subject:"\[gmx\-users\] Energy minimization"

Thanks a lot Justinn and Mark for the valuable suggestions.

I will start over again by choosing a force field which is suitable for the
RNA molecules.




*Anurag Dobhal*
*Graduate Student (Bioprocess Technology)*
*Institute of Chemical Technology, Mumbai*
*Contact: +91 8898486877*


On Thu, Jun 23, 2016 at 4:55 PM, Justin Lemkul  wrote:

>
>
> On 6/23/16 7:17 AM, Anurag Dobhal wrote:
>
>> Dear Justin,
>>
>> The main aim of the study is to study the interaction between a polymer
>> (chitosan) and RNA molecules by simulating them togather. I have already
>> successfully simulated my polymer system using OPLS AA force field.
>>
>> To simulate them together I need to write the OPLS AA parameters for RNA
>> molecules. I was suggested (Link Below) earlier that I can take the
>> charges
>> from any other forcefield.
>>
>> (http://permalink.gmane.org/gmane.science.biology.gromacs.user/85228)
>>
>> please enlight me where I am going wrong.
>>
>>
> I think you misunderstood what I said in that thread.
>
>
> https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2016-June/106520.html
>
> "You should find force field parameters specifically for the base from
> published literature or from another force field."
>
> This means: find a force field that has parametrized the species you need
> and use it.  This does not mean: hack together something from "any other
> force field" you like and try to make it OPLS-AA.  You did not say before
> that you were dealing with a complex system like this.  You just said your
> guanine charges didn't add up.  So I addressed that problem.
>
> Putting CHARMM27 charges into the OPLS-AA force field is unequivocally an
> invalid approach.
>
> Pick a force field.  Use that force field.  Do not try to kludge together
> some hybrid entity.  Force fields are designed to be internally
> self-consistent.  If you do not have a proper balance of interactions, you
> are not doing a useful simulation.  You are generating random numbers.
>
>
> -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
>
> ==
> --
> 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] Energy minimization has stopped




On 6/23/16 7:17 AM, Anurag Dobhal wrote:

Dear Justin,

The main aim of the study is to study the interaction between a polymer
(chitosan) and RNA molecules by simulating them togather. I have already
successfully simulated my polymer system using OPLS AA force field.

To simulate them together I need to write the OPLS AA parameters for RNA
molecules. I was suggested (Link Below) earlier that I can take the charges
from any other forcefield.

(http://permalink.gmane.org/gmane.science.biology.gromacs.user/85228)

please enlight me where I am going wrong.



I think you misunderstood what I said in that thread.

https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2016-June/106520.html

"You should find force field parameters specifically for the base from published 
literature or from another force field."


This means: find a force field that has parametrized the species you need and 
use it.  This does not mean: hack together something from "any other force 
field" you like and try to make it OPLS-AA.  You did not say before that you 
were dealing with a complex system like this.  You just said your guanine 
charges didn't add up.  So I addressed that problem.


Putting CHARMM27 charges into the OPLS-AA force field is unequivocally an 
invalid approach.


Pick a force field.  Use that force field.  Do not try to kludge together some 
hybrid entity.  Force fields are designed to be internally self-consistent.  If 
you do not have a proper balance of interactions, you are not doing a useful 
simulation.  You are generating random numbers.


-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

==
--
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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Re: [gmx-users] Energy minimization has stopped

2016-06-23 Thread Mark Abraham

Hi,

You were recommended to pick a force field, not to combine parts of force
fields. Choosing to simulate your polymer OPLS/AA if you then want to
combine with RNA is not a good experimental design, unless you can do the
combined simulation also in OPLS/AA. I would repeat the polymer experiment
in whatever forcefield is also good for the experiment with RNA.

Mark

On Thu, Jun 23, 2016 at 1:18 PM Anurag Dobhal <
anurag.dob...@nano-medicine.co.in> wrote:

> Dear Justin,
>
> The main aim of the study is to study the interaction between a polymer
> (chitosan) and RNA molecules by simulating them togather. I have already
> successfully simulated my polymer system using OPLS AA force field.
>
> To simulate them together I need to write the OPLS AA parameters for RNA
> molecules. I was suggested (Link Below) earlier that I can take the charges
> from any other forcefield.
>
> (http://permalink.gmane.org/gmane.science.biology.gromacs.user/85228)
>
> please enlight me where I am going wrong.
>
> Thank You
>
>
>
>
>
>
>
>
> *Anurag Dobhal*
> *Graduate Student (Bioprocess Technology)*
> *Institute of Chemical Technology, Mumbai*
> *Contact: +91 8898486877*
>
>
> On Thu, Jun 23, 2016 at 4:33 PM, Justin Lemkul  wrote:
>
> >
> >
> > On 6/23/16 7:00 AM, Anurag Dobhal wrote:
> >
> >> I am using OPLS AA force field. parameters (charges) for the atoms are
> >> taken from the charmm27 force field.
> >>
> >>
> > So, by using some hybridized force field, you can't successfully minimize
> > a structure.  That should tell you something.  Why are you trying to do
> > this, and what leads you to believe that some hybrid OPLS/CHARMM
> > combination is even sensible?  You can't just mix the charges from one
> > force field with another to create some kind of Frankenforcefield.
> >
> > Recent RNA force fields like CHARMM36 and recent AMBER updates are highly
> > optimized for RNA simulations.
> >
> > -Justin
> >
> >
> >>
> >>
> >> *Anurag Dobhal*
> >> *Graduate Student (Bioprocess Technology)*
> >> *Institute of Chemical Technology, Mumbai*
> >> *Contact: +91 8898486877*
> >>
> >>
> >>
> >> On Thu, Jun 23, 2016 at 4:15 PM, Justin Lemkul  wrote:
> >>
> >>
> >>>
> >>> On 6/23/16 6:44 AM, Justin Lemkul wrote:
> >>>
> >>>
> 
>  On 6/23/16 6:35 AM, Anurag Dobhal wrote:
> 
>  Dear Gromacs Users, I am Simulating a  RNA molecule using OPLS AA
> force
> > field. I have written parameters using CHARMM27 force field for RNA
> > molecules.
> >
> >
> > What does this mean?  Are you using OPLS-AA or CHARMM27?
> 
> 
>  Also, if you are actually using CHARMM27, don't.  CHARMM36 is vastly
> >>> superior for RNA.
> >>>
> >>> -Justin
> >>>
> >>>
> >>> Minimising the molecule by invoking mdrun gives me the follwoing error.
> >>>
> 
> > Energy minimization has stopped, but the forces have not converged to
> > the
> > requested precision Fmax < 1000 (which may not be possible for your
> > system).
> > It stopped because the algorithm tried to make a new step whose size
> > was
> > too
> > small, or there was no change in the energy since last step. Either
> > way,
> > we
> > regard the minimization as converged to within the available machine
> > precision, given your starting configuration and EM parameters.
> >
> > Double precision normally gives you higher accuracy, but this is
> often
> > not
> > needed for preparing to run molecular dynamics.
> > You might need to increase your constraint accuracy, or turn
> > off constraints altogether (set constraints = none in mdp file)
> >
> >
> >
> >
> -
> >
> > The contents of the .mdp file are the following
> >
> > ; minim.mdp - used as input into grompp to generate em.tpr
> > integrator = steep ; Algorithm (steep = steepest descent
> minimization)
> > emtol = 1000.0   ; Stop minimization when the maximum force < 1000.0
> > kJ/mol/nm
> > emstep  = 0.01  ; Energy step size
> > nsteps = 5   ; Maximum number of (minimization) steps to perform
> >
> > ; 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)
> > coulombtype= PME ; Treatment of long range electrostatic
> > interactions
> > rcoulomb= 1.0 ; Short-range electrostatic cut-off
> > rvdw= 1.0 ; Short-range Van der Waals cut-off
> > pbc= xyz ; Periodic Boundary Conditions (yes/no)
> >
> > any suggestions ?
> >
> >
> >
> 
> 
>

Re: [gmx-users] Energy minimization has stopped

Dear Justin,

The main aim of the study is to study the interaction between a polymer
(chitosan) and RNA molecules by simulating them togather. I have already
successfully simulated my polymer system using OPLS AA force field.

To simulate them together I need to write the OPLS AA parameters for RNA
molecules. I was suggested (Link Below) earlier that I can take the charges
from any other forcefield.

(http://permalink.gmane.org/gmane.science.biology.gromacs.user/85228)

please enlight me where I am going wrong.

Thank You








*Anurag Dobhal*
*Graduate Student (Bioprocess Technology)*
*Institute of Chemical Technology, Mumbai*
*Contact: +91 8898486877*


On Thu, Jun 23, 2016 at 4:33 PM, Justin Lemkul  wrote:

>
>
> On 6/23/16 7:00 AM, Anurag Dobhal wrote:
>
>> I am using OPLS AA force field. parameters (charges) for the atoms are
>> taken from the charmm27 force field.
>>
>>
> So, by using some hybridized force field, you can't successfully minimize
> a structure.  That should tell you something.  Why are you trying to do
> this, and what leads you to believe that some hybrid OPLS/CHARMM
> combination is even sensible?  You can't just mix the charges from one
> force field with another to create some kind of Frankenforcefield.
>
> Recent RNA force fields like CHARMM36 and recent AMBER updates are highly
> optimized for RNA simulations.
>
> -Justin
>
>
>>
>>
>> *Anurag Dobhal*
>> *Graduate Student (Bioprocess Technology)*
>> *Institute of Chemical Technology, Mumbai*
>> *Contact: +91 8898486877*
>>
>>
>>
>> On Thu, Jun 23, 2016 at 4:15 PM, Justin Lemkul  wrote:
>>
>>
>>>
>>> On 6/23/16 6:44 AM, Justin Lemkul wrote:
>>>
>>>

 On 6/23/16 6:35 AM, Anurag Dobhal wrote:

 Dear Gromacs Users, I am Simulating a  RNA molecule using OPLS AA force
> field. I have written parameters using CHARMM27 force field for RNA
> molecules.
>
>
> What does this mean?  Are you using OPLS-AA or CHARMM27?


 Also, if you are actually using CHARMM27, don't.  CHARMM36 is vastly
>>> superior for RNA.
>>>
>>> -Justin
>>>
>>>
>>> Minimising the molecule by invoking mdrun gives me the follwoing error.
>>>

> Energy minimization has stopped, but the forces have not converged to
> the
> requested precision Fmax < 1000 (which may not be possible for your
> system).
> It stopped because the algorithm tried to make a new step whose size
> was
> too
> small, or there was no change in the energy since last step. Either
> way,
> we
> regard the minimization as converged to within the available machine
> precision, given your starting configuration and EM parameters.
>
> Double precision normally gives you higher accuracy, but this is often
> not
> needed for preparing to run molecular dynamics.
> You might need to increase your constraint accuracy, or turn
> off constraints altogether (set constraints = none in mdp file)
>
>
>
> -
>
> The contents of the .mdp file are the following
>
> ; minim.mdp - used as input into grompp to generate em.tpr
> integrator = steep ; Algorithm (steep = steepest descent minimization)
> emtol = 1000.0   ; Stop minimization when the maximum force < 1000.0
> kJ/mol/nm
> emstep  = 0.01  ; Energy step size
> nsteps = 5   ; Maximum number of (minimization) steps to perform
>
> ; 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)
> coulombtype= PME ; Treatment of long range electrostatic
> interactions
> rcoulomb= 1.0 ; Short-range electrostatic cut-off
> rvdw= 1.0 ; Short-range Van der Waals cut-off
> pbc= xyz ; Periodic Boundary Conditions (yes/no)
>
> any suggestions ?
>
>
>

 http://www.gromacs.org/Documentation/Errors#Stepsize_too_small.2c_or_no_change_in_energy._Converged_to_machine_precision.2c_but_not_to_the_requested_precision


 mdrun prints which atom is feeling the maximum force, so that's a good
 place to
 start looking to see if there is an actual problem.

 -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
>>>
>>>

Re: [gmx-users] Energy minimization has stopped

On 6/23/16 7:00 AM, Anurag Dobhal wrote:

I am using OPLS AA force field. parameters (charges) for the atoms are
taken from the charmm27 force field.

