Re: [gmx-users] LINCS warning during energy minimization of nitrogen with virtual site

2017-08-02 Thread Justin Lemkul 



On 8/2/17 9:12 AM, Ali Ahmed wrote:

Dear all,
Thank you for helping me. All I get from grompp is this
--

gmx grompp -f grompp.mdp -c N2_box.gro -po mdout.mdp -p topol.top -o
topol.tpr

Ignoring obsolete mdp entry 'title'
Ignoring obsolete mdp entry 'cpp'

Back Off! I just backed up mdout.mdp to ./#mdout.mdp.2#

NOTE 1 [file grompp.mdp]:
   The group cutoff scheme is deprecated since GROMACS 5.0 and will be
   removed in a future release when all interaction forms are supported for
   the verlet scheme. The verlet scheme already scales better, and it is
   compatible with GPUs and other accelerators.

Setting the LD random seed to 1000542586
Generated 120 of the 120 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 120 of the 120 1-4 parameter combinations
Excluding 2 bonded neighbours molecule type 'N_2'
Cleaning up constraints and constant bonded interactions with virtual sites
Analysing residue names:
There are:  2493  Other residues


Simplify your system - work with one molecule and print out the forces at each 
step to see if there is something haywire going on.


-Justin


Analysing residues not classified as Protein/DNA/RNA/Water and splitting
into groups...
Number of degrees of freedom in T-Coupling group System is 12462.00

NOTE 2 [file grompp.mdp]:
   You are using a plain Coulomb cut-off, which might produce artifacts.
   You might want to consider using PME electrostatics.


Largest charge group radii for Van der Waals: 0.056, 0.056 nm
Largest charge group radii for Coulomb:   0.056, 0.056 nm
This run will generate roughly 90 Mb of data

There were 2 notes

Back Off! I just backed up topol.tpr to ./#topol.tpr.1#

gcq#454: "I never see what has been done; I only see what remains to be
done." (Marie Curie)


On Tue, Aug 1, 2017 at 5:08 PM, Justin Lemkul  wrote:




On 8/1/17 6:07 PM, Ali Ahmed wrote:


Dear Dr. Dallas,
Thank you for your reply. Actually, I'm new to GROMACS and
I appreciate your support.


--
Here is what I get before crashing. Too many warning then crush.



This is not diagnostic of anything useful.  You've been asked several
times to provide the output of grompp, not mdrun.  The grompp output can be
suggestive of issues you may not have considered.

-Justin


Step 37, time 0.037 (ps)  LINCS WARNING


relative constraint deviation after LINCS:

rms 0.002768, max 0.195102 (between atoms 34930 and 34931)

bonds that rotated more than 30 degrees:

   atom 1 atom 2  angle  previous, current, constraint length

  193194   51.70.1100   0.1100  0.1100

54409  54410   32.30.1100   0.1100  0.1100

On Tue, Aug 1, 2017 at 4:49 PM, Dallas Warren 
wrote:

Copy the output from both of those commands, most importantly (as Mark

has asked) that from the first one gmx grompp

You need to show people exactly what you are seeing, not what you say
you are seeing.  The latter you are filtering it, and most likely not
providing all the important information.  The former allows those
trying to help to see all the information that they need to see.
Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.war...@monash.edu
-
When the only tool you own is a hammer, every problem begins to resemble
a
nail.


On 2 August 2017 at 04:05, Ali Ahmed  wrote:


Hi,
Thank you for your help.

well I used this command

gmx grompp -f em.mdp -c box.gro -p topol.top -o em.tpr
gmx mdrun -v -deffnm em

and I got all the warnings. Here is my em.mdp



-



integrator = steep

emtol   = 10.0

emstep  = 0.001

nsteps  = 5

energygrps   = system

; Parameters describing how to find the neighbors of each atom and how
to
calculate the interactions

nstlist   = 1

cutoff-scheme   = group

ns_type= grid

coulombtype= PME

rcoulomb = 1.0

rvdw= 1.0

pbc  = xyz

On Tue, Aug 1, 2017 at 11:07 AM, Mark Abraham  wrote:

Dear Mark

Yes, all the warnings are from grompp.
I have no idea where is the problem in the structure or the topology
Thank you

On Mon, Jul 31, 2017 at 2:34 PM, Mark

Re: [gmx-users] LINCS warning during energy minimization of nitrogen with virtual site

2017-08-02 Thread Ali Ahmed 
Dear all,
Thank you for helping me. All I get from grompp is this
--

gmx grompp -f grompp.mdp -c N2_box.gro -po mdout.mdp -p topol.top -o
topol.tpr

Ignoring obsolete mdp entry 'title'
Ignoring obsolete mdp entry 'cpp'

Back Off! I just backed up mdout.mdp to ./#mdout.mdp.2#

NOTE 1 [file grompp.mdp]:
  The group cutoff scheme is deprecated since GROMACS 5.0 and will be
  removed in a future release when all interaction forms are supported for
  the verlet scheme. The verlet scheme already scales better, and it is
  compatible with GPUs and other accelerators.

