Re: [gmx-users] gen-pairs

[Justin Lemkul]

On 6/3/16 6:40 PM, Alexander Alexander wrote:

Thanks, although, each of them is a 2 ns NVT calculation, not a
single-point energy.



Then the comparison, in the context of the effect of gen-pairs, is useless.


By the way, then why does "gmx grompp" shows below when gen-pairs is yes if
no pair is present?



Because you're telling it to by setting it to "yes" - there is no [pairtypes] 
entry for a given combination of atom types, so grompp generates it.  Whether or 
not it's actually used for the simulation is a different question.  In your 
case, pairs can be generated or not, and in neither case will they actually be 
used in the simulation.


-Justin


Generating 1-4 interactions: fudge = 0.5
Generated 3 of the 3 1-4 parameter combinations

Best regards,
Alex

On Sat, Jun 4, 2016 at 12:20 AM, Justin Lemkul  wrote:




On 6/3/16 6:14 PM, Alexander Alexander wrote:


I have this system in two different states, and I am interested in the
difference between total energy of these states, I found out that the
result changes when gen-pairs is YES and NO.

I mean [ \delta(S1(tot-ene)-S2(tot-ene))(NO) ] is not the same as [
\delta(S1(tot-ene)-S2(tot-ene))(YES) ] !?



That's not a definitive test.  If you do a single-point energy evaluation
of a given set of coordinates with gen-pairs set to "no" and "yes" and get
a different answer, something is wrong.  Your topology shows no bonds,
therefore there can be no 1-4, therefore no pairs.  Pairs are what
gen-pairs affects.

-Justin


Regards,

Alex

On Fri, Jun 3, 2016 at 11:59 PM, Justin Lemkul  wrote:




On 6/3/16 5:58 PM, Alexander Alexander wrote:

Many thanks for your response.


So, do you mean that the "gen-pairs" can be freely NO or YES for this
system with no change in any of the results?


Yes, it's completely irrelevant.


-Justin


The best,


Alex

On Fri, Jun 3, 2016 at 11:03 PM, Justin Lemkul  wrote:




On 6/3/16 8:49 AM, Alexander Alexander wrote:

Dear Gromacs user,



Surprisingly I am wondering why I have no warning while I assigned
"NO"
for
the "gen-pairs" in [ default ] section of my .top file, although I
have
no
pair type neither in my .top file nor in ffnonbonded.itp for these
atoms?


Pairs are 1-4 (intramolecular) interactions.  You have two atom types


that
are not bonded, so there are no pair interactions.

-Justin


I am referring to this statement in gromacs-manual: "When gen-pairs is
set

to “no,” grompp will give a warning for each pair type for which no

parameters are given".

My system is a pure transition metal solid that it's topol file comes
below:

topol.top
-
; topol file for A3B
; force field parameters in below
[ Defaults ]
;  nbfunccomb-rule   gen-pairs   fudgeLJ  fudgeQQ
 1   3 no
0.5   0.5

[ atomtypes ]
;   name  masschargeptype   sigma
 epsilon
 A32.00  0.21  A2.27357e-01
25.1
 B6.700 -0.63  A1.714534e-01
4.4

[ moleculetype ]
; Namenrexcl
  A   1
[ atoms ]
;  nr at type  resnr   residue   atom name   cgnr charge
 mass
   1A 1  A   A
1   0.21   32.00

[ position_restraints ]
; ai  funct  fcxfcyfcz
   112000   2000   2000

[ moleculetype ]
; Namenrexcl
  B   1
[ atoms ]
;  nr at type  resnr   residue   atom name   cgnr charge
 mass
   1  B1  B  B
1  -0.630 6.70

[ position_restraints ]
; ai  funct  fcxfcyfcz
   112000   2000   2000

[ system ]
; Name
   A3B

[ molecules ]
;mol_name number
   A14400
   B 4800
-


--


==

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

Re: [gmx-users] gen-pairs

[Alexander Alexander]

Thanks, although, each of them is a 2 ns NVT calculation, not a
single-point energy.

By the way, then why does "gmx grompp" shows below when gen-pairs is yes if
no pair is present?

Generating 1-4 interactions: fudge = 0.5
Generated 3 of the 3 1-4 parameter combinations

Best regards,
Alex

On Sat, Jun 4, 2016 at 12:20 AM, Justin Lemkul  wrote:

>
>
> On 6/3/16 6:14 PM, Alexander Alexander wrote:
>
>> I have this system in two different states, and I am interested in the
>> difference between total energy of these states, I found out that the
>> result changes when gen-pairs is YES and NO.
>>
>> I mean [ \delta(S1(tot-ene)-S2(tot-ene))(NO) ] is not the same as [
>> \delta(S1(tot-ene)-S2(tot-ene))(YES) ] !?
>>
>>
> That's not a definitive test.  If you do a single-point energy evaluation
> of a given set of coordinates with gen-pairs set to "no" and "yes" and get
> a different answer, something is wrong.  Your topology shows no bonds,
> therefore there can be no 1-4, therefore no pairs.  Pairs are what
> gen-pairs affects.
>
> -Justin
>
>
> Regards,
>> Alex
>>
>> On Fri, Jun 3, 2016 at 11:59 PM, Justin Lemkul  wrote:
>>
>>
>>>
>>> On 6/3/16 5:58 PM, Alexander Alexander wrote:
>>>
>>> Many thanks for your response.