So, by using some hybridized force field, you can't successfully minimize a
structure. That should tell you something. Why are you trying to do this, and
what leads you to believe that some hybrid OPLS/CHARMM combination is even
sensible? You can't just mix the charges from one force field with another to
create some kind of Frankenforcefield.

Recent RNA force fields like CHARMM36 and recent AMBER updates are highly
optimized for RNA simulations.

-Justin

*Anurag Dobhal*
*Graduate Student (Bioprocess Technology)*
*Institute of Chemical Technology, Mumbai*
*Contact: +91 8898486877*

On Thu, Jun 23, 2016 at 4:15 PM, Justin Lemkul wrote:

On 6/23/16 6:44 AM, Justin Lemkul wrote:

On 6/23/16 6:35 AM, Anurag Dobhal wrote:

Dear Gromacs Users, I am Simulating a RNA molecule using OPLS AA force
field. I have written parameters using CHARMM27 force field for RNA
molecules.

What does this mean? Are you using OPLS-AA or CHARMM27?

Also, if you are actually using CHARMM27, don't. CHARMM36 is vastly
superior for RNA.

-Justin

Minimising the molecule by invoking mdrun gives me the follwoing error.

Energy minimization has stopped, but the forces have not converged to the
requested precision Fmax < 1000 (which may not be possible for your
system).
It stopped because the algorithm tried to make a new step whose size was
too
small, or there was no change in the energy since last step. Either way,
we
regard the minimization as converged to within the available machine
precision, given your starting configuration and EM parameters.

Double precision normally gives you higher accuracy, but this is often
not
needed for preparing to run molecular dynamics.
You might need to increase your constraint accuracy, or turn
off constraints altogether (set constraints = none in mdp file)

The contents of the .mdp file are the following

; minim.mdp - used as input into grompp to generate em.tpr
integrator = steep ; Algorithm (steep = steepest descent minimization)
emtol = 1000.0 ; Stop minimization when the maximum force < 1000.0
kJ/mol/nm
emstep = 0.01 ; Energy step size
nsteps = 5 ; Maximum number of (minimization) steps to perform

; 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)
coulombtype= PME ; Treatment of long range electrostatic interactions
rcoulomb= 1.0 ; Short-range electrostatic cut-off
rvdw= 1.0 ; Short-range Van der Waals cut-off
pbc= xyz ; Periodic Boundary Conditions (yes/no)

any suggestions ?

http://www.gromacs.org/Documentation/Errors#Stepsize_too_small.2c_or_no_change_in_energy._Converged_to_machine_precision.2c_but_not_to_the_requested_precision

mdrun prints which atom is feeling the maximum force, so that's a good
place to
start looking to see if there is an actual problem.

-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

==
--
Gromacs Users mailing list

* Please search the archive at
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posting!

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

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

--
==

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
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* 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] Energy minimization has stopped

I am using OPLS AA force field. parameters (charges) for the atoms are
taken from the charmm27 force field.




*Anurag Dobhal*
*Graduate Student (Bioprocess Technology)*
*Institute of Chemical Technology, Mumbai*
*Contact: +91 8898486877*


On Thu, Jun 23, 2016 at 4:15 PM, Justin Lemkul  wrote:

>
>
> On 6/23/16 6:44 AM, Justin Lemkul wrote:
>
>>
>>
>> On 6/23/16 6:35 AM, Anurag Dobhal wrote:
>>
>>> Dear Gromacs Users, I am Simulating a  RNA molecule using OPLS AA force
>>> field. I have written parameters using CHARMM27 force field for RNA
>>> molecules.
>>>
>>>
>> What does this mean?  Are you using OPLS-AA or CHARMM27?
>>
>>
> Also, if you are actually using CHARMM27, don't.  CHARMM36 is vastly
> superior for RNA.
>
> -Justin
>
>
> Minimising the molecule by invoking mdrun gives me the follwoing error.
>>>
>>> Energy minimization has stopped, but the forces have not converged to the
>>> requested precision Fmax < 1000 (which may not be possible for your
>>> system).
>>> It stopped because the algorithm tried to make a new step whose size was
>>> too
>>> small, or there was no change in the energy since last step. Either way,
>>> we
>>> regard the minimization as converged to within the available machine
>>> precision, given your starting configuration and EM parameters.
>>>
>>> Double precision normally gives you higher accuracy, but this is often
>>> not
>>> needed for preparing to run molecular dynamics.
>>> You might need to increase your constraint accuracy, or turn
>>> off constraints altogether (set constraints = none in mdp file)
>>>
>>>
>>> -
>>>
>>> The contents of the .mdp file are the following
>>>
>>> ; minim.mdp - used as input into grompp to generate em.tpr
>>> integrator = steep ; Algorithm (steep = steepest descent minimization)
>>> emtol = 1000.0   ; Stop minimization when the maximum force < 1000.0
>>> kJ/mol/nm
>>> emstep  = 0.01  ; Energy step size
>>> nsteps = 5   ; Maximum number of (minimization) steps to perform
>>>
>>> ; 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)
>>> coulombtype= PME ; Treatment of long range electrostatic interactions
>>> rcoulomb= 1.0 ; Short-range electrostatic cut-off
>>> rvdw= 1.0 ; Short-range Van der Waals cut-off
>>> pbc= xyz ; Periodic Boundary Conditions (yes/no)
>>>
>>> any suggestions ?
>>>
>>>
>>
>> http://www.gromacs.org/Documentation/Errors#Stepsize_too_small.2c_or_no_change_in_energy._Converged_to_machine_precision.2c_but_not_to_the_requested_precision
>>
>>
>> mdrun prints which atom is feeling the maximum force, so that's a good
>> place to
>> start looking to see if there is an actual problem.
>>
>> -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
>
> ==
> --
> 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.
>

-- 


*DISCLAIMER:*

*This communication is intended only for the person or entity to which it 
is addressed and may contain confidential and / or privileged material. Any 
review, retransmission, dissemination or other use is prohibited. If you 
have received this in error, please contact the sender and delete this 
material from your computer. Any comments or statements made herein do not 
necessarily reflect those of Nanomedicine Research Group.  Before opening 
the email or accessing any attachments, please check and scan for virus.*
-- 
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] Energy minimization has stopped




On 6/23/16 6:44 AM, Justin Lemkul wrote:



On 6/23/16 6:35 AM, Anurag Dobhal wrote:

Dear Gromacs Users, I am Simulating a  RNA molecule using OPLS AA force
field. I have written parameters using CHARMM27 force field for RNA
molecules.



What does this mean?  Are you using OPLS-AA or CHARMM27?



Also, if you are actually using CHARMM27, don't.  CHARMM36 is vastly superior 
for RNA.


-Justin


Minimising the molecule by invoking mdrun gives me the follwoing error.

Energy minimization has stopped, but the forces have not converged to the
requested precision Fmax < 1000 (which may not be possible for your system).
It stopped because the algorithm tried to make a new step whose size was too
small, or there was no change in the energy since last step. Either way, we
regard the minimization as converged to within the available machine
precision, given your starting configuration and EM parameters.

Double precision normally gives you higher accuracy, but this is often not
needed for preparing to run molecular dynamics.
You might need to increase your constraint accuracy, or turn
off constraints altogether (set constraints = none in mdp file)

-

The contents of the .mdp file are the following

; minim.mdp - used as input into grompp to generate em.tpr
integrator = steep ; Algorithm (steep = steepest descent minimization)
emtol = 1000.0   ; Stop minimization when the maximum force < 1000.0
kJ/mol/nm
emstep  = 0.01  ; Energy step size
nsteps = 5   ; Maximum number of (minimization) steps to perform

; 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)
coulombtype= PME ; Treatment of long range electrostatic interactions
rcoulomb= 1.0 ; Short-range electrostatic cut-off
rvdw= 1.0 ; Short-range Van der Waals cut-off
pbc= xyz ; Periodic Boundary Conditions (yes/no)

any suggestions ?



http://www.gromacs.org/Documentation/Errors#Stepsize_too_small.2c_or_no_change_in_energy._Converged_to_machine_precision.2c_but_not_to_the_requested_precision


mdrun prints which atom is feeling the maximum force, so that's a good place to
start looking to see if there is an actual problem.

-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] Energy minimization has stopped




On 6/23/16 6:35 AM, Anurag Dobhal wrote:

Dear Gromacs Users, I am Simulating a  RNA molecule using OPLS AA force
field. I have written parameters using CHARMM27 force field for RNA
molecules.



What does this mean?  Are you using OPLS-AA or CHARMM27?


Minimising the molecule by invoking mdrun gives me the follwoing error.

Energy minimization has stopped, but the forces have not converged to the
requested precision Fmax < 1000 (which may not be possible for your system).
It stopped because the algorithm tried to make a new step whose size was too
small, or there was no change in the energy since last step. Either way, we
regard the minimization as converged to within the available machine
precision, given your starting configuration and EM parameters.

Double precision normally gives you higher accuracy, but this is often not
needed for preparing to run molecular dynamics.
You might need to increase your constraint accuracy, or turn
off constraints altogether (set constraints = none in mdp file)

-
The contents of the .mdp file are the following

; minim.mdp - used as input into grompp to generate em.tpr
integrator = steep ; Algorithm (steep = steepest descent minimization)
emtol = 1000.0   ; Stop minimization when the maximum force < 1000.0
kJ/mol/nm
emstep  = 0.01  ; Energy step size
nsteps = 5   ; Maximum number of (minimization) steps to perform

; 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)
coulombtype= PME ; Treatment of long range electrostatic interactions
rcoulomb= 1.0 ; Short-range electrostatic cut-off
rvdw= 1.0 ; Short-range Van der Waals cut-off
pbc= xyz ; Periodic Boundary Conditions (yes/no)

any suggestions ?



http://www.gromacs.org/Documentation/Errors#Stepsize_too_small.2c_or_no_change_in_energy._Converged_to_machine_precision.2c_but_not_to_the_requested_precision

mdrun prints which atom is feeling the maximum force, so that's a good place to 
start looking to see if there is an actual problem.


-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] Energy minimization has stopped

Dear Gromacs Users, I am Simulating a  RNA molecule using OPLS AA force
field. I have written parameters using CHARMM27 force field for RNA
molecules.

Minimising the molecule by invoking mdrun gives me the follwoing error.

Energy minimization has stopped, but the forces have not converged to the
requested precision Fmax < 1000 (which may not be possible for your system).
It stopped because the algorithm tried to make a new step whose size was too
small, or there was no change in the energy since last step. Either way, we
regard the minimization as converged to within the available machine
precision, given your starting configuration and EM parameters.

Double precision normally gives you higher accuracy, but this is often not
needed for preparing to run molecular dynamics.
You might need to increase your constraint accuracy, or turn
off constraints altogether (set constraints = none in mdp file)

-
The contents of the .mdp file are the following

; minim.mdp - used as input into grompp to generate em.tpr
integrator = steep ; Algorithm (steep = steepest descent minimization)
emtol = 1000.0   ; Stop minimization when the maximum force < 1000.0
kJ/mol/nm
emstep  = 0.01  ; Energy step size
nsteps = 5   ; Maximum number of (minimization) steps to perform

; 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)
coulombtype= PME ; Treatment of long range electrostatic interactions
rcoulomb= 1.0 ; Short-range electrostatic cut-off
rvdw= 1.0 ; Short-range Van der Waals cut-off
pbc= xyz ; Periodic Boundary Conditions (yes/no)

any suggestions ?


