROMACS version 4.5.5 instead of the latest one (5.X)
> Is there an specific reason to do these? (maybe martini works in a better
> way with older version of gromacs? )
> I’m asking you these, because in Martini forums all the tutorial are still
> using gromacs version 4.6.X as the standard.
> Kind regards,
> Carlos
>
> --
> Carlos Navarro Retamal
> Bioinformatics Engineering
> Ph. D (c) Applied Sciences.
> Center of Bioinformatics and Molecular Simulations. CBSM
> University of Talca
> Av. Lircay S/N, Talca, Chile
> T: (+56) 712201 798
> E: carlos.navarr...@gmail.com or cnava...@utalca.cl
>
>
>
> On March 6, 2015 at 4:08:21 PM, Tsjerk Wassenaar (tsje...@gmail.com
> ) wrote:
>
> Hi Carlos,
>
> Other things to consider are doing a first short equilibration on a single
> processor and increasing the dom.dec. radius to 1.6 or 1.8 (mdrun -rdd
> 1.6). Maybe you might want to check the just accepted manuscript on
> thylakoid membranes from the Martini group (
> http://dx.doi.org/10.1016/j.bbamem.2015.02.025), which also includes MGDG.
> Those simulations were run with a 10 fs time step.
>
> Hope it helps,
>
> Tsjerk
>
> On Fri, Mar 6, 2015 at 7:07 PM, Carlos Navarro Retamal  >
> wrote:
>
> > Dear Justin,
> > I was looking into the paper where the ‘martini’ group described the
> > parameters for glycolipids, and the mention that in order to equilibrate
> > some glycolipids the had to used a timestep of 5fs. Sadly they not
> mention
> > which glycolipid were, so i reduced the timestep from 20fs to 10fs.
> > I was able to perform performed the equilibration (NPT) with the changes
> > you suggest me (a short one of 5ns).
> > But later, when i ran the production step of 100ns, at about 60ns the
> > simulation crashed again (using a timestep of 10fs again).
> > This is the production .mdp file:
> >
> > integrator = md
> > dt = 0.01
> > nsteps = 1000
> > nstcomm = 10
> > comm-grps =
> >
> > nstxout = 0
> > nstvout = 0
> > nstfout = 0
> > nstlog = 1000
> > nstenergy = 100
> > nstxtcout = 1000
> > xtc_precision = 100
> > xtc-grps =
> > energygrps = Protein MGDG W_ION
> >
> > nstlist = 10
> > ns_type = grid
> > pbc = xyz
> > rlist = 1.4
> >
> > cutoff-scheme = verlet
> > coulomb-modifier = Potential-shift
> > vdw-modifier = Potential-shift
> > epsilon_rf = 0 ; epsilon_rf = 0 really means epsilon_rf =
> > infinity
> > verlet-buffer-drift = 0.005
> >
> > tcoupl = v-rescale
> > tc-grps = Protein MGDG W_ION
> > tau_t = 1.0 1.0 1.0
> > ref_t = 320 320 320
> > Pcoupl = parrinello-rahman
> > Pcoupltype = semiisotropic
> > tau_p = 12.0 12.0 ;parrinello-rahman is more stable
> > with larger tau-p, DdJ, 20130422
> > compressibility = 3e-4 3e-4
> > ref_p = 1.0 1.0
> >
> > gen_vel = no
> > gen_temp = 320
> > gen_seed = 473529
> >
> > constraints = none
> > constraint_algorithm = Lincs
> > unconstrained_start = no
> > lincs_order = 4
> > lincs_warnangle = 30
> > I’m currently increasing the time of equilibration step to 50ns.
> > What else do you suggest me?
> > Best regards,
> > Carlos
> > --
> > Carlos Navarro Retamal
> > Bioinformatics Engineering
> > Ph. D (c) Applied Sciences.
> > Center of Bioinformatics and Molecular Simulations. CBSM
> > University of Talca
> > Av. Lircay S/N, Talca, Chile
> > T: (+56) 712201 798
> > E: carlos.navarr...@gmail.com or cnava...@utalca.cl
> >
> >
> >
> > On March 6, 2015 at 12:26:28 PM, Carlos Navarro Retamal (
> > cnava...@utalca.cl) wrote:
> >
> > Dear Justin,
> > Thanks for your kind reply.
> > Is there a way to set up a bilayer membrane system without a protein
> using
> > insane? I’ve already several CG simulations with this protein, so i'm
> > pretty sure that its parameters are ok. I do have some issues with the
> > glycolipid used (MGDG) This is the first time i used the parameters
> gotten
> > from
> >
> http://md.chem.rug.nl/cgmartini/images/parameters/ITP/martini_v2.0_glycolipids.itp
> > so i don’t know if this kind of molecules requieres an specific
> > temperature (for example)
> > Best regards,
> > Carlos
> > --
> > Carlos Navarro Retamal
> > Bioinformatics Engineering
> > Ph. D (c) Applied Sciences.
> > Center of Bioinformatics and Molecular Simulations. CBSM
> > University of Talca
> > Av. Lircay S/N, Talca, Chile
> > T: (+56) 712201 798
> > E: carlos.navarr...@gmail.com or cnava...@utalca.cl
> >
> >
> >
> > On March 6, 2015 at 11:56:01 AM, Justin Lemkul (jalem...@vt.edu > jalem...@vt.edu>) wrote:
> >
> >
> > On 3/6/15 8:15 AM, Carlos Navarro Retamal wrote:
> > > Dear Gromacs users,
> > > I'm trying to per