 So, do you mean that the "gen-pairs" can be freely NO or YES for this
 system with no change in any of the results?


 Yes, it's completely irrelevant.
>>>
>>> -Justin
>>>
>>>
>>> The best,
>>>
 Alex

 On Fri, Jun 3, 2016 at 11:03 PM, Justin Lemkul  wrote:



> On 6/3/16 8:49 AM, Alexander Alexander wrote:
>
> Dear Gromacs user,
>
>>
>> Surprisingly I am wondering why I have no warning while I assigned
>> "NO"
>> for
>> the "gen-pairs" in [ default ] section of my .top file, although I
>> have
>> no
>> pair type neither in my .top file nor in ffnonbonded.itp for these
>> atoms?
>>
>>
>> Pairs are 1-4 (intramolecular) interactions.  You have two atom types
>>
> that
> are not bonded, so there are no pair interactions.
>
> -Justin
>
>
> I am referring to this statement in gromacs-manual: "When gen-pairs is
> set
>
> to “no,” grompp will give a warning for each pair type for which no
>> parameters are given".
>>
>> My system is a pure transition metal solid that it's topol file comes
>> below:
>>
>> topol.top
>> -
>> ; topol file for A3B
>> ; force field parameters in below
>> [ Defaults ]
>> ;  nbfunccomb-rule   gen-pairs   fudgeLJ  fudgeQQ
>>  1   3 no
>> 0.5   0.5
>>
>> [ atomtypes ]
>> ;   name  masschargeptype   sigma
>>  epsilon
>>  A32.00  0.21  A2.27357e-01
>> 25.1
>>  B6.700 -0.63  A1.714534e-01
>> 4.4
>>
>> [ moleculetype ]
>> ; Namenrexcl
>>   A   1
>> [ atoms ]
>> ;  nr at type  resnr   residue   atom name   cgnr charge
>>  mass
>>1A 1  A   A
>> 1   0.21   32.00
>>
>> [ position_restraints ]
>> ; ai  funct  fcxfcyfcz
>>112000   2000   2000
>>
>> [ moleculetype ]
>> ; Namenrexcl
>>   B   1
>> [ atoms ]
>> ;  nr at type  resnr   residue   atom name   cgnr charge
>>  mass
>>1  B1  B  B
>> 1  -0.630 6.70
>>
>> [ position_restraints ]
>> ; ai  funct  fcxfcyfcz
>>112000   2000   2000
>>
>> [ system ]
>> ; Name
>>A3B
>>
>> [ molecules ]
>> ;mol_name number
>>A14400
>>B 4800
>> -
>>
>>
>> --
>>
> ==
>
> 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
> 

Re: [gmx-users] gen-pairs

[Justin Lemkul]

On 6/3/16 6:14 PM, Alexander Alexander wrote:

I have this system in two different states, and I am interested in the
difference between total energy of these states, I found out that the
result changes when gen-pairs is YES and NO.

I mean [ \delta(S1(tot-ene)-S2(tot-ene))(NO) ] is not the same as [
\delta(S1(tot-ene)-S2(tot-ene))(YES) ] !?



That's not a definitive test.  If you do a single-point energy evaluation of a 
given set of coordinates with gen-pairs set to "no" and "yes" and get a 
different answer, something is wrong.  Your topology shows no bonds, therefore 
there can be no 1-4, therefore no pairs.  Pairs are what gen-pairs affects.


-Justin


Regards,
Alex

On Fri, Jun 3, 2016 at 11:59 PM, Justin Lemkul  wrote:




On 6/3/16 5:58 PM, Alexander Alexander wrote:


Many thanks for your response.

So, do you mean that the "gen-pairs" can be freely NO or YES for this
system with no change in any of the results?



Yes, it's completely irrelevant.

-Justin


The best,

Alex

On Fri, Jun 3, 2016 at 11:03 PM, Justin Lemkul  wrote:




On 6/3/16 8:49 AM, Alexander Alexander wrote:

Dear Gromacs user,


Surprisingly I am wondering why I have no warning while I assigned "NO"
for
the "gen-pairs" in [ default ] section of my .top file, although I have
no
pair type neither in my .top file nor in ffnonbonded.itp for these
atoms?


Pairs are 1-4 (intramolecular) interactions.  You have two atom types

that
are not bonded, so there are no pair interactions.

-Justin


I am referring to this statement in gromacs-manual: "When gen-pairs is
set


to “no,” grompp will give a warning for each pair type for which no
parameters are given".