*Anurag Dobhal*
*Graduate Student (Bioprocess Technology)*
*Institute of Chemical Technology, Mumbai*

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Re: [gmx-users] energy minimization error

2015-10-23 Thread faride badalkhani

Hi,

Thanks a lot for your time and patience. This time, I chose a very simple
structure and then inspected the generated topology. The interesting point
was that, there were some missing interactions. When I inspected them. I
found that I had defined those interactions in ffbonded.itp file, but
pdb2gmx has not assigned those definitions to these interactions. However,
I added the appropriate gb_, ga_, or gd_ manually, and then performed the
MD simulations and received an error as follows:

Step=  210, Dmax= 6.6e-03 nm, Epot= -8.80977e+04 Fmax= 1.48278e+05, atom= 46
Step=  212, Dmax= 4.0e-03 nm, Epot= -8.90453e+04 Fmax= 1.76644e+05, atom= 44
Step=  216, Dmax= 5.9e-04 nm, Epot= -8.90760e+04 Fmax= 1.48643e+05, atom= 46
Step=  218, Dmax= 3.6e-04 nm, Epot= -8.91295e+04 Fmax= 1.75349e+05, atom= 44
Step=  221, Dmax= 1.1e-04 nm, Epot= -8.91493e+04 Fmax= 1.48437e+05, atom= 46
Step=  224, Dmax= 3.2e-05 nm, Epot= -8.91556e+04 Fmax= 1.74146e+05, atom= 44
Step=  227, Dmax= 9.6e-06 nm, Epot= -8.91559e+04 Fmax= 1.51118e+05, atom= 46
Step=  229, Dmax= 5.8e-06 nm, Epot= -8.91570e+04 Fmax= 1.71312e+05, atom= 44
Step=  232, Dmax= 1.7e-06 nm, Epot= -8.91571e+04 Fmax= 1.54271e+05, atom= 46
Step=  234, Dmax= 1.0e-06 nm, Epot= -8.91572e+04 Fmax= 1.70893e+05, atom= 44
Step=  235, Dmax= 1.2e-06 nm, Epot= -8.91570e+04 Fmax= 1.57473e+05, atom= 46
Energy minimization has stopped, but the forces have not converged to the
requested precision Fmax < 100 (which may not be possible for your system).
It stopped because the algorithm tried to make a new step whose size was too
small, or there was no change in the energy since last step. Either way, we
regard the minimization as converged to within the available machine
precision, given your starting configuration and EM parameters.

Double precision normally gives you higher accuracy, but this is often not
needed for preparing to run molecular dynamics.
You might need to increase your constraint accuracy, or turn
off constraints altogether (set constraints = none in mdp file)

writing lowest energy coordinates.

Steepest Descents converged to machine precision in 236 steps,
but did not reach the requested Fmax < 100.
Potential Energy  = -8.9157188e+04
Maximum force =  1.7089320e+05 on atom 44
Norm of force =  3.3110510e+03

gcq#220: "Let's Go Hang Out In a Mall" (LIVE)

farideh@farideh-P61A-D3:~/multiple/G0$

you can access all the files via the following link:
https://www.dropbox.com/s/m1kxafyu1n749hb/G0.zip?dl=0

Truly yours,
Farideh

On Thu, Oct 22, 2015 at 11:24 AM, Mark Abraham 
wrote:

> Hi,
>
> Did you inspect your topology like I suggested? You need to know that there
> are bonds exactly where you intend them, before doing any calculations with
> them.
>
> Mark
>
> On Thu, Oct 22, 2015 at 9:35 AM faride badalkhani <
> farideh.kham...@gmail.com>
> wrote:
>
> > Hi,
> >
> > I am trying to simulate a hyper-branched polymer (a dendrimer) in water.
> > But, every time the system blows up at energy minimization step.
> Therefore,
> > according to what Mark had recommended I decided to start with a much
> > smaller dendrimer (i.e. G1 PAMAM dendrimer) , rather than a G3 one. I had
> > optimized it at M062x/6-31G* level, before starting the MD simulations.
> > Then, I generated .pdb file from .log (Gaussian 09) file, and sorted it
> > residue by residue. After that, I started simulation procedure and
> > continued step by step. In spite of G3 PAMAM dendrimer I didn't face any
> > errors in energy minimization step, and the potential energy - EM step
> plot
> > was reasonable. But, when I loaded em.gro file in VMD, the structure was
> > completely messed up as in G3 dendrimer. This time I continued the MD
> > simulation until production MD, and there was no error. However, the
> system
> > is blown up. You can access all the simulation files, pdb structure, and
> > the photos of G1 structure before and after EM step via:
> >
> > https://www.dropbox.com/s/sdggfaklg530hq0/G1.zip?dl=0
> >
> > Since I am a beginner in this area, I do not know what is the solution
> for
> > this problem.
> > Do you think errors that occur during the G3 simulation are relevant to
> the
> > initial structure?
> > any suggestion or recommendation is appreciated.
> >
> > Thanks in advance
> > Farideh
> > --
> > 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] energy minimization error

2015-10-23 Thread Mark Abraham

Hi,

pdb2gmx and grompp are pretty talkative about things like missing
parameters and bonds - go back and read what they had to say, and
particularly what pdb2gmx thought about your specbonds.

Mark

On Fri, Oct 23, 2015 at 5:51 PM faride badalkhani 
wrote:

> Hi,
>
> Thanks a lot for your time and patience. This time, I chose a very simple
> structure and then inspected the generated topology. The interesting point
> was that, there were some missing interactions. When I inspected them. I
> found that I had defined those interactions in ffbonded.itp file, but
> pdb2gmx has not assigned those definitions to these interactions. However,
> I added the appropriate gb_, ga_, or gd_ manually, and then performed the
> MD simulations and received an error as follows:
>
> Step=  210, Dmax= 6.6e-03 nm, Epot= -8.80977e+04 Fmax= 1.48278e+05, atom=
> 46
> Step=  212, Dmax= 4.0e-03 nm, Epot= -8.90453e+04 Fmax= 1.76644e+05, atom=
> 44
> Step=  216, Dmax= 5.9e-04 nm, Epot= -8.90760e+04 Fmax= 1.48643e+05, atom=
> 46
> Step=  218, Dmax= 3.6e-04 nm, Epot= -8.91295e+04 Fmax= 1.75349e+05, atom=
> 44
> Step=  221, Dmax= 1.1e-04 nm, Epot= -8.91493e+04 Fmax= 1.48437e+05, atom=
> 46
> Step=  224, Dmax= 3.2e-05 nm, Epot= -8.91556e+04 Fmax= 1.74146e+05, atom=
> 44
> Step=  227, Dmax= 9.6e-06 nm, Epot= -8.91559e+04 Fmax= 1.51118e+05, atom=
> 46
> Step=  229, Dmax= 5.8e-06 nm, Epot= -8.91570e+04 Fmax= 1.71312e+05, atom=
> 44
> Step=  232, Dmax= 1.7e-06 nm, Epot= -8.91571e+04 Fmax= 1.54271e+05, atom=
> 46
> Step=  234, Dmax= 1.0e-06 nm, Epot= -8.91572e+04 Fmax= 1.70893e+05, atom=
> 44
> Step=  235, Dmax= 1.2e-06 nm, Epot= -8.91570e+04 Fmax= 1.57473e+05, atom=
> 46
> Energy minimization has stopped, but the forces have not converged to the
> requested precision Fmax < 100 (which may not be possible for your system).
> It stopped because the algorithm tried to make a new step whose size was
> too
> small, or there was no change in the energy since last step. Either way, we
> regard the minimization as converged to within the available machine
> precision, given your starting configuration and EM parameters.
>
> Double precision normally gives you higher accuracy, but this is often not
> needed for preparing to run molecular dynamics.
> You might need to increase your constraint accuracy, or turn
> off constraints altogether (set constraints = none in mdp file)
>
> writing lowest energy coordinates.
>
> Steepest Descents converged to machine precision in 236 steps,
> but did not reach the requested Fmax < 100.
> Potential Energy  = -8.9157188e+04
> Maximum force =  1.7089320e+05 on atom 44
> Norm of force =  3.3110510e+03
>
> gcq#220: "Let's Go Hang Out In a Mall" (LIVE)
>
> farideh@farideh-P61A-D3:~/multiple/G0$
>
> you can access all the files via the following link:
> https://www.dropbox.com/s/m1kxafyu1n749hb/G0.zip?dl=0
>
> Truly yours,
> Farideh
>
> On Thu, Oct 22, 2015 at 11:24 AM, Mark Abraham 
> wrote:
>
> > Hi,
> >
> > Did you inspect your topology like I suggested? You need to know that
> there
> > are bonds exactly where you intend them, before doing any calculations
> with
> > them.
> >
> > Mark
> >
> > On Thu, Oct 22, 2015 at 9:35 AM faride badalkhani <
> > farideh.kham...@gmail.com>
> > wrote:
> >
> > > Hi,
> > >
> > > I am trying to simulate a hyper-branched polymer (a dendrimer) in
> water.
> > > But, every time the system blows up at energy minimization step.
> > Therefore,
> > > according to what Mark had recommended I decided to start with a much
> > > smaller dendrimer (i.e. G1 PAMAM dendrimer) , rather than a G3 one. I
> had
> > > optimized it at M062x/6-31G* level, before starting the MD simulations.
> > > Then, I generated .pdb file from .log (Gaussian 09) file, and sorted it
> > > residue by residue. After that, I started simulation procedure and
> > > continued step by step. In spite of G3 PAMAM dendrimer I didn't face
> any
> > > errors in energy minimization step, and the potential energy - EM step
> > plot
> > > was reasonable. But, when I loaded em.gro file in VMD, the structure
> was
> > > completely messed up as in G3 dendrimer. This time I continued the MD
> > > simulation until production MD, and there was no error. However, the
> > system
> > > is blown up. You can access all the simulation files, pdb structure,
> and
> > > the photos of G1 structure before and after EM step via:
> > >
> > > https://www.dropbox.com/s/sdggfaklg530hq0/G1.zip?dl=0
> > >
> > > Since I am a beginner in this area, I do not know what is the solution
> > for
> > > this problem.
> > > Do you think errors that occur during the G3 simulation are relevant to
> > the
> > > initial structure?
> > > any suggestion or recommendation is appreciated.
> > >
> > > Thanks in advance
> > > Farideh
> > > --
> > > Gromacs Users mailing list
> > >
> > > * Please search the archive at
> > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > > posting!
> > >
> > > *

[gmx-users] energy minimization error

2015-10-22 Thread faride badalkhani

Hi,

I am trying to simulate a hyper-branched polymer (a dendrimer) in water.
But, every time the system blows up at energy minimization step. Therefore,
according to what Mark had recommended I decided to start with a much
smaller dendrimer (i.e. G1 PAMAM dendrimer) , rather than a G3 one. I had
optimized it at M062x/6-31G* level, before starting the MD simulations.
Then, I generated .pdb file from .log (Gaussian 09) file, and sorted it
residue by residue. After that, I started simulation procedure and
continued step by step. In spite of G3 PAMAM dendrimer I didn't face any
errors in energy minimization step, and the potential energy - EM step plot
was reasonable. But, when I loaded em.gro file in VMD, the structure was
completely messed up as in G3 dendrimer. This time I continued the MD
simulation until production MD, and there was no error. However, the system
is blown up. You can access all the simulation files, pdb structure, and
the photos of G1 structure before and after EM step via:

https://www.dropbox.com/s/sdggfaklg530hq0/G1.zip?dl=0

Since I am a beginner in this area, I do not know what is the solution for
this problem.
Do you think errors that occur during the G3 simulation are relevant to the
initial structure?
any suggestion or recommendation is appreciated.

Thanks in advance
Farideh
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Re: [gmx-users] energy minimization error

2015-10-22 Thread Mark Abraham

Hi,

Did you inspect your topology like I suggested? You need to know that there
are bonds exactly where you intend them, before doing any calculations with
them.

