[gmx-users] About using GLYCAM force field in Gromacs

2017-05-22 Thread ???? 
Dear Gromacs Users,

  I want to know that if there is a easy way of using GLYCAM force field in 
Gromacs. Thanks in advance!

Best regards
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Re: [gmx-users] Minimisation

2017-05-22 Thread Justin Lemkul 



On 5/22/17 4:59 PM, Pandya, Akash wrote:

Sorry I meant 20 A. But I'll look into expanding the box size and see if it 
works. Thanks for your help.



Making the box larger is unlikely to be useful.  You should simplify the system 
by simulating individual components as the link I provided before describes.  A 
2-A box would clearly cause clashes.  A 20-A box should not, but you should be 
mindful of cutoffs and the requirement of satisfying the minimum image convention.


-Justin


Akash

-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: 22 May 2017 21:52
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Minimisation



On 5/22/17 4:42 PM, Pandya, Akash wrote:

Is there a chance that as my simulation box is quite small 2 angstroms and 
citrate is a charged anion, this could be a cause of my system blowing up?



I don't see how any sensible system can be that small.  Are you sure it's 2 A 
and not 2 nm?  Even 2 nm is too small given conventional cutoffs for most force 
fields, and you will always have an absurdly high concentration of any species 
in such a box.

-Justin


-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: 22 May 2017 13:26
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Minimisation



On 5/22/17 7:25 AM, Pandya, Akash wrote:

What could be wrong with the topology could you please elaborate? I added 
glycine and citrate molecules  to the simulation box randomly. Could it be the 
fact I added topology for glycine and citrate in the wrong way?

This is how my topol.top file looks:

; Include Citrate Topology
#include "Citrate.itp"
#ifdef POSRES
#include "Citrate_posre.itp"
#endif

; Include GLY Topology
#include "GLY.itp"
#ifdef POSRES
#include "GLY_posre.itp"
#endif

[ moleculetype ]
; Namenrexcl
Protein_chain_H 3



A series of #include statements is not a useful diagnostic.  You should start 
by inspecting your coordinates, particularly whatever atom 6640 is, and its 
surroundings.  There may simply be a bad clash there that can be resolved 
easily.  Otherwise, follow 
http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System
  Glycine should come from the force field itself and likely is not 
topologically problematic, but if you constructed your own citrate parameters, 
you should check their correctness, as well.

-Justin


Akash

-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: 22 May 2017 12:13
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Minimisation



On 5/22/17 6:47 AM, Pandya, Akash wrote:

Hi all,


During Minimisation I get the following output that the simulation ended 
prematurely.



Steepest Descents:
   Tolerance (Fmax)   =  1.0e+03
   Number of steps=   50
Step=0, Dmax= 1.0e-02 nm, Epot=  7.39413e+26 Fmax= inf, atom= 6640
Step=   14, Dmax= 1.2e-06 nm, Epot=  7.39413e+26 Fmax= inf, atom= 6640

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)

How do I increase my constraint accuracy? Which file do I have to change?



That's not your problem.  You have infinite force, which means you have some 
catastrophic problem with either your coordinates or topology.

-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] Minimisation

2017-05-22 Thread Pandya, Akash 
One quick question what would you suggest a suitable box size is?


-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: 22 May 2017 21:52
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Minimisation



On 5/22/17 4:42 PM, Pandya, Akash wrote:
> Is there a chance that as my simulation box is quite small 2 angstroms and 
> citrate is a charged anion, this could be a cause of my system blowing up?
>

I don't see how any sensible system can be that small.  Are you sure it's 2 A 
and not 2 nm?  Even 2 nm is too small given conventional cutoffs for most force 
fields, and you will always have an absurdly high concentration of any species 
in such a box.

-Justin

> -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: 22 May 2017 13:26
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] Minimisation
>
>
>
> On 5/22/17 7:25 AM, Pandya, Akash wrote:
>> What could be wrong with the topology could you please elaborate? I added 
>> glycine and citrate molecules  to the simulation box randomly. Could it be 
>> the fact I added topology for glycine and citrate in the wrong way?
>>
>> This is how my topol.top file looks:
>>
>> ; Include Citrate Topology
>> #include "Citrate.itp"
>> #ifdef POSRES
>> #include "Citrate_posre.itp"
>> #endif
>>
>> ; Include GLY Topology
>> #include "GLY.itp"
>> #ifdef POSRES
>> #include "GLY_posre.itp"
>> #endif
>>
>> [ moleculetype ]
>> ; Namenrexcl
>> Protein_chain_H 3
>>
>
> A series of #include statements is not a useful diagnostic.  You should start 
> by inspecting your coordinates, particularly whatever atom 6640 is, and its 
> surroundings.  There may simply be a bad clash there that can be resolved 
> easily.  Otherwise, follow 
> http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System
>   Glycine should come from the force field itself and likely is not 
> topologically problematic, but if you constructed your own citrate 
> parameters, you should check their correctness, as well.
>
> -Justin
>
>> Akash
>>
>> -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: 22 May 2017 12:13
>> To: gmx-us...@gromacs.org
>> Subject: Re: [gmx-users] Minimisation
>>
>>
>>
>> On 5/22/17 6:47 AM, Pandya, Akash wrote:
>>> Hi all,
>>>
>>>
>>> During Minimisation I get the following output that the simulation ended 
>>> prematurely.
>>>
>>>
>>>
>>> Steepest Descents:
>>>Tolerance (Fmax)   =  1.0e+03
>>>Number of steps=   50
>>> Step=0, Dmax= 1.0e-02 nm, Epot=  7.39413e+26 Fmax= inf, atom= 
>>> 6640
>>> Step=   14, Dmax= 1.2e-06 nm, Epot=  7.39413e+26 Fmax= inf, atom= 
>>> 6640
>>>
>>> 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)
>>>
>>> How do I increase my constraint accuracy? Which file do I have to change?
>>>
>>
>> That's not your problem.  You have infinite force, which means you have some 
>> catastrophic problem with either your coordinates or topology.
>>
>> -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.
>>
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA

Re: [gmx-users] Minimisation

2017-05-22 Thread Pandya, Akash 
Sorry I meant 20 A. But I'll look into expanding the box size and see if it 
works. Thanks for your help.

Akash

-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: 22 May 2017 21:52
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Minimisation



On 5/22/17 4:42 PM, Pandya, Akash wrote:
> Is there a chance that as my simulation box is quite small 2 angstroms and 
> citrate is a charged anion, this could be a cause of my system blowing up?
>

I don't see how any sensible system can be that small.  Are you sure it's 2 A 
and not 2 nm?  Even 2 nm is too small given conventional cutoffs for most force 
fields, and you will always have an absurdly high concentration of any species 
in such a box.