My system is a pure transition metal solid that it's topol file comes
below:

topol.top
-
; topol file for A3B
; force field parameters in below
[ Defaults ]
;  nbfunccomb-rule   gen-pairs   fudgeLJ  fudgeQQ
 1   3 no
0.5   0.5

[ atomtypes ]
;   name  masschargeptype   sigma   epsilon
 A32.00  0.21  A2.27357e-01
25.1
 B6.700 -0.63  A1.714534e-01
4.4

[ moleculetype ]
; Namenrexcl
  A   1
[ atoms ]
;  nr at type  resnr   residue   atom name   cgnr charge
 mass
   1A 1  A   A
1   0.21   32.00

[ position_restraints ]
; ai  funct  fcxfcyfcz
   112000   2000   2000

[ moleculetype ]
; Namenrexcl
  B   1
[ atoms ]
;  nr at type  resnr   residue   atom name   cgnr charge
 mass
   1  B1  B  B
1  -0.630 6.70

[ position_restraints ]
; ai  funct  fcxfcyfcz
   112000   2000   2000

[ system ]
; Name
   A3B

[ molecules ]
;mol_name number
   A14400
   B 4800
-


--

==

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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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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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

Re: [gmx-users] gen-pairs

[Alexander Alexander]

I have this system in two different states, and I am interested in the
difference between total energy of these states, I found out that the
result changes when gen-pairs is YES and NO.

I mean [ \delta(S1(tot-ene)-S2(tot-ene))(NO) ] is not the same as [
\delta(S1(tot-ene)-S2(tot-ene))(YES) ] !?

Regards,
Alex

On Fri, Jun 3, 2016 at 11:59 PM, Justin Lemkul  wrote:

>
>
> On 6/3/16 5:58 PM, Alexander Alexander wrote:
>
>> Many thanks for your response.
>>
>> So, do you mean that the "gen-pairs" can be freely NO or YES for this
>> system with no change in any of the results?
>>
>>
> Yes, it's completely irrelevant.
>
> -Justin
>
>
> The best,
>> Alex
>>
>> On Fri, Jun 3, 2016 at 11:03 PM, Justin Lemkul  wrote:
>>
>>
>>>
>>> On 6/3/16 8:49 AM, Alexander Alexander wrote:
>>>
>>> Dear Gromacs user,

 Surprisingly I am wondering why I have no warning while I assigned "NO"
 for
 the "gen-pairs" in [ default ] section of my .top file, although I have
 no
 pair type neither in my .top file nor in ffnonbonded.itp for these
 atoms?


 Pairs are 1-4 (intramolecular) interactions.  You have two atom types
>>> that
>>> are not bonded, so there are no pair interactions.
>>>
>>> -Justin
>>>
>>>
>>> I am referring to this statement in gromacs-manual: "When gen-pairs is
>>> set
>>>
 to “no,” grompp will give a warning for each pair type for which no
 parameters are given".

 My system is a pure transition metal solid that it's topol file comes
 below:

 topol.top
 -
 ; topol file for A3B
 ; force field parameters in below
 [ Defaults ]
 ;  nbfunccomb-rule   gen-pairs   fudgeLJ  fudgeQQ
  1   3 no
 0.5   0.5

 [ atomtypes ]
 ;   name  masschargeptype   sigma   epsilon
  A32.00  0.21  A2.27357e-01
 25.1
  B6.700 -0.63  A1.714534e-01
 4.4

 [ moleculetype ]
 ; Namenrexcl
   A   1
 [ atoms ]
 ;  nr at type  resnr   residue   atom name   cgnr charge
  mass
1A 1  A   A
 1   0.21   32.00

 [ position_restraints ]
 ; ai  funct  fcxfcyfcz
112000   2000   2000

 [ moleculetype ]
 ; Namenrexcl
   B   1
 [ atoms ]
 ;  nr at type  resnr   residue   atom name   cgnr charge
  mass
1  B1  B  B
 1  -0.630 6.70

 [ position_restraints ]
 ; ai  funct  fcxfcyfcz
112000   2000   2000

 [ system ]
 ; Name
A3B

 [ molecules ]
 ;mol_name number
A14400
B 4800
 -


 --
>>> ==
>>>
>>> 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
> 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] gen-pairs

[Justin Lemkul]

On 6/3/16 5:58 PM, Alexander Alexander wrote:

Many thanks for your response.

So, do you mean that the "gen-pairs" can be freely NO or YES for this
system with no change in any of the results?



Yes, it's completely irrelevant.

-Justin


The best,
Alex

On Fri, Jun 3, 2016 at 11:03 PM, Justin Lemkul  wrote:




On 6/3/16 8:49 AM, Alexander Alexander wrote:


Dear Gromacs user,

Surprisingly I am wondering why I have no warning while I assigned "NO"
for
the "gen-pairs" in [ default ] section of my .top file, although I have no
pair type neither in my .top file nor in ffnonbonded.itp for these atoms?



Pairs are 1-4 (intramolecular) interactions.  You have two atom types that
are not bonded, so there are no pair interactions.

-Justin


I am referring to this statement in gromacs-manual: "When gen-pairs is set

to “no,” grompp will give a warning for each pair type for which no
parameters are given".

My system is a pure transition metal solid that it's topol file comes
below:

topol.top
-
; topol file for A3B
; force field parameters in below
[ Defaults ]
;  nbfunccomb-rule   gen-pairs   fudgeLJ  fudgeQQ
 1   3 no
0.5   0.5

[ atomtypes ]
;   name  masschargeptype   sigma   epsilon
 A32.00  0.21  A2.27357e-01
25.1
 B6.700 -0.63  A1.714534e-01
4.4

[ moleculetype ]
; Namenrexcl
  A   1
[ atoms ]
;  nr at type  resnr   residue   atom name   cgnr charge
 mass
   1A 1  A   A
1   0.21   32.00

[ position_restraints ]
; ai  funct  fcxfcyfcz
   112000   2000   2000

[ moleculetype ]
; Namenrexcl
  B   1
[ atoms ]
;  nr at type  resnr   residue   atom name   cgnr charge
 mass
   1  B1  B  B
1  -0.630 6.70

[ position_restraints ]
; ai  funct  fcxfcyfcz
   112000   2000   2000

[ system ]
; Name
   A3B

[ molecules ]
;mol_name number
   A14400
   B 4800
-



--
==

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

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

Re: [gmx-users] gen-pairs

[Alexander Alexander]

Many thanks for your response.