Mark

On Thu, Oct 22, 2015 at 9:35 AM faride badalkhani 
wrote:

> Hi,
>
> I am trying to simulate a hyper-branched polymer (a dendrimer) in water.
> But, every time the system blows up at energy minimization step. Therefore,
> according to what Mark had recommended I decided to start with a much
> smaller dendrimer (i.e. G1 PAMAM dendrimer) , rather than a G3 one. I had
> optimized it at M062x/6-31G* level, before starting the MD simulations.
> Then, I generated .pdb file from .log (Gaussian 09) file, and sorted it
> residue by residue. After that, I started simulation procedure and
> continued step by step. In spite of G3 PAMAM dendrimer I didn't face any
> errors in energy minimization step, and the potential energy - EM step plot
> was reasonable. But, when I loaded em.gro file in VMD, the structure was
> completely messed up as in G3 dendrimer. This time I continued the MD
> simulation until production MD, and there was no error. However, the system
> is blown up. You can access all the simulation files, pdb structure, and
> the photos of G1 structure before and after EM step via:
>
> https://www.dropbox.com/s/sdggfaklg530hq0/G1.zip?dl=0
>
> Since I am a beginner in this area, I do not know what is the solution for
> this problem.
> Do you think errors that occur during the G3 simulation are relevant to the
> initial structure?
> any suggestion or recommendation is appreciated.
>
> Thanks in advance
> Farideh
> --
> 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] Energy minimization error

2015-10-20 Thread faride badalkhani

Hi,

As you said, I started with a G1 PAMAM dendrimer, rather than a G3 one. I
had optimized it at M062x/6-31G* level, before starting the MD simulations.
Then, I generated .pdb file from .log (Gaussian 09) file, and sorted it
residue by residue. After that, I started simulation procedure and
continued step by step. In spite of G3 PAMAM dendrimer I didn't face any
errors in energy minimization step, and the potential energy - EM step plot
was reasonable. But, when I loaded em.gro file in VMD, the structure was
completely messed up as in G3 dendrimer. This time I continued the MD
simulation until production MD, and there was no error. However, the system
is blown up. You can access all the simulation files, pdb structure, and
the photos of G1 structure before and after EM step via:

https://www.dropbox.com/s/sdggfaklg530hq0/G1.zip?dl=0

Since I am a beginner in this area, I do not know what is the solution for
this problem.
Do you think errors that occur during the G3 simulation are relevant to the
initial structure?
any suggestion or recommendation is appreciated.

Thanks in advance
Farideh

On Sat, Oct 17, 2015 at 6:29 PM, Mark Abraham 
wrote:

> Hi,
>
> What some visualization program shows about bonds doesn't mean anything -
> it has not parsed your topology. You have no option but to look at the .top
> produced and reason about what it shows, but yours is very complex. I
> strongly recommend starting with something simpler than a multiply branched
> dendrimer. Join two units with a specbond, inspect the .top so that you
> know it has what you think it has, and get that to EM and simulation
> stably. Then you can get more complex.
>
> Mark
>
> On Sat, Oct 17, 2015 at 3:58 PM faride badalkhani <
> farideh.kham...@gmail.com>
> wrote:
>
> > Dear gromacs users,
> >
> > As I said before I faced with the minimization error, so I changed
> > coordinates of atoms in pdb file, but the problem is the same. the only
> > thing that changes in every run is atom number. I modified pdb for many
> > times.
> >
> > Steepest Descents converged to Fmax < 1000 in 530 steps
> > Potential Energy  = -5.5180181e+05
> > Maximum force =  7.4496063e+02 on atom 501
> > Norm of force =  3.8248455e+01
> >
> >
> > Moreover gro structure was completely messed up when was visualized in
> vmd.
> > you can see the picture of my structure in below dropbox link:
> >
> > https://www.dropbox.com/s/78v2cvii4gkd8ev/gro.bmp?dl=0
> > https://www.dropbox.com/s/nyzyu3zmy1vvevg/pdb.bmp?dl=0
> >
> > and this is the pdb file dropbox link:
> >
> > https://www.dropbox.com/s/yvxpl2igzi5ccad/120.pdb?dl=0
> >
> >
> > I used cg algorithm after steep for minimization, too. But it did not
> work.
> > is there any way to solve this problem?
> >
> > any help is appreciated.
> >
> > On Mon, Oct 5, 2015 at 2:08 PM, Mark Abraham 
> > wrote:
> >
> > > Hi,
> > >
> > > Look at atom 380 and see why the forces might be high.
> > >
> > > Mark
> > >
> > > On Mon, Oct 5, 2015 at 10:15 AM faride badalkhani <
> > > farideh.kham...@gmail.com>
> > > wrote:
> > >
> > > > Thank you for your great help on specbond.dat file. I defined it and
> I
> > > > could go ahead until Energy minimization step. I have used this
> > minim.mdp
> > > > file
> > > >
> > > > ; minim.mdp - used as input into grompp to generate em.tpr
> > > > ; 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 <
> > > > 1000.0 kJ/mol/nm
> > > > emstep   = 0.01  ; Energy step size
> > > > nsteps= 5  ; Maximum number of (minimization)
> steps
> > > to
> > > > perform
> > > >
> > > > ; 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
> > > > 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; Short-range electrostatic cut-off
> > > > rvdw   = 1.0; Short-range Van der Waals cut-off
> > > > pbc = xyz ; Periodic Boundary Conditions
> > (yes/no)
> > > >
> > > > But when I run mdrun -v -deffnm em command, I get this error:
> > > >
> > > > Energy minimization has stopped, but the forces have not converged to
> > the
> > > > requested precision Fmax < 1000 (which may not be possible for your
> > > > system).
> > > > It stopped because the algorithm tried to make a new step whose size
> > was
> > > > too
> > > > small, or there was no change

Re: [gmx-users] Energy minimization error

2015-10-17 Thread faride badalkhani

Dear gromacs users,

As I said before I faced with the minimization error, so I changed
coordinates of atoms in pdb file, but the problem is the same. the only
thing that changes in every run is atom number. I modified pdb for many
times.

Steepest Descents converged to Fmax < 1000 in 530 steps
Potential Energy  = -5.5180181e+05
Maximum force =  7.4496063e+02 on atom 501
Norm of force =  3.8248455e+01


Moreover gro structure was completely messed up when was visualized in vmd.
you can see the picture of my structure in below dropbox link:

https://www.dropbox.com/s/78v2cvii4gkd8ev/gro.bmp?dl=0
https://www.dropbox.com/s/nyzyu3zmy1vvevg/pdb.bmp?dl=0

and this is the pdb file dropbox link:

https://www.dropbox.com/s/yvxpl2igzi5ccad/120.pdb?dl=0


I used cg algorithm after steep for minimization, too. But it did not work.
is there any way to solve this problem?

any help is appreciated.

On Mon, Oct 5, 2015 at 2:08 PM, Mark Abraham 
wrote:

> Hi,
>
> Look at atom 380 and see why the forces might be high.
>
> Mark
>
> On Mon, Oct 5, 2015 at 10:15 AM faride badalkhani <
> farideh.kham...@gmail.com>
> wrote:
>
> > Thank you for your great help on specbond.dat file. I defined it and I
> > could go ahead until Energy minimization step. I have used this minim.mdp
> > file
> >
> > ; minim.mdp - used as input into grompp to generate em.tpr
> > ; 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 <
> > 1000.0 kJ/mol/nm
> > emstep   = 0.01  ; Energy step size
> > nsteps= 5  ; Maximum number of (minimization) steps
> to
> > perform
> >
> > ; 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
> > 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; Short-range electrostatic cut-off
> > rvdw   = 1.0; Short-range Van der Waals cut-off
> > pbc = xyz ; Periodic Boundary Conditions (yes/no)
> >
> > But when I run mdrun -v -deffnm em command, I get this error:
> >
> > Energy minimization has stopped, but the forces have not converged to the
> > requested precision Fmax < 1000 (which may not be possible for your
> > system).
> > It stopped because the algorithm tried to make a new step whose size was
> > too
> > small, or there was no change in the energy since last step. Either way,
> we
> > regard the minimization as converged to within the available machine
> > precision, given your starting configuration and EM parameters.
> >
> > Double precision normally gives you higher accuracy, but this is often
> not
> > needed for preparing to run molecular dynamics.
> > You might need to increase your constraint accuracy, or turn
> > off constraints altogether (set constraints = none in mdp file)
> >
> > writing lowest energy coordinates.
> >
> > Steepest Descents converged to machine precision in 90 steps,
> > but did not reach the requested Fmax < 1000.
> > Potential Energy  = -2.3956744e+05
> > Maximum force =  1.5824519e+05 on atom 380
> > Norm of force =  1.7695243e+03
> >
> > gcq#187: "Been There, Done It" (Beavis and Butthead)
> >
> > farideh@farideh-P61A-D3:~/FARIDEH$
> >
> > I changed the emtol, emstep, and nsteps for a few times. However, I
> > couldn't resolve this problem. Could you tell me if there is something
> > wrong with the minim.mdp file?
> >
> > You can see all the files via:
> > https://www.dropbox.com/s/sq2c103yxi4mc28/Farideh.zip?dl=0
> >
> > Truly yours,
> > Farideh
> > --
> > 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!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
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Re: [gmx-users] Energy minimization error

2015-10-17 Thread Mark Abraham

Hi,

What some visualization program shows about bonds doesn't mean anything -
it has not parsed your topology. You have no option but to look at the .top
produced and reason about what it shows, but yours is very complex. I
strongly recommend starting with something simpler than a multiply branched
dendrimer. Join two units with a specbond, inspect the .top so that you
know it has what you think it has, and get that to EM and simulation
stably. Then you can get more complex.

Mark

On Sat, Oct 17, 2015 at 3:58 PM faride badalkhani 
wrote:

> Dear gromacs users,
>
> As I said before I faced with the minimization error, so I changed
> coordinates of atoms in pdb file, but the problem is the same. the only
> thing that changes in every run is atom number. I modified pdb for many
> times.
>
> Steepest Descents converged to Fmax < 1000 in 530 steps
> Potential Energy  = -5.5180181e+05
> Maximum force =  7.4496063e+02 on atom 501
> Norm of force =  3.8248455e+01
>
>
> Moreover gro structure was completely messed up when was visualized in vmd.
> you can see the picture of my structure in below dropbox link:
>
> https://www.dropbox.com/s/78v2cvii4gkd8ev/gro.bmp?dl=0
> https://www.dropbox.com/s/nyzyu3zmy1vvevg/pdb.bmp?dl=0
>
> and this is the pdb file dropbox link:
>
> https://www.dropbox.com/s/yvxpl2igzi5ccad/120.pdb?dl=0
>
>
> I used cg algorithm after steep for minimization, too. But it did not work.
> is there any way to solve this problem?
>
> any help is appreciated.
>
> On Mon, Oct 5, 2015 at 2:08 PM, Mark Abraham 
> wrote:
>
> > Hi,
> >
> > Look at atom 380 and see why the forces might be high.
> >
> > Mark
> >
> > On Mon, Oct 5, 2015 at 10:15 AM faride badalkhani <
> > farideh.kham...@gmail.com>
> > wrote:
> >
> > > Thank you for your great help on specbond.dat file. I defined it and I
> > > could go ahead until Energy minimization step. I have used this
> minim.mdp
> > > file
> > >
> > > ; minim.mdp - used as input into grompp to generate em.tpr
> > > ; 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 <
> > > 1000.0 kJ/mol/nm
> > > emstep   = 0.01  ; Energy step size
> > > nsteps= 5  ; Maximum number of (minimization) steps
> > to
> > > perform
> > >
> > > ; 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
> > > 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; Short-range electrostatic cut-off
> > > rvdw   = 1.0; Short-range Van der Waals cut-off
> > > pbc = xyz ; Periodic Boundary Conditions
> (yes/no)
> > >
> > > But when I run mdrun -v -deffnm em command, I get this error:
> > >
> > > Energy minimization has stopped, but the forces have not converged to
> the
> > > requested precision Fmax < 1000 (which may not be possible for your
> > > system).
> > > It stopped because the algorithm tried to make a new step whose size
> was
> > > too
> > > small, or there was no change in the energy since last step. Either
> way,
> > we
> > > regard the minimization as converged to within the available machine
> > > precision, given your starting configuration and EM parameters.
> > >
> > > Double precision normally gives you higher accuracy, but this is often
> > not
> > > needed for preparing to run molecular dynamics.
> > > You might need to increase your constraint accuracy, or turn
> > > off constraints altogether (set constraints = none in mdp file)
> > >
> > > writing lowest energy coordinates.
> > >
> > > Steepest Descents converged to machine precision in 90 steps,
> > > but did not reach the requested Fmax < 1000.
> > > Potential Energy  = -2.3956744e+05
> > > Maximum force =  1.5824519e+05 on atom 380
> > > Norm of force =  1.7695243e+03
> > >
> > > gcq#187: "Been There, Done It" (Beavis and Butthead)
> > >
> > > farideh@farideh-P61A-D3:~/FARIDEH$
> > >
> > > I changed the emtol, emstep, and nsteps for a few times. However, I
> > > couldn't resolve this problem. Could you tell me if there is something
> > > wrong with the minim.mdp file?
> > >
> > > You can see all the files via:
> > > https://www.dropbox.com/s/sq2c103yxi4mc28/Farideh.zip?dl=0
> > >
> > > Truly yours,
> > > Farideh
> > > --
> > > Gromacs Users mailing list
> > >
> > > * Please search the archive at
> > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > >

[gmx-users] Energy minimization error

2015-10-05 Thread faride badalkhani

Thank you for your great help on specbond.dat file. I defined it and I
could go ahead until Energy minimization step. I have used this minim.mdp
file

; minim.mdp - used as input into grompp to generate em.tpr
; 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 <
1000.0 kJ/mol/nm
emstep   = 0.01  ; Energy step size
nsteps= 5  ; Maximum number of (minimization) steps to
perform

; 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
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; Short-range electrostatic cut-off
rvdw   = 1.0; Short-range Van der Waals cut-off
pbc = xyz ; Periodic Boundary Conditions (yes/no)

But when I run mdrun -v -deffnm em command, I get this error:

Energy minimization has stopped, but the forces have not converged to the
requested precision Fmax < 1000 (which may not be possible for your system).
It stopped because the algorithm tried to make a new step whose size was too
small, or there was no change in the energy since last step. Either way, we
regard the minimization as converged to within the available machine
precision, given your starting configuration and EM parameters.