Re: [gmx-users] System blowing up - equilibration step - CG simulation

[Carlos Navarro Retamal]

Hi Tsjerk,
Thanks for your kind reply. I just start to reading your manuscript and notice 
that you used GROMACS version 4.5.5 instead of the latest one (5.X)
Is there an specific reason to do these? (maybe martini works in a better way 
with older version of gromacs? )
I’m asking you these, because in Martini forums all the tutorial are still 
using gromacs version 4.6.X as the standard.
Kind regards,
Carlos

--
Carlos Navarro Retamal
Bioinformatics Engineering
Ph. D (c) Applied Sciences.
Center of Bioinformatics and Molecular Simulations. CBSM
University of Talca
Av. Lircay S/N, Talca, Chile
T: (+56) 712201 798
E: carlos.navarr...@gmail.com or cnava...@utalca.cl



On March 6, 2015 at 4:08:21 PM, Tsjerk Wassenaar 
(tsje...@gmail.com) wrote:

Hi Carlos,

Other things to consider are doing a first short equilibration on a single
processor and increasing the dom.dec. radius to 1.6 or 1.8 (mdrun -rdd
1.6). Maybe you might want to check the just accepted manuscript on
thylakoid membranes from the Martini group (
http://dx.doi.org/10.1016/j.bbamem.2015.02.025), which also includes MGDG.
Those simulations were run with a 10 fs time step.

Hope it helps,

Tsjerk

On Fri, Mar 6, 2015 at 7:07 PM, Carlos Navarro Retamal 
wrote:

> Dear Justin,
> I was looking into the paper where the ‘martini’ group described the
> parameters for glycolipids, and the mention that in order to equilibrate
> some glycolipids the had to used a timestep of 5fs. Sadly they not mention
> which glycolipid were, so i reduced the timestep from 20fs to 10fs.
> I was able to perform performed the equilibration (NPT) with the changes
> you suggest me (a short one of 5ns).
> But later, when i ran the production step of 100ns, at about 60ns the
> simulation crashed again (using a timestep of 10fs again).
> This is the production .mdp file:
>
> integrator = md
> dt = 0.01
> nsteps = 1000
> nstcomm = 10
> comm-grps =
>
> nstxout = 0
> nstvout = 0
> nstfout = 0
> nstlog = 1000
> nstenergy = 100
> nstxtcout = 1000
> xtc_precision = 100
> xtc-grps =
> energygrps = Protein MGDG W_ION
>
> nstlist = 10
> ns_type = grid
> pbc = xyz
> rlist = 1.4
>
> cutoff-scheme = verlet
> coulomb-modifier = Potential-shift
> vdw-modifier = Potential-shift
> epsilon_rf = 0 ; epsilon_rf = 0 really means epsilon_rf =
> infinity
> verlet-buffer-drift = 0.005
>
> tcoupl = v-rescale
> tc-grps = Protein MGDG W_ION
> tau_t = 1.0 1.0 1.0
> ref_t = 320 320 320
> Pcoupl = parrinello-rahman
> Pcoupltype = semiisotropic
> tau_p = 12.0 12.0 ;parrinello-rahman is more stable
> with larger tau-p, DdJ, 20130422
> compressibility = 3e-4 3e-4
> ref_p = 1.0 1.0
>
> gen_vel = no
> gen_temp = 320
> gen_seed = 473529
>
> constraints = none
> constraint_algorithm = Lincs
> unconstrained_start = no
> lincs_order = 4
> lincs_warnangle = 30
> I’m currently increasing the time of equilibration step to 50ns.
> What else do you suggest me?
> Best regards,
> Carlos
> --
> Carlos Navarro Retamal
> Bioinformatics Engineering
> Ph. D (c) Applied Sciences.
> Center of Bioinformatics and Molecular Simulations. CBSM
> University of Talca
> Av. Lircay S/N, Talca, Chile
> T: (+56) 712201 798
> E: carlos.navarr...@gmail.com or cnava...@utalca.cl
>
>
>
> On March 6, 2015 at 12:26:28 PM, Carlos Navarro Retamal (
> cnava...@utalca.cl) wrote:
>
> Dear Justin,
> Thanks for your kind reply.
> Is there a way to set up a bilayer membrane system without a protein using
> insane? I’ve already several CG simulations with this protein, so i'm
> pretty sure that its parameters are ok. I do have some issues with the
> glycolipid used (MGDG) This is the first time i used the parameters gotten
> from
> http://md.chem.rug.nl/cgmartini/images/parameters/ITP/martini_v2.0_glycolipids.itp
> so i don’t know if this kind of molecules requieres an specific
> temperature (for example)
> Best regards,
> Carlos
> --
> Carlos Navarro Retamal
> Bioinformatics Engineering
> Ph. D (c) Applied Sciences.
> Center of Bioinformatics and Molecular Simulations. CBSM
> University of Talca
> Av. Lircay S/N, Talca, Chile
> T: (+56) 712201 798
> E: carlos.navarr...@gmail.com or cnava...@utalca.cl
>
>
>
> On March 6, 2015 at 11:56:01 AM, Justin Lemkul (jalem...@vt.edu jalem...@vt.edu>) wrote:
>
>
> On 3/6/15 8:15 AM, Carlos Navarro Retamal wrote:
> > Dear Gromacs users,
> > I'm trying to perform a CG simulations of a system consisting in a
> protein locate at 5 nm with respect to the charged groups of a MGDG
> membrane.
> > I first performed an EM in vaccum.
> > After that, to constructed the system i use insane.py as following:
> > ./insane.py -f minimization-vaccum.gro -o system.gro -pbc square -dm 5
> -box 10,10,10 -l MGDG -sol W -orient
> >
> > Later, i ran a EM with the whole system, with the respective output:
> > Steepest Descents converged to machine precision in 2081 steps,
> > but did not reach the requested Fmax < 10.
> > Potential Energy = -2.6833109e+05
> > Maximum force = 3.519394

Re: [gmx-users] System blowing up - equilibration step - CG simulation

[Tsjerk Wassenaar]

Hi Carlos,

Other things to consider are doing a first short equilibration on a single
processor and increasing the dom.dec. radius to 1.6 or 1.8 (mdrun -rdd
1.6). Maybe you might want to check the just accepted manuscript on
thylakoid membranes from the Martini group (
http://dx.doi.org/10.1016/j.bbamem.2015.02.025), which also includes MGDG.
Those simulations were run with a 10 fs time step.