-Justin

> -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: 22 May 2017 13:26
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] Minimisation
>
>
>
> On 5/22/17 7:25 AM, Pandya, Akash wrote:
>> What could be wrong with the topology could you please elaborate? I added 
>> glycine and citrate molecules  to the simulation box randomly. Could it be 
>> the fact I added topology for glycine and citrate in the wrong way?
>>
>> This is how my topol.top file looks:
>>
>> ; Include Citrate Topology
>> #include "Citrate.itp"
>> #ifdef POSRES
>> #include "Citrate_posre.itp"
>> #endif
>>
>> ; Include GLY Topology
>> #include "GLY.itp"
>> #ifdef POSRES
>> #include "GLY_posre.itp"
>> #endif
>>
>> [ moleculetype ]
>> ; Namenrexcl
>> Protein_chain_H 3
>>
>
> A series of #include statements is not a useful diagnostic.  You should start 
> by inspecting your coordinates, particularly whatever atom 6640 is, and its 
> surroundings.  There may simply be a bad clash there that can be resolved 
> easily.  Otherwise, follow 
> http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System
>   Glycine should come from the force field itself and likely is not 
> topologically problematic, but if you constructed your own citrate 
> parameters, you should check their correctness, as well.
>
> -Justin
>
>> Akash
>>
>> -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: 22 May 2017 12:13
>> To: gmx-us...@gromacs.org
>> Subject: Re: [gmx-users] Minimisation
>>
>>
>>
>> On 5/22/17 6:47 AM, Pandya, Akash wrote:
>>> Hi all,
>>>
>>>
>>> During Minimisation I get the following output that the simulation ended 
>>> prematurely.
>>>
>>>
>>>
>>> Steepest Descents:
>>>Tolerance (Fmax)   =  1.0e+03
>>>Number of steps=   50
>>> Step=0, Dmax= 1.0e-02 nm, Epot=  7.39413e+26 Fmax= inf, atom= 
>>> 6640
>>> Step=   14, Dmax= 1.2e-06 nm, Epot=  7.39413e+26 Fmax= inf, atom= 
>>> 6640
>>>
>>> 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)
>>>
>>> How do I increase my constraint accuracy? Which file do I have to change?
>>>
>>
>> That's not your problem.  You have infinite force, which means you have some 
>> catastrophic problem with either your coordinates or topology.
>>
>> -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.
>>
>
> --
> ==
>
> Justin

Re: [gmx-users] Minimisation

2017-05-22 Thread Justin Lemkul 



On 5/22/17 4:42 PM, Pandya, Akash wrote:

Is there a chance that as my simulation box is quite small 2 angstroms and 
citrate is a charged anion, this could be a cause of my system blowing up?



I don't see how any sensible system can be that small.  Are you sure it's 2 A 
and not 2 nm?  Even 2 nm is too small given conventional cutoffs for most force 
fields, and you will always have an absurdly high concentration of any species 
in such a box.


-Justin


-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: 22 May 2017 13:26
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Minimisation



On 5/22/17 7:25 AM, Pandya, Akash wrote:

What could be wrong with the topology could you please elaborate? I added 
glycine and citrate molecules  to the simulation box randomly. Could it be the 
fact I added topology for glycine and citrate in the wrong way?

This is how my topol.top file looks:

; Include Citrate Topology
#include "Citrate.itp"
#ifdef POSRES
#include "Citrate_posre.itp"
#endif

; Include GLY Topology
#include "GLY.itp"
#ifdef POSRES
#include "GLY_posre.itp"
#endif

[ moleculetype ]
; Namenrexcl
Protein_chain_H 3



A series of #include statements is not a useful diagnostic.  You should start 
by inspecting your coordinates, particularly whatever atom 6640 is, and its 
surroundings.  There may simply be a bad clash there that can be resolved 
easily.  Otherwise, follow 
http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System
  Glycine should come from the force field itself and likely is not 
topologically problematic, but if you constructed your own citrate parameters, 
you should check their correctness, as well.

-Justin


Akash

-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: 22 May 2017 12:13
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Minimisation



On 5/22/17 6:47 AM, Pandya, Akash wrote:

Hi all,


During Minimisation I get the following output that the simulation ended 
prematurely.



Steepest Descents:
   Tolerance (Fmax)   =  1.0e+03
   Number of steps=   50
Step=0, Dmax= 1.0e-02 nm, Epot=  7.39413e+26 Fmax= inf, atom= 6640
Step=   14, Dmax= 1.2e-06 nm, Epot=  7.39413e+26 Fmax= inf, atom= 6640

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)

How do I increase my constraint accuracy? Which file do I have to change?



That's not your problem.  You have infinite force, which means you have some 
catastrophic problem with either your coordinates or topology.

-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.



--
==

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

Re: [gmx-users] Minimisation

2017-05-22 Thread Pandya, Akash 
Is there a chance that as my simulation box is quite small 2 angstroms and 
citrate is a charged anion, this could be a cause of my system blowing up?   

-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: 22 May 2017 13:26
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Minimisation



On 5/22/17 7:25 AM, Pandya, Akash wrote:
> What could be wrong with the topology could you please elaborate? I added 
> glycine and citrate molecules  to the simulation box randomly. Could it be 
> the fact I added topology for glycine and citrate in the wrong way?
>
> This is how my topol.top file looks:
>
> ; Include Citrate Topology
> #include "Citrate.itp"
> #ifdef POSRES
> #include "Citrate_posre.itp"
> #endif
>
> ; Include GLY Topology
> #include "GLY.itp"
> #ifdef POSRES
> #include "GLY_posre.itp"
> #endif
>
> [ moleculetype ]
> ; Namenrexcl
> Protein_chain_H 3
>

A series of #include statements is not a useful diagnostic.  You should start 
by inspecting your coordinates, particularly whatever atom 6640 is, and its 
surroundings.  There may simply be a bad clash there that can be resolved 
easily.  Otherwise, follow 
http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System
  Glycine should come from the force field itself and likely is not 
topologically problematic, but if you constructed your own citrate parameters, 
you should check their correctness, as well.

-Justin

> Akash
>
> -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: 22 May 2017 12:13
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] Minimisation
>
>
>
> On 5/22/17 6:47 AM, Pandya, Akash wrote:
>> Hi all,
>>
>>
>> During Minimisation I get the following output that the simulation ended 
>> prematurely.
>>
>>
>>
>> Steepest Descents:
>>Tolerance (Fmax)   =  1.0e+03
>>Number of steps=   50
>> Step=0, Dmax= 1.0e-02 nm, Epot=  7.39413e+26 Fmax= inf, atom= 
>> 6640
>> Step=   14, Dmax= 1.2e-06 nm, Epot=  7.39413e+26 Fmax= inf, atom= 
>> 6640
>>
>> 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)
>>
>> How do I increase my constraint accuracy? Which file do I have to change?
>>
>
> That's not your problem.  You have infinite force, which means you have some 
> catastrophic problem with either your coordinates or topology.
>
> -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
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==

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Ruth L. Kirschstein NRSA Postdoctoral Fellow

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

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Re: [gmx-users] Need to confirm parameters.

2017-05-22 Thread Justin Lemkul 



On 5/22/17 10:00 AM, Sailesh Bataju wrote:

Hi Sir,

Right, CHARMM force field is what I'm looking for. Thank you very much
sir for your advice. I've made parameter file of isobutane using
CHARMM36 force field files shown below so I've a few questions
regarding it.