Double precision normally gives you higher accuracy, but this is often not
needed for preparing to run molecular dynamics.
You might need to increase your constraint accuracy, or turn
off constraints altogether (set constraints = none in mdp file)

writing lowest energy coordinates.

Steepest Descents converged to machine precision in 90 steps,
but did not reach the requested Fmax < 1000.
Potential Energy  = -2.3956744e+05
Maximum force =  1.5824519e+05 on atom 380
Norm of force =  1.7695243e+03

gcq#187: "Been There, Done It" (Beavis and Butthead)

farideh@farideh-P61A-D3:~/FARIDEH$

I changed the emtol, emstep, and nsteps for a few times. However, I
couldn't resolve this problem. Could you tell me if there is something
wrong with the minim.mdp file?

You can see all the files via:
https://www.dropbox.com/s/sq2c103yxi4mc28/Farideh.zip?dl=0

Truly yours,
Farideh
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Re: [gmx-users] Energy minimization error

2015-10-05 Thread Mark Abraham

Hi,

Look at atom 380 and see why the forces might be high.

Mark

On Mon, Oct 5, 2015 at 10:15 AM faride badalkhani 
wrote:

> Thank you for your great help on specbond.dat file. I defined it and I
> could go ahead until Energy minimization step. I have used this minim.mdp
> file
>
> ; minim.mdp - used as input into grompp to generate em.tpr
> ; 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 <
> 1000.0 kJ/mol/nm
> emstep   = 0.01  ; Energy step size
> nsteps= 5  ; Maximum number of (minimization) steps to
> perform
>
> ; 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
> 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; Short-range electrostatic cut-off
> rvdw   = 1.0; Short-range Van der Waals cut-off
> pbc = xyz ; Periodic Boundary Conditions (yes/no)
>
> But when I run mdrun -v -deffnm em command, I get this error:
>
> Energy minimization has stopped, but the forces have not converged to the
> requested precision Fmax < 1000 (which may not be possible for your
> system).
> It stopped because the algorithm tried to make a new step whose size was
> too
> small, or there was no change in the energy since last step. Either way, we
> regard the minimization as converged to within the available machine
> precision, given your starting configuration and EM parameters.
>
> Double precision normally gives you higher accuracy, but this is often not
> needed for preparing to run molecular dynamics.
> You might need to increase your constraint accuracy, or turn
> off constraints altogether (set constraints = none in mdp file)
>
> writing lowest energy coordinates.
>
> Steepest Descents converged to machine precision in 90 steps,
> but did not reach the requested Fmax < 1000.
> Potential Energy  = -2.3956744e+05
> Maximum force =  1.5824519e+05 on atom 380
> Norm of force =  1.7695243e+03
>
> gcq#187: "Been There, Done It" (Beavis and Butthead)
>
> farideh@farideh-P61A-D3:~/FARIDEH$
>
> I changed the emtol, emstep, and nsteps for a few times. However, I
> couldn't resolve this problem. Could you tell me if there is something
> wrong with the minim.mdp file?
>
> You can see all the files via:
> https://www.dropbox.com/s/sq2c103yxi4mc28/Farideh.zip?dl=0
>
> Truly yours,
> Farideh
> --
> 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] energy minimization

 Hi;
I've alreadyconverted the amber topology and coordinate files to gromacs 
format.But when I want to start running theenergy minimization first by using 
the grompp to generate .tpr file,I get this error:
Program gmx, VERSION5.0.2Source code 
file:/build/buildd/gromacs-5.0.2/src/gromacs/gmxpreprocess/toppush.c,line: 1353
Fatal error:Atomtype IP notfoundFor more informationand tips for 
troubleshooting, please check the GROMACSwebsite 
athttp://www.gromacs.org/Documentation/Errors
I think that itcannot recognize the atoms. I don't know how to fix it.
Best regards, Mohammad. 
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[gmx-users] energy minimization

Hi;
I've alreadyconverted the amber topology and coordinate files to gromacs 
format.But when I want to start running theenergy minimization first by using 
the grompp to generate .tpr file,I get this error:
Program gmx, VERSION5.0.2Source code 
file:/build/buildd/gromacs-5.0.2/src/gromacs/gmxpreprocess/toppush.c,line: 1353
Fatal error:Atomtype IP notfoundFor more informationand tips for 
troubleshooting, please check the GROMACSwebsite 
athttp://www.gromacs.org/Documentation/Errors
I think that itcannot recognize the atoms. I don't know how to fix it.
Best regards, Mohammad.
-- 
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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mail to gmx-users-requ...@gromacs.org.

[gmx-users] energy minimization

Hi;
I've alreadyconverted the amber topology and coordinate files to gromacs 
format.But when I want to start running theenergy minimization first by using 
the grompp to generate .tpr file,I get this error:
Program gmx, VERSION5.0.2Source code 
file:/build/buildd/gromacs-5.0.2/src/gromacs/gmxpreprocess/toppush.c,line: 1353
Fatal error:Atomtype IP notfoundFor more informationand tips for 
troubleshooting, please check the GROMACSwebsite 
athttp://www.gromacs.org/Documentation/Errors
I think that itcannot recognize the atoms. I don't know how to fix it.
Best regards, Mohammad.
-- 
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.

[gmx-users] energy minimization

 Hi;I've alreadyconverted the amber topology and coordinate files to gromacs 
format.But when I want to start running theenergy minimization first by using 
the grompp to generate .tpr file,I get this error:
Program gmx, VERSION5.0.2Source code 
file:/build/buildd/gromacs-5.0.2/src/gromacs/gmxpreprocess/toppush.c,line: 1353
Fatal error:Atomtype IP notfoundFor more informationand tips for 
troubleshooting, please check the GROMACSwebsite 
athttp://www.gromacs.org/Documentation/Errors
I think that itcannot recognize the atoms. I don't know how to fix it.
Best regards, Mohammad.

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http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

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Re: [gmx-users] Energy minimization

2015-07-09 Thread Justin Lemkul




On 7/8/15 8:03 PM, Malihe Hasanzadeh wrote:

Hi,
I want to do MD simulation of protein-DNA-ligand using Gromacs 5.0.4.,when I
do energy minimization, my system is converged but has positive potential
energy. also this step only takes 3 second! for next step (pr), gives error:
your system is not equilibrated well and blowing up! I chcked my em.pdb
file and
I saw the Sol box is separated from protein and DNA!


This is probably just a PBC effect; use trjconv.


Could you please help me, what should I do?what part of my set is wrong?



Your EM outcome suggests an unresolvable clash in the system, so it's pointless 
to try dynamics unless you get a force below the specified tolerance (or at 
least of some other reasonable magnitude).  mdrun tells you where the maximum 
force is, so that's where you should start looking.  Beyond that, you'll have to 
give us a complete description of what you've done to prepare the system, 
parametrize the ligand, etc.  General troubleshooting that you should always follow:


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


my em.mdp:
define = -DFLEXIBLE


I'm assuming you're trying to use rigid water during the subsequent dynamics 
(you should), so you'll want to re-minimize without flexible water. 
Occasionally, the waters distort and SETTLE cannot fix the geometry.  This is 
not likely the source of your problem, just an FYI.


-Justin


integrator = cg ; steep
nsteps = 4000
nstlist = 1
constraints = none
emtol = 100.0
nstcgsteep = 10 ; do a steep every 10 steps of cg
emstep = 0.01 ; used with steep
nstcomm = 1
nstcalcenergy = 1.2
ewald_rtol = 1e-05
coulombtype = PME
cutoff-scheme = Group
ns_type = grid
rlist = 1.4
rcoulomb =1.4
rvdw = 1.4
Tcoupl = no
Pcoupl = no
gen_vel = no
nstxout = 0 ; write coords every # step
optimize_fft = yes

Sincerely,
Malihe



--
==

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] Energy minimization

2015-07-08 Thread Malihe Hasanzadeh

Hi,
I want to do MD simulation of protein-DNA-ligand using Gromacs 5.0.4.,when I
do energy minimization, my system is converged but has positive potential
energy. also this step only takes 3 second! for next step (pr), gives error:
your system is not equilibrated well and blowing up! I chcked my em.pdb
file and
I saw the Sol box is separated from protein and DNA!
Could you please help me, what should I do?what part of my set is wrong?

my em.mdp:
define = -DFLEXIBLE
integrator = cg ; steep
nsteps = 4000
nstlist = 1
constraints = none
emtol = 100.0
nstcgsteep = 10 ; do a steep every 10 steps of cg
emstep = 0.01 ; used with steep
nstcomm = 1
nstcalcenergy = 1.2
ewald_rtol = 1e-05
coulombtype = PME
cutoff-scheme = Group
ns_type = grid
rlist = 1.4
rcoulomb =1.4
rvdw = 1.4
Tcoupl = no
Pcoupl = no
gen_vel = no
nstxout = 0 ; write coords every # step
optimize_fft = yes

Sincerely,
Malihe
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Re: [gmx-users] energy minimization error

2015-06-27 Thread James Lord

Hi Justin
For now I  used


*mdrun -nt 1*


* and got rid of this error so hopefully the simulation wont crash. *

*Cheers*

*James*


On Sat, Jun 27, 2015 at 11:19 AM, James Lord jjamesgreen...@gmail.com
wrote:

 Hi Justin,
 I have asked this before, but this time I started up from scratch and used
 the input files that I know they are fine but again I am getting this
 error, Would you please tell me what is wrong in my topology files and
 where about in .top files the bond length are defined?


 https://drive.google.com/file/d/0B0YMTXH1gmQsbkpjTU9tWGFkSDA/view?usp=sharing

 Cheers
 James

 On Mon, May 18, 2015 at 1:13 AM, Justin Lemkul jalem...@vt.edu wrote:



 On 5/16/15 11:35 PM, James Lord wrote:

 Hi Justin
 Thanks for this. Can you tell me which step(s) this bond length is
 defined
 What should I do (redo) to resolve this issue?


 The bonds are defined in the topology.  The DD algorithm reads what's in
 the coordinate file and builds cells based on the geometry it finds there.

 Without a full description of what's in your system, what steps you've
 taken to prepare it (full commands, in order), there's little I can suggest
 because it would all be guesswork.