Setting the LD random seed to 1000542586
Generated 120 of the 120 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 120 of the 120 1-4 parameter combinations
Excluding 2 bonded neighbours molecule type 'N_2'
Cleaning up constraints and constant bonded interactions with virtual sites
Analysing residue names:
There are:  2493  Other residues
Analysing residues not classified as Protein/DNA/RNA/Water and splitting
into groups...
Number of degrees of freedom in T-Coupling group System is 12462.00

NOTE 2 [file grompp.mdp]:
  You are using a plain Coulomb cut-off, which might produce artifacts.
  You might want to consider using PME electrostatics.


Largest charge group radii for Van der Waals: 0.056, 0.056 nm
Largest charge group radii for Coulomb:   0.056, 0.056 nm
This run will generate roughly 90 Mb of data

There were 2 notes

Back Off! I just backed up topol.tpr to ./#topol.tpr.1#

gcq#454: "I never see what has been done; I only see what remains to be
done." (Marie Curie)


On Tue, Aug 1, 2017 at 5:08 PM, Justin Lemkul  wrote:

>
>
> On 8/1/17 6:07 PM, Ali Ahmed wrote:
>
>> Dear Dr. Dallas,
>> Thank you for your reply. Actually, I'm new to GROMACS and
>> I appreciate your support.
>> 
>> 
>> --
>> Here is what I get before crashing. Too many warning then crush.
>>
>>
> This is not diagnostic of anything useful.  You've been asked several
> times to provide the output of grompp, not mdrun.  The grompp output can be
> suggestive of issues you may not have considered.
>
> -Justin
>
>
> Step 37, time 0.037 (ps)  LINCS WARNING
>>
>> relative constraint deviation after LINCS:
>>
>> rms 0.002768, max 0.195102 (between atoms 34930 and 34931)
>>
>> bonds that rotated more than 30 degrees:
>>
>>   atom 1 atom 2  angle  previous, current, constraint length
>>
>>  193194   51.70.1100   0.1100  0.1100
>>
>>54409  54410   32.30.1100   0.1100  0.1100
>>
>> On Tue, Aug 1, 2017 at 4:49 PM, Dallas Warren 
>> wrote:
>>
>> Copy the output from both of those commands, most importantly (as Mark
>>> has asked) that from the first one gmx grompp
>>>
>>> You need to show people exactly what you are seeing, not what you say
>>> you are seeing.  The latter you are filtering it, and most likely not
>>> providing all the important information.  The former allows those
>>> trying to help to see all the information that they need to see.
>>> Catch ya,
>>>
>>> Dr. Dallas Warren
>>> Drug Delivery, Disposition and Dynamics
>>> Monash Institute of Pharmaceutical Sciences, Monash University
>>> 381 Royal Parade, Parkville VIC 3052
>>> dallas.war...@monash.edu
>>> -
>>> When the only tool you own is a hammer, every problem begins to resemble
>>> a
>>> nail.
>>>
>>>
>>> On 2 August 2017 at 04:05, Ali Ahmed  wrote:
>>>
 Hi,
 Thank you for your help.

 well I used this command

 gmx grompp -f em.mdp -c box.gro -p topol.top -o em.tpr
 gmx mdrun -v -deffnm em

 and I got all the warnings. Here is my em.mdp
 

>>> -
>>>

 integrator = steep

 emtol   = 10.0

 emstep  = 0.001

 nsteps  = 5

 energygrps   = system

 ; Parameters describing how to find the neighbors of each atom and how
 to
 calculate the interactions

 nstlist   = 1

 cutoff-scheme   = group

 ns_type= grid

 coulombtype= PME

 rcoulomb = 1.0

 rvdw= 1.0

 pbc  = xyz

 On Tue, Aug 1, 2017 at 11:07 AM, Mark Abraham 
 wrote:

 Hi,
>
> No, only mdrun issues LINCS warnings. grompp issues different warnings,
>
 and
>>>
 I would like you to check whether you had any from grompp that you may
>
 not
>>>
 have considered. :-)
>
> Mark
>
> On

Re: [gmx-users] LINCS warning during energy minimization of nitrogen with virtual site

2017-08-01 Thread Justin Lemkul 



On 8/1/17 6:07 PM, Ali Ahmed wrote:

Dear Dr. Dallas,
Thank you for your reply. Actually, I'm new to GROMACS and
I appreciate your support.
--
Here is what I get before crashing. Too many warning then crush.