Hope it helps,

Tsjerk

On Fri, Mar 6, 2015 at 7:07 PM, Carlos Navarro Retamal 
wrote:

> Dear Justin,
> I was looking into the paper where the ‘martini’ group described the
> parameters for glycolipids, and the mention that in order to equilibrate
> some glycolipids the had to used a timestep of 5fs. Sadly they not mention
> which glycolipid were, so i reduced the timestep from 20fs to 10fs.
> I was able to perform performed the equilibration (NPT) with the changes
> you suggest me (a short one of 5ns).
> But later, when i ran the production step of 100ns, at about 60ns the
> simulation crashed again (using a timestep of 10fs again).
> This is the production .mdp file:
>
> integrator   = md
> dt   = 0.01
> nsteps   = 1000
> nstcomm  = 10
> comm-grps =
>
> nstxout  = 0
> nstvout  = 0
> nstfout  = 0
> nstlog   = 1000
> nstenergy= 100
> nstxtcout= 1000
> xtc_precision= 100
> xtc-grps =
> energygrps   = Protein MGDG W_ION
>
> nstlist  = 10
> ns_type  = grid
> pbc  = xyz
> rlist= 1.4
>
> cutoff-scheme= verlet
> coulomb-modifier = Potential-shift
> vdw-modifier = Potential-shift
> epsilon_rf   = 0   ; epsilon_rf = 0 really means epsilon_rf =
> infinity
> verlet-buffer-drift  = 0.005
>
> tcoupl   = v-rescale
> tc-grps  = Protein MGDG W_ION
> tau_t= 1.0  1.0 1.0
> ref_t= 320 320 320
> Pcoupl   = parrinello-rahman
> Pcoupltype   = semiisotropic
> tau_p= 12.0 12.0  ;parrinello-rahman is more stable
> with larger tau-p, DdJ, 20130422
> compressibility  = 3e-4  3e-4
> ref_p= 1.0  1.0
>
> gen_vel  = no
> gen_temp = 320
> gen_seed = 473529
>
> constraints  = none
> constraint_algorithm = Lincs
> unconstrained_start  = no
> lincs_order  = 4
> lincs_warnangle  = 30
> I’m currently increasing the time of equilibration step to 50ns.
> What else do you suggest me?
> Best regards,
> Carlos
> --
> Carlos Navarro Retamal
> Bioinformatics Engineering
> Ph. D (c) Applied Sciences.
> Center of Bioinformatics and Molecular Simulations. CBSM
> University of Talca
> Av. Lircay S/N, Talca, Chile
> T: (+56) 712201 798
> E: carlos.navarr...@gmail.com or cnava...@utalca.cl
>
>
>
> On March 6, 2015 at 12:26:28 PM, Carlos Navarro Retamal (
> cnava...@utalca.cl) wrote:
>
> Dear Justin,
> Thanks for your kind reply.
> Is there a way to set up a bilayer membrane system without a protein using
> insane? I’ve already several CG simulations with this protein, so i'm
> pretty sure that its parameters are ok. I do have some issues with the
> glycolipid used (MGDG) This is the first time i used the parameters gotten
> from
> http://md.chem.rug.nl/cgmartini/images/parameters/ITP/martini_v2.0_glycolipids.itp
> so i don’t know if this kind of molecules requieres an specific
> temperature (for example)
> Best regards,
> Carlos
> --
> Carlos Navarro Retamal
> Bioinformatics Engineering
> Ph. D (c) Applied Sciences.
> Center of Bioinformatics and Molecular Simulations. CBSM
> University of Talca
> Av. Lircay S/N, Talca, Chile
> T: (+56) 712201 798
> E: carlos.navarr...@gmail.com or cnava...@utalca.cl
>
>
>
> On March 6, 2015 at 11:56:01 AM, Justin Lemkul (jalem...@vt.edu jalem...@vt.edu>) wrote:
>
>
> On 3/6/15 8:15 AM, Carlos Navarro Retamal wrote:
> > Dear Gromacs users,
> > I'm trying to perform a CG simulations of a system consisting in a
> protein locate at 5 nm with respect to the charged groups of a MGDG
> membrane.
> > I first performed an EM in vaccum.
> > After that, to constructed the system i use insane.py as following:
> > ./insane.py -f minimization-vaccum.gro -o system.gro -pbc square -dm 5
> -box 10,10,10 -l MGDG -sol W -orient
> >
> > Later, i ran a EM with the whole system, with the respective output:
> > Steepest Descents converged to machine precision in 2081 steps,
> > but did not reach the requested Fmax < 10.
> > Potential Energy = -2.6833109e+05
> > Maximum force = 3.5193942e+02 on atom 3598
> > Norm of force = 6.2432761e+00,
> >
> > Sadly, when i'm trying to perform an equilibration i got the following
> error message:
> > Step 10:
> > Atom 8449 moved more than t