 -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] energy minimization error

2015-06-27 Thread Justin Lemkul




On 6/27/15 2:29 AM, James Lord wrote:

Hi Justin
For now I  used


*mdrun -nt 1*


* and got rid of this error so hopefully the simulation wont crash. *



The DD errors have nothing to do with physical stability; you just can't 
necessarily parallelize any arbitrary system over any arbitrary number of cores 
(DD cells).  You can also parallelize with OpenMP to get some speed-up (mdrun 
-ntmpi 1 -ntomp N).


-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] energy minimization error

2015-06-26 Thread Justin Lemkul




On 6/26/15 7:19 PM, James Lord wrote:

Hi Justin,
I have asked this before, but this time I started up from scratch and used
the input files that I know they are fine but again I am getting this
error, Would you please tell me what is wrong in my topology files and
where about in .top files the bond length are defined?

https://drive.google.com/file/d/0B0YMTXH1gmQsbkpjTU9tWGFkSDA/view?usp=sharing



There's nothing I can do with a topology that's a series of #include statements.

Please also remind me what this is all about so I don't have to go digging 
through the archives for something from a month ago.  Lots of things have 
happened since then :)


-Justin


Cheers
James

On Mon, May 18, 2015 at 1:13 AM, Justin Lemkul jalem...@vt.edu wrote:




On 5/16/15 11:35 PM, James Lord wrote:


Hi Justin
Thanks for this. Can you tell me which step(s) this bond length is
defined
What should I do (redo) to resolve this issue?



The bonds are defined in the topology.  The DD algorithm reads what's in
the coordinate file and builds cells based on the geometry it finds there.

Without a full description of what's in your system, what steps you've
taken to prepare it (full commands, in order), there's little I can suggest
because it would all be guesswork.


-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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--
==

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] energy minimization error

2015-06-26 Thread James Lord

Hi Justin,
I have asked this before, but this time I started up from scratch and used
the input files that I know they are fine but again I am getting this
error, Would you please tell me what is wrong in my topology files and
where about in .top files the bond length are defined?

https://drive.google.com/file/d/0B0YMTXH1gmQsbkpjTU9tWGFkSDA/view?usp=sharing

Cheers
James

On Mon, May 18, 2015 at 1:13 AM, Justin Lemkul jalem...@vt.edu wrote:



 On 5/16/15 11:35 PM, James Lord wrote:

 Hi Justin
 Thanks for this. Can you tell me which step(s) this bond length is
 defined
 What should I do (redo) to resolve this issue?


 The bonds are defined in the topology.  The DD algorithm reads what's in
 the coordinate file and builds cells based on the geometry it finds there.

 Without a full description of what's in your system, what steps you've
 taken to prepare it (full commands, in order), there's little I can suggest
 because it would all be guesswork.


 -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] energy minimization problem

Hi,
   I am simulating a 5X5 carbon nanotube in the presence of nucleic acids
in Tip3P water. I have made this nanotube using VMD nanotube builder and
made the topology using pdb2gmx. Upto the energy minimization step every
thing was fine but when I proceed for energy minimization I get the carbon
naotube crumpled when I view the em.gro file in VMD. It is worth mentioning
that the nucleic acid remains unchanged during the em process and when I am
going for NVT equilibration it does not produce any LINCS warning or stuffs
like that. So is it happening because a visualization tool is unaware of
the molecular topology or do I need to change some parameters in the em.mdp
file?

The cnt.itp file is as follows (partwise)

;   File 'cnt.top' was generated
;   By user: onbekend (0)
;   On host: onbekend
;   At date: Sat May 30 11:07:23 2015
;
;   This is a standalone topology file
;
;   It was generated using program:
;   pdb2gmx_d - VERSION 4.5.6
;
;   Command line was:
;   pdb2gmx_d -f nishCNT.pdb -o init.gro -p cnt.top
;
;   Force field was read from current directory or a relative path -
path addeed


[ moleculetype ]
; Namenrexcl
SDG 3

[ atoms ]
;   nr   type  resnr residue  atom   cgnr charge   mass  typeB
   chargeB  massB
; residue   0 SDG rtp SDG  q  0.0
 1 CA  0SDG C1  1  0 12.011   ;
qtot 0
 2 CA  0SDG C2  2  0 12.011   ;
qtot 0
 3 CA  0SDG C3  3  0 12.011   ;
qtot 0
 4 CA  0SDG C4  4  0 12.011   ;
qtot 0
 5 CA  0SDG C5  5  0 12.011   ;
qtot 0
 6 CA  0SDG C6  6  0 12.011   ;
qtot 0
 7 CA  0SDG C7  7  0 12.011   ;
qtot 0
 8 CA  0SDG C8  8  0 12.011   ;
qtot 0
 9 CA  0SDG C9  9  0 12.011   ;
qtot 0
10 CA  0SDGC10 10  0 12.011   ;
qtot 0
11 CA  0SDGC11 11  0 12.011   ;
qtot 0
12 CA  0SDGC12 12  0 12.011   ;
qtot 0
13 CA  0SDGC13 13  0 12.011   ;
qtot 0
14 CA  0SDGC14 14  0 12.011   ;
qtot 0
15 CA  0SDGC15 15  0 12.011   ;
qtot 0
16 CA  0SDGC16 16  0 12.011   ;
qtot 0
17 CA  0SDGC17 17  0 12.011   ;
qtot 0

[ bonds ]
;  aiaj funct   b0 kb
1 2 1C6   H30.108  284512.0
1 6 1C5   H40.108  284512.0
1   403 1   0.108  284512.0
2 3 1C4   C70.1375 255224.0
2   385 1C370 C386  0.1375 255224.0
3 4 1C5  C100.1375 255224.0
3 7 1C8 C3690.1375 255224.0
4 5 1C6 C4000.1375 255224.0
5   400 1C383 C399  0.1375 255224.0
6   404 1   0.108  284512.0
7 8 1C9  C110.1375 255224.0
8 9 1C10  C14   0.1375 255224.0
811 1C12 C353   0.1375 255224.0
910 1C4 C3840.1375 255224.0
914 1C13 C368   0.1375 255224.0
   1112 1C13  C15   0.1375 255224.0
   11   353 1C338 C354  0.1375 255224.0
   1213 1C14  C18   0.1375 255224.0
   1215 1C16 C337   0.1375 255224.0
   1318 1C17 C352   0.1375 255224.0
   14   368 1C351 C367  0.1375 255224.0
   1516 1C17  C19   0.1375 255224.0
   15   337 1C322 C338  0.1375 255224.0
[ angles ]
;  aiajak functth0   cthubo
   cub
2 1 6 5   120.00334.72 0.24162
   29288.0
2 1   403 5   120.00251.04 0.21525
   18409.6
6 1   403 5   120.00251.04 0.21525
   18409.6
1 2 3 5   120.00334.72 0.24162
   29288.0
1 2   385 5   120.00334.72 0.24162
   29288.0
3 2   385 5   120.00334.72 0.24162
   29288.0
2 3 4 5   120.00334.72 0.24162
   29288.0
2 3 7 5   120.00334.72 0.24162
   29288.0
4 3 7 5   120.00334.72 0.24162
   29288.0
3 4 5 5

[gmx-users] energy minimization problem

Hi,
The mdp file has pbc= xyz in the last line. In the previous mail it was
written that pbc=full. Plaese ignore it.

Thanks and regards
Soumadwip
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Re: [gmx-users] energy minimization problem

2015-06-01 Thread Justin Lemkul




On 6/1/15 8:06 AM, soumadwip ghosh wrote:

Thanks Justin for your quick reply. What are the correct non-bonding
settings for CHARMM to be used in the .mdp file?



http://www.gromacs.org/Documentation/Terminology/Force_Fields/CHARMM

I seem to have to post this information weekly...


Here is how the CNT molecule looks like prior to energy minimization.

pre energy min CNT
https://drive.google.com/file/d/0B7SBnQ5YXQSLX0dIOHZjT3p1Y2s/view?usp=sharing



Yep, that's definitely wrong.


I am not continuing any of the equilibration steps anymore. As you can see
the CNT structure is distorted badly.

Please help me out. What settings do I need to change in order to avoid
such distortion? Is there a possibility that the cnt topology was wrong to
begin with?



The CNT topology is clearly wrong.  It's probably missing some bonds or 
something.

-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] energy minimization problem

2015-06-01 Thread Justin Lemkul




On 6/1/15 9:07 AM, soumadwip ghosh wrote:

Hi Justin,
 the snapshot I uploaded in the URL is of the SSDNA-CNT
system after energy minimization step not before it. I stripped off
water and ions from the system for the ease of visualization. I would
be grateful if you suggest me a possible way out.



I don't see how that changes what I've said.  You have a topology problem with 
the CNT.  Simplify the system - build a smaller CNT, minimize it in vacuo, etc, 
then make it bigger/more complex.  Look at the atoms that are distorting and 
check the existence of their bonded interactions and associated parameters.


-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] energy minimization problem

2015-06-01 Thread Justin Lemkul




On 6/1/15 2:28 AM, soumadwip ghosh wrote:

Hi,
I am simulating a 5X5 carbon nanotube in the presence of nucleic acids
in Tip3P water. I have made this nanotube using VMD nanotube builder and
made the topology using pdb2gmx. Upto the energy minimization step every
thing was fine but when I proceed for energy minimization I get the carbon
naotube crumpled when I view the em.gro file in VMD. It is worth mentioning


Please upload an image somewhere and provide the URL.


that the nucleic acid remains unchanged during the em process and when I am
going for NVT equilibration it does not produce any LINCS warning or stuffs
like that. So is it happening because a visualization tool is unaware of
the molecular topology or do I need to change some parameters in the em.mdp
file?



Possibly; see below.


The cnt.itp file is as follows (partwise)



Incomplete topologies are not generally useful.


;   File 'cnt.top' was generated
;   By user: onbekend (0)
;   On host: onbekend
;   At date: Sat May 30 11:07:23 2015
;
;   This is a standalone topology file
;
;   It was generated using program:
;   pdb2gmx_d - VERSION 4.5.6
;
;   Command line was:
;   pdb2gmx_d -f nishCNT.pdb -o init.gro -p cnt.top
;
;   Force field was read from current directory or a relative path -
path addeed


[ moleculetype ]
; Namenrexcl
SDG 3

[ atoms ]
;   nr   type  resnr residue  atom   cgnr charge   mass  typeB
chargeB  massB
; residue   0 SDG rtp SDG  q  0.0
  1 CA  0SDG C1  1  0 12.011   ;
qtot 0
  2 CA  0SDG C2  2  0 12.011   ;
qtot 0
  3 CA  0SDG C3  3  0 12.011   ;
qtot 0
  4 CA  0SDG C4  4  0 12.011   ;
qtot 0
  5 CA  0SDG C5  5  0 12.011   ;
qtot 0
  6 CA  0SDG C6  6  0 12.011   ;
qtot 0
  7 CA  0SDG C7  7  0 12.011   ;
qtot 0
  8 CA  0SDG C8  8  0 12.011   ;
qtot 0
  9 CA  0SDG C9  9  0 12.011   ;
qtot 0
 10 CA  0SDGC10 10  0 12.011   ;
qtot 0
 11 CA  0SDGC11 11  0 12.011   ;
qtot 0
 12 CA  0SDGC12 12  0 12.011   ;
qtot 0
 13 CA  0SDGC13 13  0 12.011   ;
qtot 0
 14 CA  0SDGC14 14  0 12.011   ;
qtot 0
 15 CA  0SDGC15 15  0 12.011   ;
qtot 0
 16 CA  0SDGC16 16  0 12.011   ;
qtot 0
 17 CA  0SDGC17 17  0 12.011   ;
qtot 0

[ bonds ]
;  aiaj funct   b0 kb
 1 2 1C6   H30.108  284512.0
 1 6 1C5   H40.108  284512.0
 1   403 1   0.108  284512.0
 2 3 1C4   C70.1375 255224.0
 2   385 1C370 C386  0.1375 255224.0
 3 4 1C5  C100.1375 255224.0
 3 7 1C8 C3690.1375 255224.0
 4 5 1C6 C4000.1375 255224.0
 5   400 1C383 C399  0.1375 255224.0
 6   404 1   0.108  284512.0
 7 8 1C9  C110.1375 255224.0
 8 9 1C10  C14   0.1375 255224.0
 811 1C12 C353   0.1375 255224.0
 910 1C4 C3840.1375 255224.0
 914 1C13 C368   0.1375 255224.0
1112 1C13  C15   0.1375 255224.0
11   353 1C338 C354  0.1375 255224.0
1213 1C14  C18   0.1375 255224.0
1215 1C16 C337   0.1375 255224.0
1318 1C17 C352   0.1375 255224.0
14   368 1C351 C367  0.1375 255224.0
1516 1C17  C19   0.1375 255224.0
15   337 1C322 C338  0.1375 255224.0
[ angles ]
;  aiajak functth0   cthubo
cub
 2 1 6 5   120.00334.72 0.24162
29288.0
 2 1   403 5   120.00251.04 0.21525
18409.6
 6 1   403 5   120.00251.04 0.21525
18409.6
 1 2 3 5   120.00334.72 0.24162
29288.0
 1 2   385 5   120.00334.72 0.24162
29288.0
 3 2   385 5   120.00334.72 0.24162
29288.0
 2 3 4 5

Re: [gmx-users] energy minimization problem

Hi Justin,
the snapshot I uploaded in the URL is of the SSDNA-CNT
system after energy minimization step not before it. I stripped off
water and ions from the system for the ease of visualization. I would
be grateful if you suggest me a possible way out.