So, do you mean that the "gen-pairs" can be freely NO or YES for this
system with no change in any of the results?

The best,
Alex

On Fri, Jun 3, 2016 at 11:03 PM, Justin Lemkul  wrote:

>
>
> On 6/3/16 8:49 AM, Alexander Alexander wrote:
>
>> Dear Gromacs user,
>>
>> Surprisingly I am wondering why I have no warning while I assigned "NO"
>> for
>> the "gen-pairs" in [ default ] section of my .top file, although I have no
>> pair type neither in my .top file nor in ffnonbonded.itp for these atoms?
>>
>>
> Pairs are 1-4 (intramolecular) interactions.  You have two atom types that
> are not bonded, so there are no pair interactions.
>
> -Justin
>
>
> I am referring to this statement in gromacs-manual: "When gen-pairs is set
>> to “no,” grompp will give a warning for each pair type for which no
>> parameters are given".
>>
>> My system is a pure transition metal solid that it's topol file comes
>> below:
>>
>> topol.top
>> -
>> ; topol file for A3B
>> ; force field parameters in below
>> [ Defaults ]
>> ;  nbfunccomb-rule   gen-pairs   fudgeLJ  fudgeQQ
>>  1   3 no
>> 0.5   0.5
>>
>> [ atomtypes ]
>> ;   name  masschargeptype   sigma   epsilon
>>  A32.00  0.21  A2.27357e-01
>> 25.1
>>  B6.700 -0.63  A1.714534e-01
>> 4.4
>>
>> [ moleculetype ]
>> ; Namenrexcl
>>   A   1
>> [ atoms ]
>> ;  nr at type  resnr   residue   atom name   cgnr charge
>>  mass
>>1A 1  A   A
>> 1   0.21   32.00
>>
>> [ position_restraints ]
>> ; ai  funct  fcxfcyfcz
>>112000   2000   2000
>>
>> [ moleculetype ]
>> ; Namenrexcl
>>   B   1
>> [ atoms ]
>> ;  nr at type  resnr   residue   atom name   cgnr charge
>>  mass
>>1  B1  B  B
>> 1  -0.630 6.70
>>
>> [ position_restraints ]
>> ; ai  funct  fcxfcyfcz
>>112000   2000   2000
>>
>> [ system ]
>> ; Name
>>A3B
>>
>> [ molecules ]
>> ;mol_name number
>>A14400
>>B 4800
>> -
>>
>>
> --
> ==
>
> 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
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> * Please search the archive at
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Re: [gmx-users] error installing trj_cavity with gromacs

[Williams Miranda]

Hi
I recompiled gromacs from my synaptic manager and it worked now
Thanks

Williams


From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on behalf of Tsjerk 
Wassenaar 
Sent: Friday, June 3, 2016 3:49:01 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] error installing trj_cavity with gromacs

Hi Williams,

It looks like you didn't set the Gromacs include directory. What
command/procedure did you use to compile?

Cheers,

Tsjerk
On Jun 3, 2016 21:25, "Williams Miranda" 
wrote:

> Dear GROMACS users
> I use gromacs 4.6.5, then, I downloaded trj_cavity v1.1 for installation.
> But I am getting this error:
>
>
> src/AtomReaderGromacs.cpp:13:19: fatal error: xtcio.h: No such file or
> directory
>
>
> Actually, the AtomReaderGromacs.cpp includes the following files:
>
> include "xtcio.h"
> include "trajana.h"
> include "statutil.h"
> include "typedefs.h"
> include "smalloc.h"
> include "copyrite.h"
> include "tpxio.h"
> include "names.h"
> include "gmx_random.h"
> include "gmx_ana.h"
> include "filenm.h"
> include "macros.h"
> include "pbc.h"
> include "vec.h"
> include "xvgr.h"
> include "pdb2top.h"
>
> However, only typedefs.h is found in my GROMACS library. What could I do
> to fix this problem?
> Regards
>
> --
> 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] gen-pairs

[Justin Lemkul]

On 6/3/16 8:49 AM, Alexander Alexander wrote:

Dear Gromacs user,

Surprisingly I am wondering why I have no warning while I assigned "NO" for
the "gen-pairs" in [ default ] section of my .top file, although I have no
pair type neither in my .top file nor in ffnonbonded.itp for these atoms?



Pairs are 1-4 (intramolecular) interactions.  You have two atom types that are 
not bonded, so there are no pair interactions.


-Justin


I am referring to this statement in gromacs-manual: "When gen-pairs is set
to “no,” grompp will give a warning for each pair type for which no
parameters are given".