This is not diagnostic of anything useful.  You've been asked several times to 
provide the output of grompp, not mdrun.  The grompp output can be suggestive of 
issues you may not have considered.


-Justin


Step 37, time 0.037 (ps)  LINCS WARNING

relative constraint deviation after LINCS:

rms 0.002768, max 0.195102 (between atoms 34930 and 34931)

bonds that rotated more than 30 degrees:

  atom 1 atom 2  angle  previous, current, constraint length

 193194   51.70.1100   0.1100  0.1100

   54409  54410   32.30.1100   0.1100  0.1100

On Tue, Aug 1, 2017 at 4:49 PM, Dallas Warren 
wrote:


Copy the output from both of those commands, most importantly (as Mark
has asked) that from the first one gmx grompp

You need to show people exactly what you are seeing, not what you say
you are seeing.  The latter you are filtering it, and most likely not
providing all the important information.  The former allows those
trying to help to see all the information that they need to see.
Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.war...@monash.edu
-
When the only tool you own is a hammer, every problem begins to resemble a
nail.


On 2 August 2017 at 04:05, Ali Ahmed  wrote:

Hi,
Thank you for your help.

well I used this command

gmx grompp -f em.mdp -c box.gro -p topol.top -o em.tpr
gmx mdrun -v -deffnm em

and I got all the warnings. Here is my em.mdp


-


integrator = steep

emtol   = 10.0

emstep  = 0.001

nsteps  = 5

energygrps   = system

; Parameters describing how to find the neighbors of each atom and how to
calculate the interactions

nstlist   = 1

cutoff-scheme   = group

ns_type= grid

coulombtype= PME

rcoulomb = 1.0

rvdw= 1.0

pbc  = xyz

On Tue, Aug 1, 2017 at 11:07 AM, Mark Abraham 
wrote:


Hi,

No, only mdrun issues LINCS warnings. grompp issues different warnings,

and

I would like you to check whether you had any from grompp that you may

not

have considered. :-)

Mark

On Tue, Aug 1, 2017 at 5:04 PM Ali Ahmed  wrote:


Dear Mark
Yes, all the warnings are from grompp.
I have no idea where is the problem in the structure or the topology
Thank you

On Mon, Jul 31, 2017 at 2:34 PM, Mark Abraham <

mark.j.abra...@gmail.com>

wrote:


Hi,

Did you get any warnings from grompp?

Mark

On Mon, Jul 31, 2017 at 5:48 PM Ali Ahmed 

wrote:



Hello GROMACS users,

I'm doing MD for nitrogen, and for better electrostatic

interactions

I

need

to use massless and charged virtual site. I did that but when I

try

to

do

energy minimization gives me LINCS warning and crush. I don't know

where

is

the error I tried a lot but could not find a solution.
Anyone has an idea where is my error

Here is the topology file (hand written)

--

[ defaults ]

1 3 yes 0.5 0.5



;


[ atomtypes ]

; name  bond_typemasscharge   ptype  sigma

epsilon


   OP   OP0.000   0.000A  0.330

0.3062

;

nitrogen

   M  M  0.000   0.000V  0.000

0.000

;

virtual site







[ moleculetype ]

; name  nrexcl

N2 2



[ atoms ]

;   nr   typeresnr residue  atom   cgnr   charge mass

  1 OP  1N2 N1  1-0.482

14.0067


  2 M 1N2 M1  1 0.964 0.000

  3 OP   1N2 N2  1-0.482

  14.0067




[ constraints ]

; the N-N is fixed

 1   3   1   0.11



[ virtual_sites2 ]

; site  ai  aj  funct   a

  2   1   3  1   0.5000  ; right in the mid





[ system ]

N2 in vacuo



[ molecules ]

N2 1500


--

Here is the structure (N2.pdb)

---

TITLE N2 with dummy masses

REMARKTHIS IS A SIMULATION BOX

MODEL1

COMPNDUNNAMED

AUTHORGENERATED BY OPEN BABEL 2.3.2

CRYST1   50.000   50.000   50.000

Re: [gmx-users] LINCS warning during energy minimization of nitrogen with virtual site

2017-08-01 Thread Ali Ahmed 
Dear Dr. Dallas,
Thank you for your reply. Actually, I'm new to GROMACS and
I appreciate your support.
--
Here is what I get before crashing. Too many warning then crush.