[ defaults ]
; nbfunccomb-rule   gen-pairs   fudgeLJ fudgeQQ
  1 1   yes 1.0 1.0

[ atomtypes ]
;   name  at.num   masscharge ptype   sigma epsilon
   CC31A 612.011000   -0.090A   0.356359487256  0.13389
   CC33A 612.011000   -0.270A   0.363486677001  0.32635
   HCA1A 1 1.0080000.090A   0.238760856462  0.18828
   HCA3A 1 1.0080000.090A   0.238760856462  0.10042

[ moleculetype ]
; Namenrexcl
isobutane   3

[ atoms ]
;   nr  typeresnr   residue atomcgnrcharge  mass
typeBchargeB  massB
; residue   1 IBUT rtp IBUT q  0.0
1   CC33A   1   IBUTC1  1   -0.270  ; qtot
-0.270
2   HCA3A   1   IBUTH2  20.090  ; qtot -0.180
3   HCA3A   1   IBUTH3  30.090  ; qtot -0.090
4   HCA3A   1   IBUTH4  40.090  ; qtot  0.000
5   CC31A   1   IBUTC5  5   -0.090  ; qtot -0.090
6   HCA1A   1   IBUTH6  60.090  ; qtot  0.000
7   CC33A   1   IBUTC7  7   -0.270  ; qtot -0.270
8   HCA3A   1   IBUTH8  80.090  ; qtot -0.180
9   HCA3A   1   IBUTH9  90.090  ; qtot -0.090
10  HCA3A   1   IBUTH10 10   0.090  ; qtot  0.000
11  CC33A   1   IBUTC11 11  -0.270  ; qtot -0.270
12  HCA3A   1   IBUTH12 12   0.090  ; qtot -0.180
13  HCA3A   1   IBUTH13 13   0.090  ; qtot -0.090
14  HCA3A   1   IBUTH14 14   0.090  ; qtot  0.000

[ bonds ]
:   ai  aj  funct   b0(nm)  kb[KJ mol^(-1) nm^(-2)] ; 13 bonds
1   2   1   0.  269449.60
1   3   1   0.  269449.60
1   4   1   0.  269449.60   ;
 C13
1   5   1   0.1538  186188.00   ;
 |
5   6   1   0.  258571.20   ;
H14--C11--H12
5   7   1   0.1538  186188.00   ;
 |
5   11  1   0.1538  186188.00   ;
 H2  |   H8
7   8   1   0.  269449.60   ;
 |   |   |
7   9   1   0.  269449.60   ;
 H3--C1--C5--C7--H9
7   10  1   0.  269449.60   ;
 |   |   |
11  12  1   0.  269449.60   ;
 H4  H6  H10
11  13  1   0.  269449.60   ;
11  14  1   0.  269449.60

[ pairs ]
;ai aj funct; 27 pairs
 1  8  1
 1  9  1
 1 10  1
 1 12  1
 1 13  1
 1 14  1
 2  6  1
 2  7  1
 2 11  1
 3  6  1
 3  7  1
 3 11  1
 4  6  1
 4  7  1
 4 11  1
 6  8  1
 6  9  1
 6 10  1
 6 12  1
 6 13  1
 6 14  1
 7 12  1
 7 13  1
 7 14  1
 8 11  1
 9 11  1
10 11  1

[ angles ]
;  ai   aj  ak  funct   theta0(deg) ktheta(KJ mol^(-1) rad^(-2))
 ub0(nm)  kub(KJ mol^(-1) nm^(-2)) ; 24 angles
2   1   3   5   108.40  297.064000
 0.1802   4518.72; HCA3A-CC33A-HCA3A
2   1   4   5   108.40  297.064000
 0.1802   4518.72
3   1   4   5   108.40  297.064000
 0.1802   4518.72
8   7   9   5   108.40  297.064000
 0.1802   4518.72
8   7   10  5   108.40  297.064000
 0.1802   4518.72
9   7   10  5   108.40  297.064000
 0.1802   4518.72
12  11  13  5   108.40  297.064000
 0.1802   4518.72
12  11  14  5   108.40  297.064000
 0.1802   4518.72
13  11  14  5   108.40  297.064000
 0.1802   4518.72
5   1   2   5   110.10  279.742240
 0.2179   18853.10   ; CC31A-CC33A-HCA3A
5   1   3   5   110.10  279.742240
 0.2179   18853.10
5   1   4   5   110.10  279.742240
 0.2179   18853.10
5   7   8   5   110.10  279.742240
 0.2179   18853.10
5   7   9   5   110.10

Re: [gmx-users] PBC fix for visualization

2017-05-22 Thread Mohsen Ramezanpour 
Hi Dallas,

Thanks for your reply.
I did try -pbc cluster for waters. It could fix it somehow but not
completely.
After that, I had to use -pbc center to fix it. Still, I do not get what I
want.
Unfortunately, some waters and lipids are appearing from the other side of
the box.

Cheers,
Mohsen


On Sun, May 21, 2017 at 8:12 PM, Dallas Warren 
wrote:

> I have found the cluster option of -pbc to work well for putting
> aggregates back together correctly. Some times you do need an index
> file and appropriate groups to assist with it getting it right.
>
> gmx trjconv -pbc cluster
> Catch ya,
>
> Dr. Dallas Warren
> Drug Delivery, Disposition and Dynamics
> Monash Institute of Pharmaceutical Sciences, Monash University
> 381 Royal Parade, Parkville VIC 3052
> dallas.war...@monash.edu
> -
> When the only tool you own is a hammer, every problem begins to resemble a
> nail.
>
>
> On 16 May 2017 at 07:50, Mohsen Ramezanpour
>  wrote:
> > Dear Gromacs users,
> >
> > I have an HII phase made of one inverted cylinder (and waters inside) in
> a
> > triclinic box with 90, 90, 60 angles. After running the simulation, this
> > cylinder become bent like a curve. I.e. is not a perfect cylinder
> anymore.
> > As a result, some water molecules and lipids pass the box sides and enter
> > from the other side of box because of PBC.
> > Now, I want to make the cylinder again but I am not sure how to do so.
> >
> > The best I could do was to use "-pbc mol  -ur compact" options in
> trjconv.
> > However, here are still some lipids and molecules which are not part of
> the
> > cylinder.
> >
> > Any idea how could I fix the effect of these PBC in visualization?
> >
> > Thanks
> > Mohsen
> >
> > --
> > *Rewards work better than punishment ...*
> > --
> > Gromacs Users mailing list
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Re: [gmx-users] Need to confirm parameters.

2017-05-22 Thread Sailesh Bataju 
Hi Sir,

Right, CHARMM force field is what I'm looking for. Thank you very much
sir for your advice. I've made parameter file of isobutane using
CHARMM36 force field files shown below so I've a few questions
regarding it.