Regards,
Soumadwip
Research Fellow
IITB
India
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Re: [gmx-users] energy minimization problem

Thanks Justin for your quick reply. What are the correct non-bonding
settings for CHARMM to be used in the .mdp file?

Here is how the CNT molecule looks like prior to energy minimization.

pre energy min CNT
https://drive.google.com/file/d/0B7SBnQ5YXQSLX0dIOHZjT3p1Y2s/view?usp=sharing

I am not continuing any of the equilibration steps anymore. As you can see
the CNT structure is distorted badly.

Please help me out. What settings do I need to change in order to avoid
such distortion? Is there a possibility that the cnt topology was wrong to
begin with?

Regards,
Soumadwip
Research Fellow
IITB
India
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Re: [gmx-users] energy minimization problem

Hi Tsjerk,

I just tried, but it stopped for too many LICS warnings at step 6000. Small 
triple helix can be equilibrated for 1000ns with NPT.

-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Tsjerk 
Wassenaar
Sent: Monday, 18 May 2015 6:21 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] energy minimization problem

Hi Ming Tang,

Can you run in NVT? Then afterwards you can try NPT without position restraints.

Cheers,

Tsjerk
On May 18, 2015 10:14, Ming Tang m21.t...@qut.edu.au wrote:

 Thanks a lot, Justin

 It really makes me feel weird. The small triple helix with 30 amino 
 acids per chain(generated simply by deleting other atoms in .pdb file 
 of the real triple helix) can be equilibrated for 1ns using exactly 
 the same control files, and the real triple helix can be used for full 
 atomic simulation without any problem. The CG topology is generated 
 using the same mitinize.py downloaded from the website. I will try for 
 another time, and will tell you if I fix it.

 Thanks.

 -Original Message-
 From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:
 gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Justin 
 Lemkul
 Sent: Sunday, 17 May 2015 7:07 AM
 To: gmx-us...@gromacs.org
 Subject: Re: [gmx-users] energy minimization problem



 On 5/16/15 8:30 AM, Ming Tang wrote:
  Dear Justin,
 
  I tried to use small time step. First,  set dt=0.005ps, after 
  running
 20ps, I found one chain of the triple helix just went to another water 
 box totally. I guess there is something wrong with the martini ff 
 because of the small time step.
  Then, I increased it to 0.01ps, after running 40ps, I checked the 
  .gro,
 and found all the three chains stay together, which is reasonable. 
 However, even use dt=0.01, the simulation can only run about 1ns. And, 
 after simulating 100 ps using dt=0.01ps, the simulation can just run 
 thousands of steps when dt is increased to 0.02ps. I tried many times 
 and many different time steps, but still could not see the possibility 
 for it to run hundreds of  nanoseconds, which is quite normal when 
 using martini force. If the system can be further minimized, then it can run 
 longer maybe.
 

 This seems entirely random and suggests instead that there is 
 something simply physically unstable with the system or problematic in the 
 topology.
 I don't use MARTINI (or CG models in general) so there's little else I 
 can suggest.  Maybe someone more experienced with such systems will chime in.

 Also note that a chain moving into another box is probably just a 
 PBC effect and not a true dissociation.  If it is a dissociation, it's 
 not simply because of the time step.

 -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] energy minimization problem

Thanks a lot, Justin

It really makes me feel weird. The small triple helix with 30 amino acids per 
chain(generated simply by deleting other atoms in .pdb file of the real triple 
helix) can be equilibrated for 1ns using exactly the same control files, and 
the real triple helix can be used for full atomic simulation without any 
problem. The CG topology is generated using the same mitinize.py downloaded 
from the website. I will try for another time, and will tell you if I fix it.

Thanks.

-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Justin 
Lemkul
Sent: Sunday, 17 May 2015 7:07 AM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] energy minimization problem



On 5/16/15 8:30 AM, Ming Tang wrote:
 Dear Justin,

 I tried to use small time step. First,  set dt=0.005ps, after running 20ps, I 
 found one chain of the triple helix just went to another water box totally. I 
 guess there is something wrong with the martini ff because of the small time 
 step.
 Then, I increased it to 0.01ps, after running 40ps, I checked the .gro, and 
 found all the three chains stay together, which is reasonable. However, even 
 use dt=0.01, the simulation can only run about 1ns. And, after simulating 100 
 ps using dt=0.01ps, the simulation can just run thousands of steps when dt is 
 increased to 0.02ps. I tried many times and many different time steps, but 
 still could not see the possibility for it to run hundreds of  nanoseconds, 
 which is quite normal when using martini force. If the system can be further 
 minimized, then it can run longer maybe.


This seems entirely random and suggests instead that there is something simply 
physically unstable with the system or problematic in the topology.  I don't 
use MARTINI (or CG models in general) so there's little else I can suggest.  
Maybe someone more experienced with such systems will chime in.

Also note that a chain moving into another box is probably just a PBC effect 
and not a true dissociation.  If it is a dissociation, it's not simply because 
of the time step.

-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] energy minimization problem

2015-05-18 Thread Tsjerk Wassenaar

Hi Ming Tang,

Can you run in NVT? Then afterwards you can try NPT without position
restraints.

Cheers,

Tsjerk
On May 18, 2015 10:14, Ming Tang m21.t...@qut.edu.au wrote:

 Thanks a lot, Justin

 It really makes me feel weird. The small triple helix with 30 amino acids
 per chain(generated simply by deleting other atoms in .pdb file of the real
 triple helix) can be equilibrated for 1ns using exactly the same control
 files, and the real triple helix can be used for full atomic simulation
 without any problem. The CG topology is generated using the same
 mitinize.py downloaded from the website. I will try for another time, and
 will tell you if I fix it.

 Thanks.

 -Original Message-
 From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:
 gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Justin
 Lemkul
 Sent: Sunday, 17 May 2015 7:07 AM
 To: gmx-us...@gromacs.org
 Subject: Re: [gmx-users] energy minimization problem



 On 5/16/15 8:30 AM, Ming Tang wrote:
  Dear Justin,
 
  I tried to use small time step. First,  set dt=0.005ps, after running
 20ps, I found one chain of the triple helix just went to another water box
 totally. I guess there is something wrong with the martini ff because of
 the small time step.
  Then, I increased it to 0.01ps, after running 40ps, I checked the .gro,
 and found all the three chains stay together, which is reasonable. However,
 even use dt=0.01, the simulation can only run about 1ns. And, after
 simulating 100 ps using dt=0.01ps, the simulation can just run thousands of
 steps when dt is increased to 0.02ps. I tried many times and many different
 time steps, but still could not see the possibility for it to run hundreds
 of  nanoseconds, which is quite normal when using martini force. If the
 system can be further minimized, then it can run longer maybe.
 

 This seems entirely random and suggests instead that there is something
 simply physically unstable with the system or problematic in the topology.
 I don't use MARTINI (or CG models in general) so there's little else I can
 suggest.  Maybe someone more experienced with such systems will chime in.

 Also note that a chain moving into another box is probably just a PBC
 effect and not a true dissociation.  If it is a dissociation, it's not
 simply because of the time step.

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

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Re: [gmx-users] energy minimization problem

2015-05-18 Thread Tsjerk Wassenaar

Hi Ming Tang,

That's pretty quick. I guess that this is on multiple cores, given the size
of the system. It often helps to equilibrate on a limited number of cores,
but I'm not sure that's feasible.

Did you obtain the model by martinizing the original structure, or did you
use the relaxed structure from the atomistic simulation? How did you
solvate the system?

Cheers,

Tsjerk
On May 18, 2015 10:29, Ming Tang m21.t...@qut.edu.au wrote:

 Hi Tsjerk,

 I just tried, but it stopped for too many LICS warnings at step 6000.
 Small triple helix can be equilibrated for 1000ns with NPT.

 -Original Message-
 From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:
 gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Tsjerk
 Wassenaar
 Sent: Monday, 18 May 2015 6:21 PM
 To: Discussion list for GROMACS users
 Subject: Re: [gmx-users] energy minimization problem

 Hi Ming Tang,

 Can you run in NVT? Then afterwards you can try NPT without position
 restraints.

 Cheers,

 Tsjerk
 On May 18, 2015 10:14, Ming Tang m21.t...@qut.edu.au wrote:

  Thanks a lot, Justin
 
  It really makes me feel weird. The small triple helix with 30 amino
  acids per chain(generated simply by deleting other atoms in .pdb file
  of the real triple helix) can be equilibrated for 1ns using exactly
  the same control files, and the real triple helix can be used for full
  atomic simulation without any problem. The CG topology is generated
  using the same mitinize.py downloaded from the website. I will try for
  another time, and will tell you if I fix it.
 
  Thanks.
 
  -Original Message-
  From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:
  gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Justin
  Lemkul
  Sent: Sunday, 17 May 2015 7:07 AM
  To: gmx-us...@gromacs.org
  Subject: Re: [gmx-users] energy minimization problem
 
 
 
  On 5/16/15 8:30 AM, Ming Tang wrote:
   Dear Justin,
  
   I tried to use small time step. First,  set dt=0.005ps, after
   running
  20ps, I found one chain of the triple helix just went to another water
  box totally. I guess there is something wrong with the martini ff
  because of the small time step.
   Then, I increased it to 0.01ps, after running 40ps, I checked the
   .gro,
  and found all the three chains stay together, which is reasonable.
  However, even use dt=0.01, the simulation can only run about 1ns. And,
  after simulating 100 ps using dt=0.01ps, the simulation can just run
  thousands of steps when dt is increased to 0.02ps. I tried many times
  and many different time steps, but still could not see the possibility
  for it to run hundreds of  nanoseconds, which is quite normal when
  using martini force. If the system can be further minimized, then it can
 run longer maybe.
  
 
  This seems entirely random and suggests instead that there is
  something simply physically unstable with the system or problematic in
 the topology.
  I don't use MARTINI (or CG models in general) so there's little else I
  can suggest.  Maybe someone more experienced with such systems will
 chime in.
 
  Also note that a chain moving into another box is probably just a
  PBC effect and not a true dissociation.  If it is a dissociation, it's
  not simply because of the time step.
 
  -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
 
  ==
  --
  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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Re: [gmx-users] energy minimization problem

Hi Tsjerk,

My computer has 8 cores only, martini simulation looks much faster than full 
atomic simulation.

The command I used is here:

python martinize.py -f hyp.pdb -o system-vaccum.top -x hyp-CG.pdb -ss hyp_lys 
-p backbone -ff martini22 -collagen

editconf -f hyp-CG.pdb -c -d 1 -o hyp-CG-box.pdb

grompp -f minimization-vaccum.mdp -p system-vaccum.top -c hyp-CG-box.pdb -o 
minimization-vaccum.tpr
mdrun -deffnm minimization-vaccum -v

gmx solvate -cp minimization-vaccum.gro -cs water-box-CG_303K-1bar.gro -radius 
0.21 -o system-solvated.gro

I downloaded the CG water model from martini protein tutorial website. Is there 
anything wrong?