Step 37, time 0.037 (ps)  LINCS WARNING

relative constraint deviation after LINCS:

rms 0.002768, max 0.195102 (between atoms 34930 and 34931)

bonds that rotated more than 30 degrees:

 atom 1 atom 2  angle  previous, current, constraint length

193194   51.70.1100   0.1100  0.1100

  54409  54410   32.30.1100   0.1100  0.1100

On Tue, Aug 1, 2017 at 4:49 PM, Dallas Warren 
wrote:

> Copy the output from both of those commands, most importantly (as Mark
> has asked) that from the first one gmx grompp
>
> You need to show people exactly what you are seeing, not what you say
> you are seeing.  The latter you are filtering it, and most likely not
> providing all the important information.  The former allows those
> trying to help to see all the information that they need to see.
> Catch ya,
>
> Dr. Dallas Warren
> Drug Delivery, Disposition and Dynamics
> Monash Institute of Pharmaceutical Sciences, Monash University
> 381 Royal Parade, Parkville VIC 3052
> dallas.war...@monash.edu
> -
> When the only tool you own is a hammer, every problem begins to resemble a
> nail.
>
>
> On 2 August 2017 at 04:05, Ali Ahmed  wrote:
> > Hi,
> > Thank you for your help.
> >
> > well I used this command
> >
> > gmx grompp -f em.mdp -c box.gro -p topol.top -o em.tpr
> > gmx mdrun -v -deffnm em
> >
> > and I got all the warnings. Here is my em.mdp
> > 
> -
> >
> > integrator = steep
> >
> > emtol   = 10.0
> >
> > emstep  = 0.001
> >
> > nsteps  = 5
> >
> > energygrps   = system
> >
> > ; Parameters describing how to find the neighbors of each atom and how to
> > calculate the interactions
> >
> > nstlist   = 1
> >
> > cutoff-scheme   = group
> >
> > ns_type= grid
> >
> > coulombtype= PME
> >
> > rcoulomb = 1.0
> >
> > rvdw= 1.0
> >
> > pbc  = xyz
> >
> > On Tue, Aug 1, 2017 at 11:07 AM, Mark Abraham 
> > wrote:
> >
> >> Hi,
> >>
> >> No, only mdrun issues LINCS warnings. grompp issues different warnings,
> and
> >> I would like you to check whether you had any from grompp that you may
> not
> >> have considered. :-)
> >>
> >> Mark
> >>
> >> On Tue, Aug 1, 2017 at 5:04 PM Ali Ahmed  wrote:
> >>
> >> > Dear Mark
> >> > Yes, all the warnings are from grompp.
> >> > I have no idea where is the problem in the structure or the topology
> >> > Thank you
> >> >
> >> > On Mon, Jul 31, 2017 at 2:34 PM, Mark Abraham <
> mark.j.abra...@gmail.com>
> >> > wrote:
> >> >
> >> > > Hi,
> >> > >
> >> > > Did you get any warnings from grompp?
> >> > >
> >> > > Mark
> >> > >
> >> > > On Mon, Jul 31, 2017 at 5:48 PM Ali Ahmed 
> wrote:
> >> > >
> >> > > > Hello GROMACS users,
> >> > > >
> >> > > > I'm doing MD for nitrogen, and for better electrostatic
> interactions
> >> I
> >> > > need
> >> > > > to use massless and charged virtual site. I did that but when I
> try
> >> to
> >> > do
> >> > > > energy minimization gives me LINCS warning and crush. I don't know
> >> > where
> >> > > is
> >> > > > the error I tried a lot but could not find a solution.
> >> > > > Anyone has an idea where is my error
> >> > > >
> >> > > > Here is the topology file (hand written)
> >> > > >
> >> > > > --
> >> > > >
> >> > > > [ defaults ]
> >> > > >
> >> > > > 1 3 yes 0.5 0.5
> >> > > >
> >> > > > 
> >> > > ;
> >> > > >
> >> > > > [ atomtypes ]
> >> > > >
> >> > > > ; name  bond_typemasscharge   ptype  sigma
> >> epsilon
> >> > > >
> >> > > >   OP   OP0.000   0.000A  0.330
> >> 0.3062
> >> > ;
> >> > > > nitrogen
> >> > > >
> >> > > >   M  M  0.000   0.000V  0.000
> >> > 0.000
> >> > > ;
> >> > > > virtual site
> >> > > >
> >> > > >
> >> > > > 
> >> > > 
> >> > > >
> >> > > > [ moleculetype ]
> >> > > >
> >> > > > ; name  nrexcl
> >> > > >
> >> > > > N2 2
> >> > > >
> >> > > >
> >> > > >
> >> > > > [ atoms ]
> >> > > >
> >> > > > ;   nr   typeresnr residue  atom   cgnr   charge mass
> >> > > >
> >> > > >  1 OP  1N2 N1  1-0.482
> 14.0067
> >> > > >
> >> > > >  2 M 1N2 M1  1 0.964 0.000
> >> > > >
> >> > > >

Re: [gmx-users] LINCS warning during energy minimization of nitrogen with virtual site

2017-08-01 Thread Dallas Warren 
Copy the output from both of those commands, most importantly (as Mark
has asked) that from the first one gmx grompp

You need to show people exactly what you are seeing, not what you say
you are seeing.  The latter you are filtering it, and most likely not
providing all the important information.  The former allows those
trying to help to see all the information that they need to see.
Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.war...@monash.edu
-
When the only tool you own is a hammer, every problem begins to resemble a nail.