[ defaults ]
; nbfunccomb-rule   gen-pairs   fudgeLJ fudgeQQ
  1 1   yes 1.0 1.0

[ atomtypes ]
;   name  at.num   masscharge ptype   sigma epsilon
   CC31A 612.011000   -0.090A   0.356359487256  0.13389
   CC33A 612.011000   -0.270A   0.363486677001  0.32635
   HCA1A 1 1.0080000.090A   0.238760856462  0.18828
   HCA3A 1 1.0080000.090A   0.238760856462  0.10042

[ moleculetype ]
; Namenrexcl
isobutane   3

[ atoms ]
;   nr  typeresnr   residue atomcgnrcharge  mass
typeBchargeB  massB
; residue   1 IBUT rtp IBUT q  0.0
1   CC33A   1   IBUTC1  1   -0.270  ; qtot
-0.270
2   HCA3A   1   IBUTH2  20.090  ; qtot -0.180
3   HCA3A   1   IBUTH3  30.090  ; qtot -0.090
4   HCA3A   1   IBUTH4  40.090  ; qtot  0.000
5   CC31A   1   IBUTC5  5   -0.090  ; qtot -0.090
6   HCA1A   1   IBUTH6  60.090  ; qtot  0.000
7   CC33A   1   IBUTC7  7   -0.270  ; qtot -0.270
8   HCA3A   1   IBUTH8  80.090  ; qtot -0.180
9   HCA3A   1   IBUTH9  90.090  ; qtot -0.090
10  HCA3A   1   IBUTH10 10   0.090  ; qtot  0.000
11  CC33A   1   IBUTC11 11  -0.270  ; qtot -0.270
12  HCA3A   1   IBUTH12 12   0.090  ; qtot -0.180
13  HCA3A   1   IBUTH13 13   0.090  ; qtot -0.090
14  HCA3A   1   IBUTH14 14   0.090  ; qtot  0.000

[ bonds ]
:   ai  aj  funct   b0(nm)  kb[KJ mol^(-1) nm^(-2)] ; 13 bonds
1   2   1   0.  269449.60
1   3   1   0.  269449.60
1   4   1   0.  269449.60   ;
 C13
1   5   1   0.1538  186188.00   ;
 |
5   6   1   0.  258571.20   ;
H14--C11--H12
5   7   1   0.1538  186188.00   ;
 |
5   11  1   0.1538  186188.00   ;
 H2  |   H8
7   8   1   0.  269449.60   ;
 |   |   |
7   9   1   0.  269449.60   ;
 H3--C1--C5--C7--H9
7   10  1   0.  269449.60   ;
 |   |   |
11  12  1   0.  269449.60   ;
 H4  H6  H10
11  13  1   0.  269449.60   ;
11  14  1   0.  269449.60

[ pairs ]
;ai aj funct; 27 pairs
 1  8  1
 1  9  1
 1 10  1
 1 12  1
 1 13  1
 1 14  1
 2  6  1
 2  7  1
 2 11  1
 3  6  1
 3  7  1
 3 11  1
 4  6  1
 4  7  1
 4 11  1
 6  8  1
 6  9  1
 6 10  1
 6 12  1
 6 13  1
 6 14  1
 7 12  1
 7 13  1
 7 14  1
 8 11  1
 9 11  1
10 11  1

[ angles ]
;  ai   aj  ak  funct   theta0(deg) ktheta(KJ mol^(-1) rad^(-2))
 ub0(nm)  kub(KJ mol^(-1) nm^(-2)) ; 24 angles
2   1   3   5   108.40  297.064000
 0.1802   4518.72; HCA3A-CC33A-HCA3A
2   1   4   5   108.40  297.064000
 0.1802   4518.72
3   1   4   5   108.40  297.064000
 0.1802   4518.72
8   7   9   5   108.40  297.064000
 0.1802   4518.72
8   7   10  5   108.40  297.064000
 0.1802   4518.72
9   7   10  5   108.40  297.064000
 0.1802   4518.72
12  11  13  5   108.40  297.064000
 0.1802   4518.72
12  11  14  5   108.40  297.064000
 0.1802   4518.72
13  11  14  5   108.40  297.064000
 0.1802   4518.72
5   1   2   5   110.10  279.742240
 0.2179   18853.10   ; CC31A-CC33A-HCA3A
5   1   3   5   110.10  279.742240
 0.2179   18853.10
5   1   4   5   110.10  279.742240
 0.2179   18853.10
5   7   8   5   110.10  279.742240
 0.2179   18853.10
5   7   9   5   110.10  279.742240
 0.2179   18853.10
5   7

Re: [gmx-users] Minimisation

2017-05-22 Thread Justin Lemkul 



On 5/22/17 7:25 AM, Pandya, Akash wrote:

What could be wrong with the topology could you please elaborate? I added 
glycine and citrate molecules  to the simulation box randomly. Could it be the 
fact I added topology for glycine and citrate in the wrong way?

This is how my topol.top file looks:

; Include Citrate Topology
#include "Citrate.itp"
#ifdef POSRES
#include "Citrate_posre.itp"
#endif

; Include GLY Topology
#include "GLY.itp"
#ifdef POSRES
#include "GLY_posre.itp"
#endif

[ moleculetype ]
; Namenrexcl
Protein_chain_H 3



A series of #include statements is not a useful diagnostic.  You should start by 
inspecting your coordinates, particularly whatever atom 6640 is, and its 
surroundings.  There may simply be a bad clash there that can be resolved 
easily.  Otherwise, follow 
http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System 
 Glycine should come from the force field itself and likely is not 
topologically problematic, but if you constructed your own citrate parameters, 
you should check their correctness, as well.


-Justin


Akash

-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: 22 May 2017 12:13
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Minimisation



On 5/22/17 6:47 AM, Pandya, Akash wrote:

Hi all,


During Minimisation I get the following output that the simulation ended 
prematurely.



Steepest Descents:
   Tolerance (Fmax)   =  1.0e+03
   Number of steps=   50
Step=0, Dmax= 1.0e-02 nm, Epot=  7.39413e+26 Fmax= inf, atom= 6640
Step=   14, Dmax= 1.2e-06 nm, Epot=  7.39413e+26 Fmax= inf, atom= 6640

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)

How do I increase my constraint accuracy? Which file do I have to change?



That's not your problem.  You have infinite force, which means you have some 
catastrophic problem with either your coordinates or topology.

-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] Minimisation

2017-05-22 Thread Pandya, Akash 
What could be wrong with the topology could you please elaborate? I added 
glycine and citrate molecules  to the simulation box randomly. Could it be the 
fact I added topology for glycine and citrate in the wrong way?

This is how my topol.top file looks:

; Include Citrate Topology
#include "Citrate.itp"
#ifdef POSRES
#include "Citrate_posre.itp"
#endif

; Include GLY Topology
#include "GLY.itp"
#ifdef POSRES
#include "GLY_posre.itp"
#endif

[ moleculetype ]
; Namenrexcl
Protein_chain_H 3

Akash

-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: 22 May 2017 12:13
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Minimisation



On 5/22/17 6:47 AM, Pandya, Akash wrote:
> Hi all,
>
>
> During Minimisation I get the following output that the simulation ended 
> prematurely.
>
>
>
> Steepest Descents:
>Tolerance (Fmax)   =  1.0e+03
>Number of steps=   50
> Step=0, Dmax= 1.0e-02 nm, Epot=  7.39413e+26 Fmax= inf, atom= 6640
> Step=   14, Dmax= 1.2e-06 nm, Epot=  7.39413e+26 Fmax= inf, atom= 6640
>
> 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)
>
> How do I increase my constraint accuracy? Which file do I have to change?
>

That's not your problem.  You have infinite force, which means you have some 
catastrophic problem with either your coordinates or topology.