My system is a pure transition metal solid that it's topol file comes below:

topol.top
-
; topol file for A3B
; force field parameters in below
[ Defaults ]
;  nbfunccomb-rule   gen-pairs   fudgeLJ  fudgeQQ
 1   3 no
0.5   0.5

[ atomtypes ]
;   name  masschargeptype   sigma   epsilon
 A32.00  0.21  A2.27357e-01
25.1
 B6.700 -0.63  A1.714534e-014.4

[ moleculetype ]
; Namenrexcl
  A   1
[ atoms ]
;  nr at type  resnr   residue   atom name   cgnr charge   mass
   1A 1  A   A
1   0.21   32.00

[ position_restraints ]
; ai  funct  fcxfcyfcz
   112000   2000   2000

[ moleculetype ]
; Namenrexcl
  B   1
[ atoms ]
;  nr at type  resnr   residue   atom name   cgnr charge   mass
   1  B1  B  B
1  -0.630 6.70

[ position_restraints ]
; ai  funct  fcxfcyfcz
   112000   2000   2000

[ system ]
; Name
   A3B

[ molecules ]
;mol_name number
   A14400
   B 4800
-



--
==

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] error installing trj_cavity with gromacs

[Tsjerk Wassenaar]

Hi Williams,

It looks like you didn't set the Gromacs include directory. What
command/procedure did you use to compile?

Cheers,

Tsjerk
On Jun 3, 2016 21:25, "Williams Miranda" 
wrote:

> Dear GROMACS users
> I use gromacs 4.6.5, then, I downloaded trj_cavity v1.1 for installation.
> But I am getting this error:
>
>
> src/AtomReaderGromacs.cpp:13:19: fatal error: xtcio.h: No such file or
> directory
>
>
> Actually, the AtomReaderGromacs.cpp includes the following files:
>
> include "xtcio.h"
> include "trajana.h"
> include "statutil.h"
> include "typedefs.h"
> include "smalloc.h"
> include "copyrite.h"
> include "tpxio.h"
> include "names.h"
> include "gmx_random.h"
> include "gmx_ana.h"
> include "filenm.h"
> include "macros.h"
> include "pbc.h"
> include "vec.h"
> include "xvgr.h"
> include "pdb2top.h"
>
> However, only typedefs.h is found in my GROMACS library. What could I do
> to fix this problem?
> Regards
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
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[gmx-users] Gromacs in Mac OS 10.11 (el capitan)

[Eudes Fileti]

Hi,
I'm following the standard script below for Gromacs installation, as usual
I do:

   mkdir build
   cd build
   cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON
   make
   make check
   sudo make install


But this time I'm getting a strange error after "cmake" command:

fileti:~/Downloads/gromacs-5.1.2/build$make
[  1%] Built target fftwBuild
make[2]: *** No rule to make target
`/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk/System/Library/Frameworks/Accelerate.framework',
needed by `lib/libgromacs.1.2.0.dylib'.  Stop.
make[1]: *** [src/gromacs/CMakeFiles/libgromacs.dir/all] Error 2
make: *** [all] Error 2


Someone also had any problems withMac OS 10.11 (el capitan) to INSTALLING
gromacs?

Any suggestion?

Bests
eef
___
Eudes Eterno Fileti
Instituto de Ciência e Tecnologia da UNIFESP
Av. Cesar Lattes, 1201, Eugênio de Mello, SP, 12247-014
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[gmx-users] gen-pairs

[Alexander Alexander]

Dear Gromacs user,

Surprisingly I am wondering why I have no warning while I assigned "NO" for
the "gen-pairs" in [ default ] section of my .top file, although I have no
pair type neither in my .top file nor in ffnonbonded.itp for these atoms?

I am referring to this statement in gromacs-manual: "When gen-pairs is set
to “no,” grompp will give a warning for each pair type for which no
parameters are given".

My system is a pure transition metal solid that it's topol file comes below:

topol.top
-
; topol file for A3B
; force field parameters in below
[ Defaults ]
;  nbfunccomb-rule   gen-pairs   fudgeLJ  fudgeQQ
 1   3 no
0.5   0.5

[ atomtypes ]
;   name  masschargeptype   sigma   epsilon
 A32.00  0.21  A2.27357e-01
25.1
 B6.700 -0.63  A1.714534e-014.4

[ moleculetype ]
; Namenrexcl
  A   1
[ atoms ]
;  nr at type  resnr   residue   atom name   cgnr charge   mass
   1A 1  A   A
1   0.21   32.00

[ position_restraints ]
; ai  funct  fcxfcyfcz
   112000   2000   2000

[ moleculetype ]
; Namenrexcl
  B   1
[ atoms ]
;  nr at type  resnr   residue   atom name   cgnr charge   mass
   1  B1  B  B
1  -0.630 6.70

[ position_restraints ]
; ai  funct  fcxfcyfcz
   112000   2000   2000

[ system ]
; Name
   A3B

[ molecules ]
;mol_name number
   A14400
   B 4800
-
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[gmx-users] error installing trj_cavity with gromacs

[Williams Miranda]

Dear GROMACS users
I use gromacs 4.6.5, then, I downloaded trj_cavity v1.1 for installation. But I 
am getting this error:


src/AtomReaderGromacs.cpp:13:19: fatal error: xtcio.h: No such file or directory


Actually, the AtomReaderGromacs.cpp includes the following files:

include "xtcio.h"
include "trajana.h"
include "statutil.h"
include "typedefs.h"
include "smalloc.h"
include "copyrite.h"
include "tpxio.h"
include "names.h"
include "gmx_random.h"
include "gmx_ana.h"
include "filenm.h"
include "macros.h"
include "pbc.h"
include "vec.h"
include "xvgr.h"
include "pdb2top.h"

However, only typedefs.h is found in my GROMACS library. What could I do to fix 
this problem?
Regards

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Re: [gmx-users] top parameters for pluronic f127

[Alan]

It's too big! It will never work.