On 2 August 2017 at 04:05, Ali Ahmed  wrote:
> Hi,
> Thank you for your help.
>
> well I used this command
>
> gmx grompp -f em.mdp -c box.gro -p topol.top -o em.tpr
> gmx mdrun -v -deffnm em
>
> and I got all the warnings. Here is my em.mdp
> -
>
> integrator = steep
>
> emtol   = 10.0
>
> emstep  = 0.001
>
> nsteps  = 5
>
> energygrps   = system
>
> ; Parameters describing how to find the neighbors of each atom and how to
> calculate the interactions
>
> nstlist   = 1
>
> cutoff-scheme   = group
>
> ns_type= grid
>
> coulombtype= PME
>
> rcoulomb = 1.0
>
> rvdw= 1.0
>
> pbc  = xyz
>
> On Tue, Aug 1, 2017 at 11:07 AM, Mark Abraham 
> wrote:
>
>> Hi,
>>
>> No, only mdrun issues LINCS warnings. grompp issues different warnings, and
>> I would like you to check whether you had any from grompp that you may not
>> have considered. :-)
>>
>> Mark
>>
>> On Tue, Aug 1, 2017 at 5:04 PM Ali Ahmed  wrote:
>>
>> > Dear Mark
>> > Yes, all the warnings are from grompp.
>> > I have no idea where is the problem in the structure or the topology
>> > Thank you
>> >
>> > On Mon, Jul 31, 2017 at 2:34 PM, Mark Abraham 
>> > wrote:
>> >
>> > > Hi,
>> > >
>> > > Did you get any warnings from grompp?
>> > >
>> > > Mark
>> > >
>> > > On Mon, Jul 31, 2017 at 5:48 PM Ali Ahmed  wrote:
>> > >
>> > > > Hello GROMACS users,
>> > > >
>> > > > I'm doing MD for nitrogen, and for better electrostatic interactions
>> I
>> > > need
>> > > > to use massless and charged virtual site. I did that but when I try
>> to
>> > do
>> > > > energy minimization gives me LINCS warning and crush. I don't know
>> > where
>> > > is
>> > > > the error I tried a lot but could not find a solution.
>> > > > Anyone has an idea where is my error
>> > > >
>> > > > Here is the topology file (hand written)
>> > > >
>> > > > --
>> > > >
>> > > > [ defaults ]
>> > > >
>> > > > 1 3 yes 0.5 0.5
>> > > >
>> > > > 
>> > > ;
>> > > >
>> > > > [ atomtypes ]
>> > > >
>> > > > ; name  bond_typemasscharge   ptype  sigma
>> epsilon
>> > > >
>> > > >   OP   OP0.000   0.000A  0.330
>> 0.3062
>> > ;
>> > > > nitrogen
>> > > >
>> > > >   M  M  0.000   0.000V  0.000
>> > 0.000
>> > > ;
>> > > > virtual site
>> > > >
>> > > >
>> > > > 
>> > > 
>> > > >
>> > > > [ moleculetype ]
>> > > >
>> > > > ; name  nrexcl
>> > > >
>> > > > N2 2
>> > > >
>> > > >
>> > > >
>> > > > [ atoms ]
>> > > >
>> > > > ;   nr   typeresnr residue  atom   cgnr   charge mass
>> > > >
>> > > >  1 OP  1N2 N1  1-0.482  14.0067
>> > > >
>> > > >  2 M 1N2 M1  1 0.964 0.000
>> > > >
>> > > >  3 OP   1N2 N2  1-0.482 14.0067
>> > > >
>> > > >
>> > > >
>> > > > [ constraints ]
>> > > >
>> > > > ; the N-N is fixed
>> > > >
>> > > > 1   3   1   0.11
>> > > >
>> > > >
>> > > >
>> > > > [ virtual_sites2 ]
>> > > >
>> > > > ; site  ai  aj  funct   a
>> > > >
>> > > >  2   1   3  1   0.5000  ; right in the mid
>> > > >
>> > > >
>> > > >
>> > > > 
>> > > >
>> > > > [ system ]
>> > > >
>> > > > N2 in vacuo
>> > > >
>> > > >
>> > > >
>> > > > [ molecules ]
>> > > >
>> > > > N2 1500
>> > > >
>> > > > 
>> > > > --
>> > > >
>> > > > Here is the structure (N2.pdb)
>> > > >
>> > > > ---
>> > > >
>> > > > TITLE N2 with dummy masses
>> > > >
>> > > > REMARKTHIS IS A SIMULATION BOX
>> > > >
>> > > > MODEL1
>> > > >
>> > > > COMPNDUNNAMED
>> > > >
>> > > > AUTHORGENERATED BY OPEN BABEL 2.3.2
>> > > >
>> > > > CRYST1   50.000   50.000   50.000  90.00