-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] Fwd: Topology error

2017-05-22 Thread Justin Lemkul 



On 5/22/17 6:55 AM, Jai Krishna wrote:

Dear Sir/Ma'am,

I am trying to generate topology file for my metalloprotein that has FeS
cluster and Fe2+ atoms in it. When I run the pdb2gmx command, it fails to
generate the topology file. The error says -   Residue 'FE2' not found in
residue topology database.

Could you please help me with this query? What steps should I take to
proceed forward with it. I also like to tell you that I need these atoms in
my protein for ligand to bind and for simulation also.



This is a very difficult issue.  Additive force fields do not treat multivalent 
ions well, and transition elements are extremely challenging due to their 
complex real world behavior.  Hence any parameters that a given force field 
might have for something like Fe2+ are probably only going to be in the context 
of heme, which also likely has covalent bonds between Fe2+ and ligating atoms 
because the nonbonded treatment is badly inadequate.


The FeS cluster is even worse.  You'd have to parametrize that, along with the 
ligating residues, due to the considerable effects of polarization and charge 
transfer.  Some efforts may be made in parts of the literature, so do some 
homework first, but often these kinds of cases are treated with QM/MM to 
side-step the force field issue.  Whereas parametrizing new species (ligands, 
modified residues) is considered an expert topic, anything to do with transition 
elements and cofactors like these would be an expert expert topic.


-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] Minimisation

2017-05-22 Thread Justin Lemkul 



On 5/22/17 6:47 AM, Pandya, Akash wrote:

Hi all,


During Minimisation I get the following output that the simulation ended 
prematurely.



Steepest Descents:
   Tolerance (Fmax)   =  1.0e+03
   Number of steps=   50
Step=0, Dmax= 1.0e-02 nm, Epot=  7.39413e+26 Fmax= inf, atom= 6640
Step=   14, Dmax= 1.2e-06 nm, Epot=  7.39413e+26 Fmax= inf, atom= 6640

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)

How do I increase my constraint accuracy? Which file do I have to change?



That's not your problem.  You have infinite force, which means you have some 
catastrophic problem with either your coordinates or topology.


-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] mdp file for 370 K MD based on Justin's tutorial

2017-05-22 Thread Justin Lemkul 



On 5/22/17 6:47 AM, ZHANG Cheng wrote:

Dear Joao,
Sorry, I forgot. Thank you for reminding me. Is that all right now? Is that 
true that NVT needs to change two lines, while NPT and production run only need 
to change one line?




Yes.

-Justin


Yours sincerely
Cheng


1) In the NVT:
ref_t = 370  370   ; reference temperature, one for each group, in K
gen_temp = 370 ; temperature for Maxwell distribution



2)  In the NPT:
ref_t = 370  370; reference temperature, one for each group, in K


3) In the production run:
ref_t   = 370 370   ; reference temperature, one for each 
group, in K



--
==

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] Martini Website is not accessible

2017-05-22 Thread Anurag Dobhal 
Okay,

Thank You




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



On Mon, May 22, 2017 at 5:17 PM, Peter Kroon  wrote:

> Hi,
>
>
> we are aware of it and will probably fix it later today. It's an update
> gone wrong.
>
>
> Peter
>
>
> On 22-05-17 11:44, Anurag Dobhal wrote:
> > Hello Gromacs users,
> >
> > This query is not related to typical gromacs error. I am unable to access
> > the Martini Forcefield website (http://cgmartini.nl/) from the past few
> > days. I just wanted to know if any of the gromacs users are aware of this
> > issue ? am I opening the right website ?
> >
> > Thank you
> >
> >
> >
> > *Anurag Dobhal*
> > *Graduate Student (Bioprocess Technology)*
> > *Institute of Chemical Technology, Mumbai*
> >
>
>
>
> --
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[gmx-users] Fwd: Topology error

2017-05-22 Thread Jai Krishna 
Dear Sir/Ma'am,

I am trying to generate topology file for my metalloprotein that has FeS
cluster and Fe2+ atoms in it. When I run the pdb2gmx command, it fails to
generate the topology file. The error says -   Residue 'FE2' not found in
residue topology database.

Could you please help me with this query? What steps should I take to
proceed forward with it. I also like to tell you that I need these atoms in
my protein for ligand to bind and for simulation also.

Thank you in advance.

Regards,
Jai Krishna
IIT Roorkee
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Re: [gmx-users] Martini Website is not accessible

2017-05-22 Thread Peter Kroon 
Hi,


we are aware of it and will probably fix it later today. It's an update
gone wrong.


Peter


On 22-05-17 11:44, Anurag Dobhal wrote:
> Hello Gromacs users,
>
> This query is not related to typical gromacs error. I am unable to access
> the Martini Forcefield website (http://cgmartini.nl/) from the past few
> days. I just wanted to know if any of the gromacs users are aware of this
> issue ? am I opening the right website ?
>
> Thank you
>
>
>
> *Anurag Dobhal*
> *Graduate Student (Bioprocess Technology)*
> *Institute of Chemical Technology, Mumbai*
>


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Re: [gmx-users] mdp file for 370 K MD based on Justin's tutorial

2017-05-22 Thread ZHANG Cheng 
Dear Joao,
Sorry, I forgot. Thank you for reminding me. Is that all right now? Is that 
true that NVT needs to change two lines, while NPT and production run only need 
to change one line?


Yours sincerely
Cheng


1) In the NVT:
ref_t = 370  370   ; reference temperature, one for each group, in K
gen_temp = 370 ; temperature for Maxwell distribution



2)  In the NPT:
ref_t = 370  370; reference temperature, one for each group, in K


3) In the production run:
ref_t   = 370 370   ; reference temperature, one for each 
group, in K
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[gmx-users] Minimisation

2017-05-22 Thread Pandya, Akash 
Hi all,


During Minimisation I get the following output that the simulation ended 
prematurely.



Steepest Descents:
   Tolerance (Fmax)   =  1.0e+03
   Number of steps=   50
Step=0, Dmax= 1.0e-02 nm, Epot=  7.39413e+26 Fmax= inf, atom= 6640
Step=   14, Dmax= 1.2e-06 nm, Epot=  7.39413e+26 Fmax= inf, atom= 6640

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)

How do I increase my constraint accuracy? Which file do I have to change?

Best wishes,

Akash
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Re: [gmx-users] Using CHARMM36 in GROMACS to simulate polysaccharides

2017-05-22 Thread Justin Lemkul 



On 5/22/17 1:09 AM, Mohammad Hassan Khatami wrote:

Hi Justin,
I am asked to focus on learning how to change and update the CHARMM36 
parameters, so I could implement the future changes and patches easier. (Thus, 
I am not focused in the Glycan Reader, at the moment.)

Thank you! I think I now have a better understanding of what should I do. For 
each part of my polymer,i.e. the initial, the middle and the final part, I have 
to modify the AGLC molecule to represent each of these parts, seperately.
So, lets say to introduce the 1->4 linkage, I need to to apply 14ba patch from 
the top_all36_carb.rtf into the merged.rtp file of GROMACS CHARMM36. In this case, 
I need to create a new version of [ AGLC ] molecule (lets call it [ AGLC14 ]) in 
the merged.rtp, with the changes below from the the top_all36_carb.rtf, applied to 
it:


Note that your residue name must be limited to 4 characters so it can properly 
be read from the input coordinates.  AGLC14 won't work.