Try the following alternatives:
- to use gasteiger charge (and then you get only the topology);
- as you said it's a polymer, take the smallest common unit, join 3 pieces
of it and get the topology/charges for it, use the middle unit to extend
the charge for all internal units of your polymer and the extreme to model
your terminals.

Good luck,

Alan

On 3 June 2016 at 18:37, SAKO MIRZAIE  wrote:

> Dear All,
>
> I am trying to convert my mol2 file to amber99sb itp to do MD by
> gromacs. but, when I use ACPYPE software, it run and never finished.
> my mol2 file is pluronic F127 and contains 2500 atoms. this structure
> is a polymer and huge in size. how can I get an itp file for my
> polymer? How can I simulate it in MD by gromacs? do polymers have some
> tricks?
>
> the molecular structure of f127 is: A99B67A99
>
> where
>
> A: ethylene oxide
> B: propylene oxide
>
> best regards,
>
> --
> ***
> sako mirzaie
> PhD in biochemistry
> --
> 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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> send a mail to gmx-users-requ...@gromacs.org.
>



-- 
Alan Wilter SOUSA da SILVA, DSc
Senior Bioinformatician, UniProt
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD
United Kingdom
Tel: +44 (0)1223 494588
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[gmx-users] top parameters for pluronic f127

[SAKO MIRZAIE]

-- Forwarded message --
From: SAKO MIRZAIE 
Date: Fri, 3 Jun 2016 20:04:49 +0430
Subject: top parameters for pluronic f127
To: gromacs.org_gmx-users@maillist.sys.kth.se

Dear All,

I am trying to convert my mol2 file to amber99sb itp to do MD by
gromacs. but, when I use ACPYPE software, it run and never finished.
my mol2 file is pluronic F127 and contains 2500 atoms. this structure
is a polymer and huge in size. how can I get an itp file for my
polymer? How can I simulate it in MD by gromacs? do polymers have some
tricks?

the molecular structure of f127 is: A99B67A99

where

A: ethylene oxide
B: propylene oxide

best regards,

-- 
***
sako mirzaie
PhD in biochemistry



-- 
***
sako mirzaie
PhD in biochemistry, science faculty, Islamic azad university of
sanandaj, sanandaj, Iran
http://www.iausdj.ac.ir/fa/fa-info.aspx?p=s.mirzaie

http://www.iausdj.ac.ir/en/en.aspx?p=s.mirzaie

http://scholar.google.com/citations?user=viwZvVAJ=en

http://www.scopus.com/authid/detail.url?authorId=54886431500

http://www.ncbi.nlm.nih.gov/pubmed/?term=sako+mirzaie
https://www.researchgate.net/profile/Sako_Mirzaie/publications/
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[gmx-users] top parameters for pluronic f127

[SAKO MIRZAIE]

Dear All,

I am trying to convert my mol2 file to amber99sb itp to do MD by
gromacs. but, when I use ACPYPE software, it run and never finished.
my mol2 file is pluronic F127 and contains 2500 atoms. this structure
is a polymer and huge in size. how can I get an itp file for my
polymer? How can I simulate it in MD by gromacs? do polymers have some
tricks?

the molecular structure of f127 is: A99B67A99

where

A: ethylene oxide
B: propylene oxide

best regards,

--
***
sako mirzaie
PhD in biochemistry
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[gmx-users] top parameters for pluronic f127

[SAKO MIRZAIE]

Dear All,

I am trying to convert my mol2 file to amber99sb itp to do MD by
gromacs. but, when I use ACPYPE software, it run and never finished.
my mol2 file is pluronic F127 and contains 2500 atoms. this structure
is a polymer and huge in size. how can I get an itp file for my
polymer? How can I simulate it in MD by gromacs? do polymers have some
tricks?

the molecular structure of f127 is: A99B67A99

where

A: ethylene oxide
B: propylene oxide

best regards,

-- 
***
sako mirzaie
PhD in biochemistry



-- 
***
sako mirzaie
PhD in biochemistry, science faculty, Islamic azad university of
sanandaj, sanandaj, Iran
http://www.iausdj.ac.ir/fa/fa-info.aspx?p=s.mirzaie

http://www.iausdj.ac.ir/en/en.aspx?p=s.mirzaie

http://scholar.google.com/citations?user=viwZvVAJ=en

http://www.scopus.com/authid/detail.url?authorId=54886431500

http://www.ncbi.nlm.nih.gov/pubmed/?term=sako+mirzaie
https://www.researchgate.net/profile/Sako_Mirzaie/publications/
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Re: [gmx-users] query on performance of GTX 1080 in gromacs