Re: [gmx-users] LINCS warning during energy minimization of nitrogen with virtual site

2017-08-01 Thread Ali Ahmed 
Hi,
Thank you for your help.

well I used this command

gmx grompp -f em.mdp -c box.gro -p topol.top -o em.tpr
gmx mdrun -v -deffnm em

and I got all the warnings. Here is my em.mdp
-

integrator = steep

emtol   = 10.0

emstep  = 0.001

nsteps  = 5

energygrps   = system

; Parameters describing how to find the neighbors of each atom and how to
calculate the interactions

nstlist   = 1

cutoff-scheme   = group

ns_type= grid

coulombtype= PME

rcoulomb = 1.0

rvdw= 1.0

pbc  = xyz

On Tue, Aug 1, 2017 at 11:07 AM, Mark Abraham 
wrote:

> Hi,
>
> No, only mdrun issues LINCS warnings. grompp issues different warnings, and
> I would like you to check whether you had any from grompp that you may not
> have considered. :-)
>
> Mark
>
> On Tue, Aug 1, 2017 at 5:04 PM Ali Ahmed  wrote:
>
> > Dear Mark
> > Yes, all the warnings are from grompp.
> > I have no idea where is the problem in the structure or the topology
> > Thank you
> >
> > On Mon, Jul 31, 2017 at 2:34 PM, Mark Abraham 
> > wrote:
> >
> > > Hi,
> > >
> > > Did you get any warnings from grompp?
> > >
> > > Mark
> > >
> > > On Mon, Jul 31, 2017 at 5:48 PM Ali Ahmed  wrote:
> > >
> > > > Hello GROMACS users,
> > > >
> > > > I'm doing MD for nitrogen, and for better electrostatic interactions
> I
> > > need
> > > > to use massless and charged virtual site. I did that but when I try
> to
> > do
> > > > energy minimization gives me LINCS warning and crush. I don't know
> > where
> > > is
> > > > the error I tried a lot but could not find a solution.
> > > > Anyone has an idea where is my error
> > > >
> > > > Here is the topology file (hand written)
> > > >
> > > > --
> > > >
> > > > [ defaults ]
> > > >
> > > > 1 3 yes 0.5 0.5
> > > >
> > > > 
> > > ;
> > > >
> > > > [ atomtypes ]
> > > >
> > > > ; name  bond_typemasscharge   ptype  sigma
> epsilon
> > > >
> > > >   OP   OP0.000   0.000A  0.330
> 0.3062
> > ;
> > > > nitrogen
> > > >
> > > >   M  M  0.000   0.000V  0.000
> > 0.000
> > > ;
> > > > virtual site
> > > >
> > > >
> > > > 
> > > 
> > > >
> > > > [ moleculetype ]
> > > >
> > > > ; name  nrexcl
> > > >
> > > > N2 2
> > > >
> > > >
> > > >
> > > > [ atoms ]
> > > >
> > > > ;   nr   typeresnr residue  atom   cgnr   charge mass
> > > >
> > > >  1 OP  1N2 N1  1-0.482  14.0067
> > > >
> > > >  2 M 1N2 M1  1 0.964 0.000
> > > >
> > > >  3 OP   1N2 N2  1-0.482 14.0067
> > > >
> > > >
> > > >
> > > > [ constraints ]
> > > >
> > > > ; the N-N is fixed
> > > >
> > > > 1   3   1   0.11
> > > >
> > > >
> > > >
> > > > [ virtual_sites2 ]
> > > >
> > > > ; site  ai  aj  funct   a
> > > >
> > > >  2   1   3  1   0.5000  ; right in the mid
> > > >
> > > >
> > > >
> > > > 
> > > >
> > > > [ system ]
> > > >
> > > > N2 in vacuo
> > > >
> > > >
> > > >
> > > > [ molecules ]
> > > >
> > > > N2 1500
> > > >
> > > > 
> > > > --
> > > >
> > > > Here is the structure (N2.pdb)
> > > >
> > > > ---
> > > >
> > > > TITLE N2 with dummy masses
> > > >
> > > > REMARKTHIS IS A SIMULATION BOX
> > > >
> > > > MODEL1
> > > >
> > > > COMPNDUNNAMED
> > > >
> > > > AUTHORGENERATED BY OPEN BABEL 2.3.2
> > > >
> > > > CRYST1   50.000   50.000   50.000  90.00  90.00  90.00 P 1 1
> > > >
> > > > ATOM  1  N1  N2  1   0.000   0.000   0.000  1.00
> > > > 0.00   N
> > > >
> > > > ATOM  2  M1  N2  1   0.55000   0.000   0.000  1.00
> > > > 0.00  Xx
> > > >
> > > > ATOM  3  N2  N2  1   1.100   0.000   0.000  1.00
> > > > 0.00   N
> > > >
> > > > CONECT13
> > > >
> > > > CONECT31
> > > >
> > > > MASTER00000000303
> 0
> > > >
> > > > END0
> > > >
> > > > 
> > > > -
> > > > Thank you
> > > > --
> > > > 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
> > >