! equatorial-axial 1->4 linkage
PRES 14ba   0.02 ! (i)1->4(i-1) equatorial at C1 and axial at C4
dele atom 1HO4
dele atom 2HO1
dele atom 2O1
ATOM 1C4  CC31610.09 !
ATOM 1O4  OC301-0.36 !
ATOM 2C1  CC31620.29 !
BOND 1O4  2C1
I have to remove the HO4, HO1 and O1 lines and modify the values for the C4, O4 
and C1 atoms. Then, I need to add the bond of

[ bond ]
…
O4  +C1



Correct.


Then, I need to apply  the bonds and angles parameters in the the 
top_all36_carb.rtf (below), into the merged.vsd file of the GROMACS CHARMM36.
!IJKL  R(IK)   T(IKJ)PHI   T(JKL)   R(KL)
IC   1C3  1C4  1O4  2C11.5071  110.40  -86.30  121.00   1.3902  ! psi
IC   1C4  1O4  2C1  2O51.4560  121.00 -130.97  108.63   1.4470  ! phi
IC   2O5  1O4 *2C1  2C21.4470  108.63 -122.09  110.89   1.5316
IC   2O5  1O4 *2C1  2H11.4470  108.63  121.92  111.32   1.0837

I have figured out how to implement R(IK), T(IKJ), T(JKL) and R(KL) values into 
the merged.vsd file, except for the PHI values. Where (and/or how) should I put 
it?
Am I on the right track?


You should not do this.  The .vsd file is for defining virtual sites.  The IC 
lines are for the CHARMM program's internal coordinate builder, specifying some 
optimized geometry (one that the force field in total should produce, or come 
very close).  All the bonded parameters you need are already in the force field 
because they come from the corresponding .prm files.  Do not adjust bonded 
parameter files.


-Justin



Thanks again for your help.
MH



On May 19, 2017, at 5:36 PM, Justin Lemkul  wrote:



On 5/19/17 9:57 AM, Mohammad Hassan Khatami wrote:

First, I am looking for 1->4 and 1->6 linkages. In the top_all36_carb.rtf file 
I found different linkages for beta-glucose, but non for alpha-glucose.
I am trying to make a simple chain with 1->4 linkages like below:

alpha-D-glucose,1->4,alpha-D-glucose,1->4,alpha-D-glucose,1->4,alpha-D-glucose.



Linkages are not specific to the sugar; most are totally generic.  A few 
comments suggest specific usage and may be corner cases, but your patches will 
be among 14aa, 14ab, 14ba, 14bb.



Then, I might need to branch them with1->6 linkage.


Also totally possible.


I tried Glycan Reader, but itstill crashes.



Uploading a correctly named PDB file should work in Glycan Reader or the Quick MD 
Simulator, but "still crashes" is not diagnostic of anything.  Specific help 
with CHARMM-GUI should be brought to their attention, though.

-Justin


MH



Thanks Justin.
I have tried the CHARMM-GUI but it crashed. I might need to modify the order of 
the atoms in my PDB file, which I have created using GLYCAM-Web GUI. I have 
downloaded the “toppar_c36_feb16” but I did not find a manual on how to apply 
them (any suggestions?), so it did not go far.


What you need to do depends on linkages.  There are patches (PRES in CHARMM 
.rtf files) that tell you how each residue is manipulated in the case of a 
patch; refer to the CHARMM documentation online for specifics.  The file you'll 
need is top_all36_carb.rtf.

Otherwise, use the force field files as a template to rename your input 
structure so CHARMM-GUI can process it.  This is probably the much faster route.

-Justin


I'll play with these two, and I'll be back.
MH

On May 18, 2017, at 5:08 PM, Justin Lemkul  wrote:



On 5/18/17 4:57 PM, Mohammad Hassan Khatami wrote:

Hi,

I am trying to run simulations on alpha-D-glucose polymers. I have done these 
simulations using AMBER and I am wondering if it is possible to run them 
employing CHARMM36 in GROMACS, as well?
It seams that CHARMM36 in GROMACS has only implemented monomers of 
alpha-D-glucose as ”AGLC”. Is there a way to introduce the whole polymer to the 
GROMACS?



Sure, you can treat it like any polymer, but you'll have to create the internal 
monomer residues yourself from the patches in the original CHARMM force field 
files.

Or try CHARMM-GUI; it should handle what you need and

Re: [gmx-users] ligand moving out during umbrella sampling

2017-05-22 Thread Justin Lemkul 



On 5/22/17 4:04 AM, abhisek Mondal wrote:

I have used active site residues COM for this time with Ligand COM. As a
test case. r 6-10 | r 78-80 | r 56 | r 63 | r 35 gave me my custom group of
residues belonging to active site. Using both the COMs now I calculated the
vector PL (protein-ligand) and applied as pull-coord1-vec.
However, I hate to say, after 500-600ps md_umbrella run the ligand got out
of the active site again. It is becoming very painful.
As you asked lastly, due to flexible ligand scenario. I'm further thinking
not to use ligand COM, despite coordinate of some atoms near the ring
structure. However, I'm totally confused regarding whether this approach
will work out. Giving it a try though.



If your ligand is large and flexible or the protein rotates very quickly, then 
it will be hard to define the reaction coordinate in the manner that we've been 
trying.  You may have to move to something more generic like distance geometry 
with pull_dim = Y Y Y and a very large box (obviously computationally expensive) 
or you'll have to calculate the binding free energy another way entirely 
(alchemical transformation, MM/PBSA, etc).


-Justin




On Sun, May 21, 2017 at 8:39 PM, abhisek Mondal 
wrote:


Beg your pardon, I have not ignored your comment entirely regarding using
specific residue COM. I just recently succeeded performing md_umbrella
simulation (using protein COM) on few configurations.
.
I have not used specific residues COM so far as because of some confusions
regrading defining it. The residue stretch is not continuous e.g. residue
6-10, 78-80, 56, 63, 35 are to be active site residue. I got no idea how to
define such discrete set of residues using make_ndx command.



On Sun, May 21, 2017 at 8:13 PM, Justin Lemkul  wrote:




On 5/21/17 9:47 AM, abhisek Mondal wrote:


I did try the code successfully on a configuration generated after
pulling.
The NVT approach with direction-periodic geometry worked nicely for the
particular configuration.

However, when I tried to reapply the same code (with modified COMs and
thus
pull_vec) on a different configuration, something awkward happened. The
ligand got pulled through protein and got stuck inside it. I have put the
trajectory movie alongwith md_umbrella.mdp file here:
https://drive.google.com/drive/folders/0B6O-L5Y7BiGJQ1FIc2tIRFE2dE0

Would you please care to give some advise regarding this odd behavior.



Likely some elements of your setup are inadequate.  You have a large,
flexible ligand, so perhaps using its overall COM is inappropriate.  You're
also using the entire protein COM as the other end of the reaction
coordinate, and perhaps that's not good enough (I've suggested a number of
times to be judicious in the choice of residues taken as the group
corresponding to the protein, but it seems you're simply not doing that so
I'll stop suggesting it).  Perhaps your pull vector is calculated
incorrectly.  A lot going on.  Back up and do something simpler, a test
case that is easy to define so you can get comfortable with setting these
things up and understanding/diagnosing weird behavior.