Re: [gmx-users] System blowing up - equilibration step - CG simulation

[Carlos Navarro Retamal]

Dear Justin,
I was looking into the paper where the ‘martini’ group described the parameters 
for glycolipids, and the mention that in order to equilibrate some glycolipids 
the had to used a timestep of 5fs. Sadly they not mention which glycolipid 
were, so i reduced the timestep from 20fs to 10fs.
I was able to perform performed the equilibration (NPT) with the changes you 
suggest me (a short one of 5ns).
But later, when i ran the production step of 100ns, at about 60ns the 
simulation crashed again (using a timestep of 10fs again).
This is the production .mdp file:

integrator   = md
dt   = 0.01
nsteps   = 1000
nstcomm  = 10
comm-grps =

nstxout  = 0
nstvout  = 0
nstfout  = 0
nstlog   = 1000
nstenergy= 100
nstxtcout= 1000
xtc_precision= 100
xtc-grps =
energygrps   = Protein MGDG W_ION

nstlist  = 10
ns_type  = grid
pbc  = xyz
rlist= 1.4

cutoff-scheme= verlet
coulomb-modifier = Potential-shift
vdw-modifier = Potential-shift
epsilon_rf   = 0   ; epsilon_rf = 0 really means epsilon_rf = 
infinity
verlet-buffer-drift  = 0.005

tcoupl   = v-rescale
tc-grps  = Protein MGDG W_ION
tau_t= 1.0  1.0 1.0
ref_t= 320 320 320
Pcoupl   = parrinello-rahman
Pcoupltype   = semiisotropic
tau_p= 12.0 12.0  ;parrinello-rahman is more stable with 
larger tau-p, DdJ, 20130422
compressibility  = 3e-4  3e-4
ref_p= 1.0  1.0

gen_vel  = no
gen_temp = 320
gen_seed = 473529

constraints  = none
constraint_algorithm = Lincs
unconstrained_start  = no
lincs_order  = 4
lincs_warnangle  = 30
I’m currently increasing the time of equilibration step to 50ns.
What else do you suggest me?
Best regards,
Carlos
--
Carlos Navarro Retamal
Bioinformatics Engineering
Ph. D (c) Applied Sciences.
Center of Bioinformatics and Molecular Simulations. CBSM
University of Talca
Av. Lircay S/N, Talca, Chile
T: (+56) 712201 798
E: carlos.navarr...@gmail.com or cnava...@utalca.cl



On March 6, 2015 at 12:26:28 PM, Carlos Navarro Retamal 
(cnava...@utalca.cl) wrote:

Dear Justin,
Thanks for your kind reply.
Is there a way to set up a bilayer membrane system without a protein using 
insane? I’ve already several CG simulations with this protein, so i'm pretty 
sure that its parameters are ok. I do have some issues with the glycolipid used 
(MGDG) This is the first time i used the parameters gotten from 
http://md.chem.rug.nl/cgmartini/images/parameters/ITP/martini_v2.0_glycolipids.itp
so i don’t know if this kind of molecules requieres an specific temperature 
(for example)
Best regards,
Carlos
--
Carlos Navarro Retamal
Bioinformatics Engineering
Ph. D (c) Applied Sciences.
Center of Bioinformatics and Molecular Simulations. CBSM
University of Talca
Av. Lircay S/N, Talca, Chile
T: (+56) 712201 798
E: carlos.navarr...@gmail.com or cnava...@utalca.cl