Re: [gmx-users] LINCS warning during energy minimization of nitrogen with virtual site

2017-08-01 Thread Ali Ahmed 
Dear Mark
Yes, all the warnings are from grompp.
I have no idea where is the problem in the structure or the topology
Thank you

On Mon, Jul 31, 2017 at 2:34 PM, Mark Abraham 
wrote:

> Hi,
>
> Did you get any warnings from grompp?
>
> Mark
>
> On Mon, Jul 31, 2017 at 5:48 PM Ali Ahmed  wrote:
>
> > Hello GROMACS users,
> >
> > I'm doing MD for nitrogen, and for better electrostatic interactions I
> need
> > to use massless and charged virtual site. I did that but when I try to do
> > energy minimization gives me LINCS warning and crush. I don't know where
> is
> > the error I tried a lot but could not find a solution.
> > Anyone has an idea where is my error
> >
> > Here is the topology file (hand written)
> >
> > --
> >
> > [ defaults ]
> >
> > 1 3 yes 0.5 0.5
> >
> > 
> ;
> >
> > [ atomtypes ]
> >
> > ; name  bond_typemasscharge   ptype  sigma  epsilon
> >
> >   OP   OP0.000   0.000A  0.330  0.3062 ;
> > nitrogen
> >
> >   M  M  0.000   0.000V  0.000  0.000
> ;
> > virtual site
> >
> >
> > 
> 
> >
> > [ moleculetype ]
> >
> > ; name  nrexcl
> >
> > N2 2
> >
> >
> >
> > [ atoms ]
> >
> > ;   nr   typeresnr residue  atom   cgnr   charge mass
> >
> >  1 OP  1N2 N1  1-0.482  14.0067
> >
> >  2 M 1N2 M1  1 0.964 0.000
> >
> >  3 OP   1N2 N2  1-0.482 14.0067
> >
> >
> >
> > [ constraints ]
> >
> > ; the N-N is fixed
> >
> > 1   3   1   0.11
> >
> >
> >
> > [ virtual_sites2 ]
> >
> > ; site  ai  aj  funct   a
> >
> >  2   1   3  1   0.5000  ; right in the mid
> >
> >
> >
> > 
> >
> > [ system ]
> >
> > N2 in vacuo
> >
> >
> >
> > [ molecules ]
> >
> > N2 1500
> >
> > 
> > --
> >
> > Here is the structure (N2.pdb)
> >
> > ---
> >
> > TITLE N2 with dummy masses
> >
> > REMARKTHIS IS A SIMULATION BOX
> >
> > MODEL1
> >
> > COMPNDUNNAMED
> >
> > AUTHORGENERATED BY OPEN BABEL 2.3.2
> >
> > CRYST1   50.000   50.000   50.000  90.00  90.00  90.00 P 1 1
> >
> > ATOM  1  N1  N2  1   0.000   0.000   0.000  1.00
> > 0.00   N
> >
> > ATOM  2  M1  N2  1   0.55000   0.000   0.000  1.00
> > 0.00  Xx
> >
> > ATOM  3  N2  N2  1   1.100   0.000   0.000  1.00
> > 0.00   N
> >
> > CONECT13
> >
> > CONECT31
> >
> > MASTER000000003030
> >
> > END0
> >
> > 
> > -
> > Thank you
> > --
> > 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.
> >
> --
> 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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>
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Re: [gmx-users] LINCS warning during energy minimization of nitrogen with virtual site

2017-07-31 Thread Mark Abraham 
Hi,

Did you get any warnings from grompp?