-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Tsjerk 
Wassenaar
Sent: Monday, 18 May 2015 6:47 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] energy minimization problem

Hi Ming Tang,

That's pretty quick. I guess that this is on multiple cores, given the size of 
the system. It often helps to equilibrate on a limited number of cores, but I'm 
not sure that's feasible.

Did you obtain the model by martinizing the original structure, or did you use 
the relaxed structure from the atomistic simulation? How did you solvate the 
system?

Cheers,

Tsjerk
On May 18, 2015 10:29, Ming Tang m21.t...@qut.edu.au wrote:

 Hi Tsjerk,

 I just tried, but it stopped for too many LICS warnings at step 6000.
 Small triple helix can be equilibrated for 1000ns with NPT.

 -Original Message-
 From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:
 gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Tsjerk 
 Wassenaar
 Sent: Monday, 18 May 2015 6:21 PM
 To: Discussion list for GROMACS users
 Subject: Re: [gmx-users] energy minimization problem

 Hi Ming Tang,

 Can you run in NVT? Then afterwards you can try NPT without position 
 restraints.

 Cheers,

 Tsjerk
 On May 18, 2015 10:14, Ming Tang m21.t...@qut.edu.au wrote:

  Thanks a lot, Justin
 
  It really makes me feel weird. The small triple helix with 30 amino 
  acids per chain(generated simply by deleting other atoms in .pdb 
  file of the real triple helix) can be equilibrated for 1ns using 
  exactly the same control files, and the real triple helix can be 
  used for full atomic simulation without any problem. The CG topology 
  is generated using the same mitinize.py downloaded from the website. 
  I will try for another time, and will tell you if I fix it.
 
  Thanks.
 
  -Original Message-
  From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:
  gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of 
  Justin Lemkul
  Sent: Sunday, 17 May 2015 7:07 AM
  To: gmx-us...@gromacs.org
  Subject: Re: [gmx-users] energy minimization problem
 
 
 
  On 5/16/15 8:30 AM, Ming Tang wrote:
   Dear Justin,
  
   I tried to use small time step. First,  set dt=0.005ps, after 
   running
  20ps, I found one chain of the triple helix just went to another 
  water box totally. I guess there is something wrong with the martini 
  ff because of the small time step.
   Then, I increased it to 0.01ps, after running 40ps, I checked the 
   .gro,
  and found all the three chains stay together, which is reasonable.
  However, even use dt=0.01, the simulation can only run about 1ns. 
  And, after simulating 100 ps using dt=0.01ps, the simulation can 
  just run thousands of steps when dt is increased to 0.02ps. I tried 
  many times and many different time steps, but still could not see 
  the possibility for it to run hundreds of  nanoseconds, which is 
  quite normal when using martini force. If the system can be further 
  minimized, then it can
 run longer maybe.
  
 
  This seems entirely random and suggests instead that there is 
  something simply physically unstable with the system or problematic 
  in
 the topology.
  I don't use MARTINI (or CG models in general) so there's little else 
  I can suggest.  Maybe someone more experienced with such systems 
  will
 chime in.
 
  Also note that a chain moving into another box is probably just a 
  PBC effect and not a true dissociation.  If it is a dissociation, 
  it's not simply because of the time step.
 
  -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
 
  ==
  --
  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

Re: [gmx-users] energy minimization problem




Hi Tsjerk,

I used the original structure generated by sabbac.

My computer has 8 cores only, martini simulation looks much faster than full 
atomic simulation.

The command I used is here:

python martinize.py -f hyp.pdb -o system-vaccum.top -x hyp-CG.pdb -ss hyp_lys 
-p backbone -ff martini22 -collagen

editconf -f hyp-CG.pdb -c -d 1 -o hyp-CG-box.pdb

grompp -f minimization-vaccum.mdp -p system-vaccum.top -c hyp-CG-box.pdb -o 
minimization-vaccum.tpr mdrun -deffnm minimization-vaccum -v

gmx solvate -cp minimization-vaccum.gro -cs water-box-CG_303K-1bar.gro -radius 
0.21 -o system-solvated.gro

I downloaded the CG water model from martini protein tutorial website. Is there 
anything wrong?


-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Tsjerk 
Wassenaar
Sent: Monday, 18 May 2015 6:47 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] energy minimization problem

Hi Ming Tang,

That's pretty quick. I guess that this is on multiple cores, given the size of 
the system. It often helps to equilibrate on a limited number of cores, but I'm 
not sure that's feasible.

Did you obtain the model by martinizing the original structure, or did you use 
the relaxed structure from the atomistic simulation? How did you solvate the 
system?

Cheers,

Tsjerk
On May 18, 2015 10:29, Ming Tang m21.t...@qut.edu.au wrote:

 Hi Tsjerk,

 I just tried, but it stopped for too many LICS warnings at step 6000.
 Small triple helix can be equilibrated for 1000ns with NPT.

 -Original Message-
 From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:
 gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Tsjerk 
 Wassenaar
 Sent: Monday, 18 May 2015 6:21 PM
 To: Discussion list for GROMACS users
 Subject: Re: [gmx-users] energy minimization problem

 Hi Ming Tang,

 Can you run in NVT? Then afterwards you can try NPT without position 
 restraints.

 Cheers,

 Tsjerk
 On May 18, 2015 10:14, Ming Tang m21.t...@qut.edu.au wrote:

  Thanks a lot, Justin
 
  It really makes me feel weird. The small triple helix with 30 amino 
  acids per chain(generated simply by deleting other atoms in .pdb 
  file of the real triple helix) can be equilibrated for 1ns using 
  exactly the same control files, and the real triple helix can be 
  used for full atomic simulation without any problem. The CG topology 
  is generated using the same mitinize.py downloaded from the website.
  I will try for another time, and will tell you if I fix it.
 
  Thanks.
 
  -Original Message-
  From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:
  gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of 
  Justin Lemkul
  Sent: Sunday, 17 May 2015 7:07 AM
  To: gmx-us...@gromacs.org
  Subject: Re: [gmx-users] energy minimization problem
 
 
 
  On 5/16/15 8:30 AM, Ming Tang wrote:
   Dear Justin,
  
   I tried to use small time step. First,  set dt=0.005ps, after 
   running
  20ps, I found one chain of the triple helix just went to another 
  water box totally. I guess there is something wrong with the martini 
  ff because of the small time step.
   Then, I increased it to 0.01ps, after running 40ps, I checked the 
   .gro,
  and found all the three chains stay together, which is reasonable.
  However, even use dt=0.01, the simulation can only run about 1ns. 
  And, after simulating 100 ps using dt=0.01ps, the simulation can 
  just run thousands of steps when dt is increased to 0.02ps. I tried 
  many times and many different time steps, but still could not see 
  the possibility for it to run hundreds of  nanoseconds, which is 
  quite normal when using martini force. If the system can be further 
  minimized, then it can
 run longer maybe.
  
 
  This seems entirely random and suggests instead that there is 
  something simply physically unstable with the system or problematic 
  in
 the topology.
  I don't use MARTINI (or CG models in general) so there's little else 
  I can suggest.  Maybe someone more experienced with such systems 
  will
 chime in.
 
  Also note that a chain moving into another box is probably just a 
  PBC effect and not a true dissociation.  If it is a dissociation, 
  it's not simply because of the time step.
 
  -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
 
  ==
  --
  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

Re: [gmx-users] energy minimization problem

Besides, the martini.itp does not contain  moleculetype CL, so I edit it like 
this:

[ moleculetype ]
; molname   nrexcl
  CL1

[ atoms ]
;id typeresnr   residu  atomcgnrcharge
 1  P4  1   CL  CL  1   -1

Please help to have a look. I do not know whether it is true or not, as the 
small triple helix used for test does not carry charge, so I did not add CL.

Thanks.

-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Ming 
Tang
Sent: Monday, 18 May 2015 7:04 PM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] energy minimization problem




Hi Tsjerk,

I used the original structure generated by sabbac.

My computer has 8 cores only, martini simulation looks much faster than full 
atomic simulation.

The command I used is here:

python martinize.py -f hyp.pdb -o system-vaccum.top -x hyp-CG.pdb -ss hyp_lys 
-p backbone -ff martini22 -collagen

editconf -f hyp-CG.pdb -c -d 1 -o hyp-CG-box.pdb

grompp -f minimization-vaccum.mdp -p system-vaccum.top -c hyp-CG-box.pdb -o 
minimization-vaccum.tpr mdrun -deffnm minimization-vaccum -v

gmx solvate -cp minimization-vaccum.gro -cs water-box-CG_303K-1bar.gro -radius 
0.21 -o system-solvated.gro

I downloaded the CG water model from martini protein tutorial website. Is there 
anything wrong?


-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Tsjerk 
Wassenaar
Sent: Monday, 18 May 2015 6:47 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] energy minimization problem

Hi Ming Tang,

That's pretty quick. I guess that this is on multiple cores, given the size of 
the system. It often helps to equilibrate on a limited number of cores, but I'm 
not sure that's feasible.

Did you obtain the model by martinizing the original structure, or did you use 
the relaxed structure from the atomistic simulation? How did you solvate the 
system?

Cheers,

Tsjerk
On May 18, 2015 10:29, Ming Tang m21.t...@qut.edu.au wrote:

 Hi Tsjerk,

 I just tried, but it stopped for too many LICS warnings at step 6000.
 Small triple helix can be equilibrated for 1000ns with NPT.

 -Original Message-
 From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:
 gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Tsjerk 
 Wassenaar
 Sent: Monday, 18 May 2015 6:21 PM
 To: Discussion list for GROMACS users
 Subject: Re: [gmx-users] energy minimization problem

 Hi Ming Tang,

 Can you run in NVT? Then afterwards you can try NPT without position 
 restraints.

 Cheers,

 Tsjerk
 On May 18, 2015 10:14, Ming Tang m21.t...@qut.edu.au wrote:

  Thanks a lot, Justin
 
  It really makes me feel weird. The small triple helix with 30 amino 
  acids per chain(generated simply by deleting other atoms in .pdb 
  file of the real triple helix) can be equilibrated for 1ns using 
  exactly the same control files, and the real triple helix can be 
  used for full atomic simulation without any problem. The CG topology 
  is generated using the same mitinize.py downloaded from the website.
  I will try for another time, and will tell you if I fix it.
 
  Thanks.
 
  -Original Message-
  From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:
  gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of 
  Justin Lemkul
  Sent: Sunday, 17 May 2015 7:07 AM
  To: gmx-us...@gromacs.org
  Subject: Re: [gmx-users] energy minimization problem
 
 
 
  On 5/16/15 8:30 AM, Ming Tang wrote:
   Dear Justin,
  
   I tried to use small time step. First,  set dt=0.005ps, after 
   running
  20ps, I found one chain of the triple helix just went to another 
  water box totally. I guess there is something wrong with the martini 
  ff because of the small time step.
   Then, I increased it to 0.01ps, after running 40ps, I checked the 
   .gro,
  and found all the three chains stay together, which is reasonable.
  However, even use dt=0.01, the simulation can only run about 1ns. 
  And, after simulating 100 ps using dt=0.01ps, the simulation can 
  just run thousands of steps when dt is increased to 0.02ps. I tried 
  many times and many different time steps, but still could not see 
  the possibility for it to run hundreds of  nanoseconds, which is 
  quite normal when using martini force. If the system can be further 
  minimized, then it can
 run longer maybe.
  
 
  This seems entirely random and suggests instead that there is 
  something simply physically unstable with the system or problematic 
  in
 the topology.
  I don't use MARTINI (or CG models in general) so there's little else 
  I can suggest.  Maybe someone more experienced with such systems 
  will
 chime in.
 
  Also note that a chain moving into another box is probably just a 
  PBC effect and not a true dissociation.  If it is a dissociation

Re: [gmx-users] energy minimization problem