On March 6, 2015 at 11:56:01 AM, Justin Lemkul 
(jalem...@vt.edu) wrote:


On 3/6/15 8:15 AM, Carlos Navarro Retamal wrote:
> Dear Gromacs users,
> I'm trying to perform a CG simulations of a system consisting in a protein 
> locate at 5 nm with respect to the charged groups of a MGDG membrane.
> I first performed an EM in vaccum.
> After that, to constructed the system i use insane.py as following:
> ./insane.py -f minimization-vaccum.gro -o system.gro -pbc square -dm 5 -box 
> 10,10,10 -l MGDG -sol W -orient
>
> Later, i ran a EM with the whole system, with the respective output:
> Steepest Descents converged to machine precision in 2081 steps,
> but did not reach the requested Fmax < 10.
> Potential Energy = -2.6833109e+05
> Maximum force = 3.5193942e+02 on atom 3598
> Norm of force = 6.2432761e+00,
>
> Sadly, when i'm trying to perform an equilibration i got the following error 
> message:
> Step 10:
> Atom 8449 moved more than the distance allowed by the domain decomposition 
> (1.59) in direction Z
> distance out of cell 1330.886108
> Old coordinates: 1.667 4.809 0.710
> New coordinates: -1840.027 -454.814 1335.667
> Old cell boundaries in direction Z: 0.000 5.000
> New cell boundaries in direction Z: 0.000 4.781
> 
> Program mdrun, VERSION 5.0.4
> Source code file: 
> /home/krlitros87/Downloads/gromacs-5.0.4/src/gromacs/mdlib/domdec.c, line: 
> 4390
>
> Fatal error:
> An atom moved too far between two domain decomposition steps
> This usually means that your system is not well equilibrated
> For more information and tips for troubleshooting, please check the GROMACS
> we

Re: [gmx-users] System blowing up - equilibration step - CG simulation

[Carlos Navarro Retamal]

Dear Justin,
Thanks for your kind reply.
Is there a way to set up a bilayer membrane system without a protein using 
insane? I’ve already several CG simulations with this protein, so i'm pretty 
sure that its parameters are ok. I do have some issues with the glycolipid used 
(MGDG) This is the first time i used the parameters gotten from 
http://md.chem.rug.nl/cgmartini/images/parameters/ITP/martini_v2.0_glycolipids.itp
so i don’t know if this kind of molecules requieres an specific temperature 
(for example)
Best regards,
Carlos
--
Carlos Navarro Retamal
Bioinformatics Engineering
Ph. D (c) Applied Sciences.
Center of Bioinformatics and Molecular Simulations. CBSM
University of Talca
Av. Lircay S/N, Talca, Chile
T: (+56) 712201 798
E: carlos.navarr...@gmail.com or cnava...@utalca.cl



On March 6, 2015 at 11:56:01 AM, Justin Lemkul 
(jalem...@vt.edu) wrote:


On 3/6/15 8:15 AM, Carlos Navarro Retamal wrote:
> Dear Gromacs users,
> I'm trying to perform a CG simulations of a system consisting in a protein 
> locate at 5 nm with respect to the charged groups of a MGDG membrane.
> I first performed an EM in vaccum.
> After that, to constructed the system i use insane.py as following:
> ./insane.py -f minimization-vaccum.gro -o system.gro -pbc square -dm 5 -box 
> 10,10,10 -l MGDG -sol W -orient
>
> Later, i ran a EM with the whole system, with the respective output:
> Steepest Descents converged to machine precision in 2081 steps,
> but did not reach the requested Fmax < 10.
> Potential Energy = -2.6833109e+05
> Maximum force = 3.5193942e+02 on atom 3598
> Norm of force = 6.2432761e+00,
>
> Sadly, when i'm trying to perform an equilibration i got the following error 
> message:
> Step 10:
> Atom 8449 moved more than the distance allowed by the domain decomposition 
> (1.59) in direction Z
> distance out of cell 1330.886108
> Old coordinates: 1.667 4.809 0.710
> New coordinates: -1840.027 -454.814 1335.667
> Old cell boundaries in direction Z: 0.000 5.000
> New cell boundaries in direction Z: 0.000 4.781
> 
> Program mdrun, VERSION 5.0.4
> Source code file: 
> /home/krlitros87/Downloads/gromacs-5.0.4/src/gromacs/mdlib/domdec.c, line: 
> 4390
>
> Fatal error:
> An atom moved too far between two domain decomposition steps
> This usually means that your system is not well equilibrated
> For more information and tips for troubleshooting, please check the GROMACS
> website at 
> www.gromacs.org/Documentation/Errors
>
>
> This is the .mdp file:
> define = -DPOSRES
> dt = 0.02
> cutoff-scheme = group
> nsteps = 50
> nstxout = 0
> nstvout = 0
> nstlog = 100
> nstxtcout = 100
> xtc-precision = 10