Mark

On Mon, Jul 31, 2017 at 5:48 PM Ali Ahmed  wrote:

> Hello GROMACS users,
>
> I'm doing MD for nitrogen, and for better electrostatic interactions I need
> to use massless and charged virtual site. I did that but when I try to do
> energy minimization gives me LINCS warning and crush. I don't know where is
> the error I tried a lot but could not find a solution.
> Anyone has an idea where is my error
>
> Here is the topology file (hand written)
>
> --
>
> [ defaults ]
>
> 1 3 yes 0.5 0.5
>
> ;
>
> [ atomtypes ]
>
> ; name  bond_typemasscharge   ptype  sigma  epsilon
>
>   OP   OP0.000   0.000A  0.330  0.3062 ;
> nitrogen
>
>   M  M  0.000   0.000V  0.000  0.000 ;
> virtual site
>
>
> 
>
> [ moleculetype ]
>
> ; name  nrexcl
>
> N2 2
>
>
>
> [ atoms ]
>
> ;   nr   typeresnr residue  atom   cgnr   charge mass
>
>  1 OP  1N2 N1  1-0.482  14.0067
>
>  2 M 1N2 M1  1 0.964 0.000
>
>  3 OP   1N2 N2  1-0.482 14.0067
>
>
>
> [ constraints ]
>
> ; the N-N is fixed
>
> 1   3   1   0.11
>
>
>
> [ virtual_sites2 ]
>
> ; site  ai  aj  funct   a
>
>  2   1   3  1   0.5000  ; right in the mid
>
>
>
> 
>
> [ system ]
>
> N2 in vacuo
>
>
>
> [ molecules ]
>
> N2 1500
>
> 
> --
>
> Here is the structure (N2.pdb)
>
> ---
>
> TITLE N2 with dummy masses
>
> REMARKTHIS IS A SIMULATION BOX
>
> MODEL1
>
> COMPNDUNNAMED
>
> AUTHORGENERATED BY OPEN BABEL 2.3.2
>
> CRYST1   50.000   50.000   50.000  90.00  90.00  90.00 P 1 1
>
> ATOM  1  N1  N2  1   0.000   0.000   0.000  1.00
> 0.00   N
>
> ATOM  2  M1  N2  1   0.55000   0.000   0.000  1.00
> 0.00  Xx
>
> ATOM  3  N2  N2  1   1.100   0.000   0.000  1.00
> 0.00   N
>
> CONECT13
>
> CONECT31
>
> MASTER000000003030
>
> END0
>
> 
> -
> Thank you
> --
> 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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[gmx-users] LINCS warning during energy minimization of nitrogen with virtual site

2017-07-31 Thread Ali Ahmed 
Hello GROMACS users,

I'm doing MD for nitrogen, and for better electrostatic interactions I need
to use massless and charged virtual site. I did that but when I try to do
energy minimization gives me LINCS warning and crush. I don't know where is
the error I tried a lot but could not find a solution.
Anyone has an idea where is my error

Here is the topology file (hand written)

--

[ defaults ]

1 3 yes 0.5 0.5

;

[ atomtypes ]

; name  bond_typemasscharge   ptype  sigma  epsilon

  OP   OP0.000   0.000A  0.330  0.3062 ;
nitrogen

  M  M  0.000   0.000V  0.000  0.000 ;
virtual site



[ moleculetype ]

; name  nrexcl

N2 2



[ atoms ]

;   nr   typeresnr residue  atom   cgnr   charge mass

 1 OP  1N2 N1  1-0.482  14.0067

 2 M 1N2 M1  1 0.964 0.000

 3 OP   1N2 N2  1-0.482 14.0067



[ constraints ]

; the N-N is fixed

1   3   1   0.11



[ virtual_sites2 ]

; site  ai  aj  funct   a

 2   1   3  1   0.5000  ; right in the mid





[ system ]

N2 in vacuo



[ molecules ]

N2 1500


--

Here is the structure (N2.pdb)

---

TITLE N2 with dummy masses

REMARKTHIS IS A SIMULATION BOX

MODEL1

COMPNDUNNAMED

AUTHORGENERATED BY OPEN BABEL 2.3.2

CRYST1   50.000   50.000   50.000  90.00  90.00  90.00 P 1 1

ATOM  1  N1  N2  1   0.000   0.000   0.000  1.00
0.00   N

ATOM  2  M1  N2  1   0.55000   0.000   0.000  1.00
0.00  Xx

ATOM  3  N2  N2  1   1.100   0.000   0.000  1.00
0.00   N

CONECT13

CONECT31

MASTER000000003030

END0


-
Thank you
-- 
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