-Justin


Thank you.


On Fri, May 19, 2017 at 5:18 PM, Justin Lemkul  wrote:




On 5/19/17 5:56 AM, abhisek Mondal wrote:

On Thu, May 18, 2017 at 6:48 PM, Justin Lemkul  wrote:





On 5/17/17 8:55 AM, abhisek Mondal wrote:

This time I think I got ligand restrained successfully during the


umbrella
sampling. I have removed the restrain from protein, as per your
advice.
Defined the COM vector in md_umbrella.mdp, applied pull_k1=1000 and
used
pull_rate1=0.0.
I have uploaded the trajectory movie (and other mdp files) in the
following
link:
https://drive.google.com/drive/folders/0B6O-L5Y7BiGJQ1FIc2tIRFE2dE0

However, I'm facing a problem. Due to the withdrawal of the position
restrain of protein. The protein and ligand (together) is moving
around
the
box and resulting in "Distance of pull group 1 (10.441990 nm) is
larger
than 0.49 times the box size (10.646989)" error.

As per the video I have uploaded, if I assume this approach worked,
then
how can I avoid this error ? Is  there any way to make sure the
protein-ligand remains in the middle of the box (or nearby). I have
taken
pretty large box compared to the protein structure from the
beginning.

Please suggest me a way out.


Use a larger box or use direction-periodic geometry.






 For the sake of computational power I'm leaning towards
direction-periodic
geometry. However, from the mailing list entries I found out that
pressure
coupling should not be used for this kind of geometry setup.
NVT coupling with no velocity generation is what I'm opting for. There
are
a lot of doubt regarding the md_umbrella.mdp setup using NVT protocol.
Would you please suggest if the code (
https://drive.google.com/drive/folders/0B6O-L5Y7BiGJQ1FIc2tIRFE2dE0)
looks
sensible ?

Eagerly waiting for your opinion.


Try it and see what happens.

Re: [gmx-users] mdp file for 370 K MD based on Justin's tutorial

2017-05-22 Thread João Henriques 
You haven't adjusted the temperature on the production mdp file, it's still
300 K.

J

On Mon, May 22, 2017 at 12:37 PM, ZHANG Cheng <272699...@qq.com> wrote:

> Dear Gromacs,
> I am performing 370 K MD based on Justin's tutorial.
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/
> gmx-tutorials/lysozyme/index.html
>
>
> After "Step Five: Energy Minimization", I need to do NVT, NPT and a
> production run.
>
>
> I think I need to change 300 K to 370 K in three mdp files. Specifically,
>
>
> 1) In the NVT:
> ref_t = 370  370   ; reference temperature, one for each group, in
> K
> gen_temp = 370 ; temperature for Maxwell distribution
>
>
>
> 2)  In the NPT:
> ref_t = 370  370; reference temperature, one for each group, in K
>
>
> 3) In the production run:
> ref_t   = 300 300   ; reference temperature, one for
> each group, in K
>
>
> Can I ask if these are the adjustments I need to do, and if there are
> something else I need? Thank you.
>
>
> Yours sincerely
> Cheng
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[gmx-users] mdp file for 370 K MD based on Justin's tutorial

2017-05-22 Thread ZHANG Cheng 
Dear Gromacs,
I am performing 370 K MD based on Justin's tutorial. 
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/index.html


After "Step Five: Energy Minimization", I need to do NVT, NPT and a production 
run.


I think I need to change 300 K to 370 K in three mdp files. Specifically,


1) In the NVT:
ref_t = 370  370   ; reference temperature, one for each group, in K
gen_temp = 370 ; temperature for Maxwell distribution



2)  In the NPT:
ref_t = 370  370; reference temperature, one for each group, in K


3) In the production run:
ref_t   = 300 300   ; reference temperature, one for each 
group, in K


Can I ask if these are the adjustments I need to do, and if there are something 
else I need? Thank you.


Yours sincerely
Cheng
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[gmx-users] Martini Website is not accessible

2017-05-22 Thread Anurag Dobhal 
Hello Gromacs users,

This query is not related to typical gromacs error. I am unable to access
the Martini Forcefield website (http://cgmartini.nl/) from the past few
days. I just wanted to know if any of the gromacs users are aware of this
issue ? am I opening the right website ?

Thank you



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

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is addressed and may contain confidential and / or privileged material. Any 
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have received this in error, please contact the sender and delete this 
material from your computer. Any comments or statements made herein do not 
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[gmx-users] Tetrahedral orientational order parameter

2017-05-22 Thread ISHRAT JAHAN 
Dear All,
I am trying to calculate the tetrahedral orientational order parameter
using command g_hydorder. I get two output with option  -or option which is
of the type -
0  0   2.92500
0  1   2.92500
0  2   2.92500
0  3   2.92500
0  4   2.92500
0  5   2.92500
0  6   2.92500
0  7   2.92500
0  8   2.92500
0  9   2.92500
0  10   2.92500
0  11   3.67500
0  12   3.77500
0  13   2.92500
0  14   3.72500
0  15   2.92500
0  16   4.72500
0  17   2.92500
0  18   2.92500
0  19   2.92500
0  20   2.92500
0  21   2.92500
0  22   2.92500
0  23   2.92500
0  24   2.92500
0  25   2.92500
0  26   2.92500
0  27   2.92500
0  28   2.92500
0  29   2.92500
0  30   2.92500
0  31   2.92500
0  32   2.92500
0  33   2.92500
0  34   2.92500
0  35   2.92500

26,1  Top
can anyone help me to interpret this result. what these numbers indicate?
Thanks in advance
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Re: [gmx-users] ligand moving out during umbrella sampling

2017-05-22 Thread abhisek Mondal 
I have used active site residues COM for this time with Ligand COM. As a
test case. r 6-10 | r 78-80 | r 56 | r 63 | r 35 gave me my custom group of
residues belonging to active site. Using both the COMs now I calculated the
vector PL (protein-ligand) and applied as pull-coord1-vec.
However, I hate to say, after 500-600ps md_umbrella run the ligand got out
of the active site again. It is becoming very painful.
As you asked lastly, due to flexible ligand scenario. I'm further thinking
not to use ligand COM, despite coordinate of some atoms near the ring
structure. However, I'm totally confused regarding whether this approach
will work out. Giving it a try though.