Any reason to sacrifice so much precision? Maybe for a CG system it doesn't
matter so much.

> rlist = 1.4
> coulombtype = shift
> rcoulomb = 1.2
> epsilon_r = 15
> vdw-type = shift
> rvdw-switch = 0.9
> rvdw = 1.2
> tcoupl = Berendsen
> tc-grps = Protein MGDG W ION

Coupling water and ions separately is generally unstable.

> tau-t = 1.0 1.0 1.0 1.0
> ref-t = 323 323 323 323
> Pcoupl = Berendsen

If NPT is failing, reduce complexity and start by equilibrating with NVT.

> Pcoupltype = isotropic
> tau-p = 5.0
> compressibility = 3e-4
> ref-p = 1.0
> refcoord_scaling = all

Try refcoord-scaling = com; the all option can be unstable.

>
> I know that my system is blowing up, but what can i do to avoid this issue? I 
> tried increasing the EM step without luck.

What about all the rest of the advice at
http://www.gromacs.org/Documentation/Terminology/Blowing_Up? Your EM seems
fine, so I doubt that's it. Something is either unstable in the topology or the
dynamics. Split the system into parts to make sure you can stably simulate
everything - protein in water, membrane alone, etc.

-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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Re: [gmx-users] System blowing up - equilibration step - CG simulation

[Justin Lemkul]

On 3/6/15 8:15 AM, Carlos Navarro Retamal wrote:

Dear Gromacs users,
I'm trying to perform a CG simulations of a system consisting in a protein 
locate at 5 nm with respect to the charged groups of a MGDG membrane.
I first performed an EM in vaccum.
After that, to constructed the system i use insane.py as following:
./insane.py -f minimization-vaccum.gro -o system.gro -pbc square -dm 5 -box 
10,10,10 -l MGDG -sol W -orient

Later, i ran a EM with the whole system, with the respective output:
Steepest Descents converged to machine precision in 2081 steps,
but did not reach the requested Fmax < 10.
Potential Energy = -2.6833109e+05
Maximum force = 3.5193942e+02 on atom 3598
Norm of force = 6.2432761e+00,

Sadly, when i'm trying to perform an equilibration i got the following error 
message:
Step 10:
Atom 8449 moved more than the distance allowed by the domain decomposition 
(1.59) in direction Z
distance out of cell 1330.886108
Old coordinates: 1.667 4.809 0.710
New coordinates: -1840.027 -454.814 1335.667
Old cell boundaries in direction Z: 0.000 5.000
New cell boundaries in direction Z: 0.000 4.781

Program mdrun, VERSION 5.0.4
Source code file: 
/home/krlitros87/Downloads/gromacs-5.0.4/src/gromacs/mdlib/domdec.c, line: 4390

Fatal error:
An atom moved too far between two domain decomposition steps
This usually means that your system is not well equilibrated
For more information and tips for troubleshooting, please check the GROMACS
website at 
www.gromacs.org/Documentation/Errors


This is the .mdp file:
define = -DPOSRES
dt = 0.02
cutoff-scheme = group
nsteps = 50
nstxout = 0
nstvout = 0
nstlog = 100
nstxtcout = 100
xtc-precision = 10


Any reason to sacrifice so much precision?  Maybe for a CG system it doesn't 
matter so much.



rlist = 1.4
coulombtype = shift
rcoulomb = 1.2
epsilon_r = 15
vdw-type = shift
rvdw-switch = 0.9
rvdw = 1.2
tcoupl = Berendsen
tc-grps = Protein MGDG W ION


Coupling water and ions separately is generally unstable.


tau-t = 1.0 1.0 1.0 1.0
ref-t = 323 323 323 323
Pcoupl = Berendsen


If NPT is failing, reduce complexity and start by equilibrating with NVT.