[Jagannath Mondal]

Dear Mark
  Did you have a chance to test gromacs with GTX 1080? Can you please let
us know if it is compatible and working well.
Jagannath

On Sat, May 28, 2016 at 2:36 PM, Jagannath Mondal 
wrote:

> Dear Mark
>
>I will appreciate if you share your experience, once you tested with
> GTX 1080. I can wait for your response.
>
> Jagannath
>
>
> On Fri, May 27, 2016 at 10:36 PM, Mark Abraham 
> wrote:
>
>> Hi,
>>
>> Yes, we expect it to work, but we haven't tried it yet. NVIDIA didn't
>> manage to give us any early access, in practice. We have some cards, but
>> perhaps no actual run until early next week.
>>
>> Mark
>>
>> On Fri, 27 May 2016 18:22 Jagannath Mondal 
>> wrote:
>>
>> > Dear Gromacs users
>> >
>> >   I just wanted to check whether latest GPU of NVIDIA GTX 1080 has been
>> > tested by any one for its compatibility/performance with gromacs.
>> >
>> > I have used GTX 980 Ti and have found it compatible with gromacs with a
>> > significant performance boosting. I wanted to check if the latest
>> release
>> > of NVIDIA GTX 1080 will work with Gromacs.
>> >
>> > I will appreciate your feedback.
>> >
>> > Jagannath
>> > --
>> > Gromacs Users mailing list
>> >
>> > * Please search the archive at
>> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> > posting!
>> >
>> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>> >
>> > * For (un)subscribe requests visit
>> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> > send a mail to gmx-users-requ...@gromacs.org.
>> >
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> posting!
>>
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>>
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>> send a mail to gmx-users-requ...@gromacs.org.
>>
>
>
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[gmx-users] top parameters for pluronic f127

[SAKO MIRZAIE]

Dear All,

I am trying to convert my mol2 file to amber99sb itp to do MD by
gromacs. but, when I use ACPYPE software, it run and never finished.
my mol2 file is pluronic F127 and contains 2500 atoms. this structure
is a polymer and huge in size. how can I get an itp file for my
polymer? How can I simulate it in MD by gromacs? do polymers have some
tricks?

the molecular structure of f127 is: A99B67A99

where

A: ethylene oxide
B: propylene oxide

best regards,

-- 
***
sako mirzaie
PhD in biochemistry
-- 
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[gmx-users] multiple nodes, GPUs on a Cray system

[Jan Domanski]

Hi,

This is a continuation of this thread – i'm unable to reply to the original
post, so I'll just post a new

https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2016-January/103044.html

The original issue in the thread above – *apparent* slow performance of
Gromacs on the TITAN Cray supercomputer – was something that just affected
me. After some back and forth with TITAN help people, here is a resolution:

Are you trying to run multiple MPI ranks per node all of them accessing the
> GPU? If so, you would need to first set in your submission script:
> export CRAY_CUDA_MPS=1 (bash syntax)
> This variable is needed to allow multiple processes to share the GPU.
> Details
> about this can be found in:
> https://www.olcf.ornl.gov/tutorials/cuda-proxy-managing-gpu-context/
> .
> The
> variable was formerly called CRAY_CUDA_PROXY, both still accomplish the
> same
> task.
> Then, depending on the number of MPI ranks per node, you want to tell
> Gromacs
> how many ranks will share the GPU. For example, if you want to run an 8 MPI
> rank job across 4 nodes, you would need to add:
> aprun -n 8 -N 2 mdrun_mpi -gpu_id 00
> When OpenMP threads are added in the mix, you also need to pass that value
> to
> Gromacs and to aprun (via the -d option):
> aprun -n 8 -N 2 -d 8 mdrun_mpi -ntomp 8 -gpu_id 00
> The Gromacs site has several recommendations for running on GPU, in which
> they
> recommend running more MPI ranks and fewer OpenMP threads:
>
> http://www.gromacs.org/Documentation/Acceleration_and_parallelization#Multiple_MPI_ranks_per_GPU
> 
> More details on the different 'aprun' options can be found at:
> https://www.olcf.ornl.gov/kb_articles/using-the-aprun-command/
> 


- Jan
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Re: [gmx-users] Cross correlation map of residues

[Florent Hédin]

Hi,

I now realise that I forgot to ask something essential: do you want to 
perform this normal mode analysis cross correlation map on just one 
pdb/gro coordinates file, on on a full gromacs trajectory ?


Here is an example performing the nma-ccm analysis for one pdb file :

https://gist.github.com/FHedin/07e07e3fe695a15a002850a2e44a2df9

For documentation see :

http://thegrantlab.org/bio3d/html/dccm.nma.html

If you want to perform a dynamic cross correlation map using a 
trajectory file see:


http://thegrantlab.org/bio3d/html/dccm.xyz.html

Regards,

Florent

On 03/06/16 12:00, Qasim Pars wrote:

Hi,

@Tsjerk: I just installed GROMACS-3.3 and implemented g_correlation tool.
Unfortunately this tool generates the colorless correlation matrix (.xpm)
on atoms. Whereas I would like to have the colourful correlation matrix on
residues (not based on atoms). I think there is no way to get the colourful
correlation matrix on residues by g_correlation tool?