On Sun, May 21, 2017 at 8:39 PM, abhisek Mondal 
wrote:

> Beg your pardon, I have not ignored your comment entirely regarding using
> specific residue COM. I just recently succeeded performing md_umbrella
> simulation (using protein COM) on few configurations.
> .
> I have not used specific residues COM so far as because of some confusions
> regrading defining it. The residue stretch is not continuous e.g. residue
> 6-10, 78-80, 56, 63, 35 are to be active site residue. I got no idea how to
> define such discrete set of residues using make_ndx command.
>
>
>
> On Sun, May 21, 2017 at 8:13 PM, Justin Lemkul  wrote:
>
>>
>>
>> On 5/21/17 9:47 AM, abhisek Mondal wrote:
>>
>>> I did try the code successfully on a configuration generated after
>>> pulling.
>>> The NVT approach with direction-periodic geometry worked nicely for the
>>> particular configuration.
>>>
>>> However, when I tried to reapply the same code (with modified COMs and
>>> thus
>>> pull_vec) on a different configuration, something awkward happened. The
>>> ligand got pulled through protein and got stuck inside it. I have put the
>>> trajectory movie alongwith md_umbrella.mdp file here:
>>> https://drive.google.com/drive/folders/0B6O-L5Y7BiGJQ1FIc2tIRFE2dE0
>>>
>>> Would you please care to give some advise regarding this odd behavior.
>>>
>>>
>> Likely some elements of your setup are inadequate.  You have a large,
>> flexible ligand, so perhaps using its overall COM is inappropriate.  You're
>> also using the entire protein COM as the other end of the reaction
>> coordinate, and perhaps that's not good enough (I've suggested a number of
>> times to be judicious in the choice of residues taken as the group
>> corresponding to the protein, but it seems you're simply not doing that so
>> I'll stop suggesting it).  Perhaps your pull vector is calculated
>> incorrectly.  A lot going on.  Back up and do something simpler, a test
>> case that is easy to define so you can get comfortable with setting these
>> things up and understanding/diagnosing weird behavior.
>>
>> -Justin
>>
>>
>> Thank you.
>>>
>>> On Fri, May 19, 2017 at 5:18 PM, Justin Lemkul  wrote:
>>>
>>>

 On 5/19/17 5:56 AM, abhisek Mondal wrote:

 On Thu, May 18, 2017 at 6:48 PM, Justin Lemkul  wrote:
>
>
>
>> On 5/17/17 8:55 AM, abhisek Mondal wrote:
>>
>> This time I think I got ligand restrained successfully during the
>>
>>> umbrella
>>> sampling. I have removed the restrain from protein, as per your
>>> advice.
>>> Defined the COM vector in md_umbrella.mdp, applied pull_k1=1000 and
>>> used
>>> pull_rate1=0.0.
>>> I have uploaded the trajectory movie (and other mdp files) in the
>>> following
>>> link:
>>> https://drive.google.com/drive/folders/0B6O-L5Y7BiGJQ1FIc2tIRFE2dE0
>>>
>>> However, I'm facing a problem. Due to the withdrawal of the position
>>> restrain of protein. The protein and ligand (together) is moving
>>> around
>>> the
>>> box and resulting in "Distance of pull group 1 (10.441990 nm) is
>>> larger
>>> than 0.49 times the box size (10.646989)" error.
>>>
>>> As per the video I have uploaded, if I assume this approach worked,
>>> then
>>> how can I avoid this error ? Is  there any way to make sure the
>>> protein-ligand remains in the middle of the box (or nearby). I have
>>> taken
>>> pretty large box compared to the protein structure from the
>>> beginning.
>>>
>>> Please suggest me a way out.
>>>
>>>
>>> Use a larger box or use direction-periodic geometry.
>>>
>>
>>
>
>  For the sake of computational power I'm leaning towards
> direction-periodic
> geometry. However, from the mailing list entries I found out that
> pressure
> coupling should not be used for this kind of geometry setup.
> NVT coupling with no velocity generation is what I'm opting for. There
> are
> a lot of doubt regarding the md_umbrella.mdp setup using NVT protocol.
> Would you please suggest if the code (
> https://drive.google.com/drive/folders/0B6O-L5Y7BiGJQ1FIc2tIRFE2dE0)
> looks
> sensible ?
>
> Eagerly waiting for your

[gmx-users] mdrun failure

2017-05-22 Thread fatemeh ramezani 
Hi dear gmx-users

Iwant to simulate gold surface - protein interaction by GOLP-CHARMM 
forcefield.In md step, after 7 ps , without any reason mdrun failed. md.mdp 
contains:

 title                   = gold

cpp                     =cpp

include                 = 

 ;RUN CONTROL PARAMETERS

integrator              = md 

 ;ENERGY MINIMIZATION OPTIONS

emtol                   = 500.0

emstep                  = 0.001

tinit                   = 0.000

dt                      =0.001

nsteps = 10

 ;OUTPUT CONTROL OPTIONS

nstxout                 = 3000

nstvout                 = 3000

nstfout                 = 0

nstlog                  = 1

nstenergy               = 3000

 ;Output frequency and precision for xtc file

nstxtcout               = 3000

xtc-precision           = 3000

 ;NEIGHBORSEARCHING PARAMETERS

;Periodic boundary conditions: xyz (default), no (vacuum)

pbc                     =xyz

periodic_molecules      = yes

rlist                   = 1.10

 ;OPTIONS FOR ELECTROSTATICS AND VDW

;Method for doing electrostatics

coulombtype             = PME

r_coulomb                = 1.1

ewald_rtol              = 1e-06

ewald_geometry          = 3d

 ;Method for doing Van der Waals

vdw-type                = switch

rvdw-switch             = 0.90

rvdw                    = 1.10

 ;OPTIONS FOR BONDS    

constraints             = h-bonds

constraint-algorithm    = Lincs

lincs-order             = 8

lincs-iter              = 12

;Lincs will write a warning to the stderr if in one step a bond

;rotates over more degrees than

lincs-warnangle         = 90

 ;OPTIONS FOR WEAK COUPLING ALGORITHMS

;Temperature coupling  

Tcoupl                  = Nose-Hoover

nhchainlength = 1

;Groups to couple separately

tc-grps                 = Protein  Non-Protein

;Time constant (ps) and reference temperature (K)

tau-t                   = 0.2 0.2

ref-t                   = 310 310

 ;Non-equilibrium MD stuff

freezegrps              = slab

freezedim               = Y Y Y

 

mdrun command is:

 nohup mdrun -smd.tpr -o md.trr -c md.pdb -g md.log -e md.edr -nt 3 -dd 1 -pin 
on -pinoffset 1 &

 the last line of md.logis:

 Step          Time         Lambda

          7460        7.46000       0.0

    Energies(kJ/mol)

           U-B    Proper Dih.  Improper Dih.     CMAP Dih.          LJ-14

   5.39081e+04    1.47221e+04    3.15826e+03  -1.85050e+03    1.80904e+04

    Coulomb-14        LJ (SR)   Coulomb (SR)  Coul. recip.      Potential

   2.97824e+05    2.17254e+12   -6.91585e+06   3.01612e+04    2.17254e+12

    KineticEn.   Total Energy  Conserved En.    Temperature Pressure(bar)

   7.71065e+14    7.73237e+14    9.41950e+16   2.61554e+11    2.41578e+12

   Constr.rmsd

   1.15453e-01

 The last line ofnohup.out is:

  Changing nstlist from 10to 40, rlist from 1.1 to 1.1

 Using 1 MPI thread

Using 3 OpenMP threads

Applying core pinningoffset 1

Setting the maximumnumber of constraint warnings to -1

 Back Off! I just backedup fws_md3.trr to ./#fws_md3.trr.20#

 Back Off! I just backedup traj_comp.xtc to ./#traj_comp.xtc.22#

 Back Off! I just backedup md3.edr to ./#md3.edr.20#

starting mdrun 'Proteinin water'

10 steps,   100.0 ps.

 Can you help me toprevent from mdrun failing?

Thank you very much

 
 Fatemeh Ramezani
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