Pcoupltype = isotropic
tau-p = 5.0
compressibility = 3e-4
ref-p = 1.0
refcoord_scaling = all


Try refcoord-scaling = com; the all option can be unstable.



I know that my system is blowing up, but what can i do to avoid this issue? I 
tried increasing the EM step without luck.


What about all the rest of the advice at 
http://www.gromacs.org/Documentation/Terminology/Blowing_Up?  Your EM seems 
fine, so I doubt that's it.  Something is either unstable in the topology or the 
dynamics.  Split the system into parts to make sure you can stably simulate 
everything - protein in water, membrane alone, etc.


-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

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[gmx-users] System blowing up - equilibration step - CG simulation

[Carlos Navarro Retamal]

Dear Gromacs users,
I'm trying to perform a CG simulations of a system consisting in a protein 
locate at 5 nm with respect to the charged groups of a MGDG membrane.
I first performed an EM in vaccum.
After that, to constructed the system i use insane.py as following:
./insane.py -f minimization-vaccum.gro -o system.gro -pbc square -dm 5 -box 
10,10,10 -l MGDG -sol W -orient

Later, i ran a EM with the whole system, with the respective output:
Steepest Descents converged to machine precision in 2081 steps,
but did not reach the requested Fmax < 10.
Potential Energy = -2.6833109e+05
Maximum force = 3.5193942e+02 on atom 3598
Norm of force = 6.2432761e+00,

Sadly, when i'm trying to perform an equilibration i got the following error 
message:
Step 10:
Atom 8449 moved more than the distance allowed by the domain decomposition 
(1.59) in direction Z
distance out of cell 1330.886108
Old coordinates: 1.667 4.809 0.710
New coordinates: -1840.027 -454.814 1335.667
Old cell boundaries in direction Z: 0.000 5.000
New cell boundaries in direction Z: 0.000 4.781

Program mdrun, VERSION 5.0.4
Source code file: 
/home/krlitros87/Downloads/gromacs-5.0.4/src/gromacs/mdlib/domdec.c, line: 4390

Fatal error:
An atom moved too far between two domain decomposition steps
This usually means that your system is not well equilibrated
For more information and tips for troubleshooting, please check the GROMACS
website at 
www.gromacs.org/Documentation/Errors


This is the .mdp file:
define = -DPOSRES
dt = 0.02
cutoff-scheme = group
nsteps = 50
nstxout = 0
nstvout = 0
nstlog = 100
nstxtcout = 100
xtc-precision = 10
rlist = 1.4
coulombtype = shift
rcoulomb = 1.2
epsilon_r = 15
vdw-type = shift
rvdw-switch = 0.9
rvdw = 1.2
tcoupl = Berendsen
tc-grps = Protein MGDG W ION
tau-t = 1.0 1.0 1.0 1.0
ref-t = 323 323 323 323
Pcoupl = Berendsen
Pcoupltype = isotropic
tau-p = 5.0
compressibility = 3e-4
ref-p = 1.0
refcoord_scaling = all

I know that my system is blowing up, but what can i do to avoid this issue? I 
tried increasing the EM step without luck.
If you need more info related my problem please let me know.
Hope someone can help me.
Best regards,
Carlos

--
Carlos Navarro Retamal
Bioinformatics Engineering
Ph. D (c) Applied Sciences.
Center of Bioinformatics and Molecular Simulations. CBSM
University of Talca
Av. Lircay S/N, Talca, Chile
T: (+56) 712201 798
E: carlos.navarr...@gmail.com or cnava...@utalca.cl

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