@Florent: The R package bio3d is complex :( It would be good if you share
on the user list such a code to generate the correlation matrix?

Cheers,

On 3 June 2016 at 11:27, Florent Hédin  wrote:


Hi,

In case you really want to produce something similar, I have a solution (
2 in fact ;-) )

This plot is easy to produce with the R package bio3d, unfortunately it
only supports charmm/namd dcd and amber ncdf trajectory types.

The first option : would be to use vmd for converting a gmx trajectory to,
for example, dcd. Then follow the bio3d tutorials of R.

The second option is : R is really modular, you can write a piece of C
code reading the gromacs trajectory and returning it (frame by frame) to R.
This code is compiled as a shared library, and in R you would just easily
load it. I already have some code doing that, if interested I can share it.
On long term I plan to put this piece of code directly into a R package.

Regards,

Florent Hédin


On 03/06/16 08:02, Tsjerk Wassenaar wrote:


Hi Qasim,

The plot you refer to is the result of NMA on C-alpha only. So g_covar
-xpma using only C-alpha atoms should come close. You might also want to
try the g_correlation tool mentioned earlier on the list, but again with a
selection of only C-alpha atoms.

Cheers,

Tsjerk

On Fri, Jun 3, 2016 at 1:50 AM, Qasim Pars  wrote:

Dear gmx users,


I need to get the cross correlation map of all residues belonging to a
protein (like this figure

http://thegrantlab.org/bio3d/vignettes/Bio3D_nma/figures/ex1C-dccmplot.png
).
Is there any tool to get such a plot with GROMACS?

By the way, gmx covar -xpma gives the cross correlation for each atom
pair
but it is not what I want.

Any suggestions will be appreciated.

--
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Re: [gmx-users] Cross correlation map of residues

[Smith, Micholas D.]

If you want coloured images you can always use the xpm2ps tool. It will map the 
.xpm generated into a postscript file with the expected coloring.


===
Micholas Dean Smith, PhD.
Post-doctoral Research Associate
University of Tennessee/Oak Ridge National Laboratory
Center for Molecular Biophysics


From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on behalf of Qasim Pars 

Sent: Friday, June 03, 2016 6:00 AM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Cross correlation map of residues

Hi,

@Tsjerk: I just installed GROMACS-3.3 and implemented g_correlation tool.
Unfortunately this tool generates the colorless correlation matrix (.xpm)
on atoms. Whereas I would like to have the colourful correlation matrix on
residues (not based on atoms). I think there is no way to get the colourful
correlation matrix on residues by g_correlation tool?

@Florent: The R package bio3d is complex :( It would be good if you share
on the user list such a code to generate the correlation matrix?

Cheers,

On 3 June 2016 at 11:27, Florent Hédin  wrote:

> Hi,
>
> In case you really want to produce something similar, I have a solution (
> 2 in fact ;-) )
>
> This plot is easy to produce with the R package bio3d, unfortunately it
> only supports charmm/namd dcd and amber ncdf trajectory types.
>
> The first option : would be to use vmd for converting a gmx trajectory to,
> for example, dcd. Then follow the bio3d tutorials of R.
>
> The second option is : R is really modular, you can write a piece of C
> code reading the gromacs trajectory and returning it (frame by frame) to R.
> This code is compiled as a shared library, and in R you would just easily
> load it. I already have some code doing that, if interested I can share it.
> On long term I plan to put this piece of code directly into a R package.
>
> Regards,
>
> Florent Hédin
>
>
> On 03/06/16 08:02, Tsjerk Wassenaar wrote:
>
>> Hi Qasim,
>>
>> The plot you refer to is the result of NMA on C-alpha only. So g_covar
>> -xpma using only C-alpha atoms should come close. You might also want to
>> try the g_correlation tool mentioned earlier on the list, but again with a
>> selection of only C-alpha atoms.
>>
>> Cheers,
>>
>> Tsjerk
>>
>> On Fri, Jun 3, 2016 at 1:50 AM, Qasim Pars  wrote:
>>
>> Dear gmx users,
>>>
>>> I need to get the cross correlation map of all residues belonging to a
>>> protein (like this figure
>>>
>>> http://thegrantlab.org/bio3d/vignettes/Bio3D_nma/figures/ex1C-dccmplot.png
>>> ).
>>> Is there any tool to get such a plot with GROMACS?
>>>
>>> By the way, gmx covar -xpma gives the cross correlation for each atom
>>> pair
>>> but it is not what I want.
>>>
>>> Any suggestions will be appreciated.
>>>
>>> --
>>> Qasim Pars
>>> --
>>> 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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>>> 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] allosteric effect

[sun]

Hi Qasim
You can read below mentioned paper for analysis:
http://www.nature.com/articles/srep23830

Sent from my iPhone

> On 03-Jun-2016, at 3:28 pm, Qasim Pars  wrote:
> 
> Hi Tsjerk,
> 
> I am interested in the dynamic and conformational effect of allostery on
> protein. The RMSD doesn't show those effects clearly. I would appreciate if
> someone gives me any example of such analysis that provides the information
> about the dynamic and conformational effect of allostery on protein.
> 
> Cheers,
> 
>> On 3 June 2016 at 11:10,  wrote:
>> 
>> Hi,
>> 
>> I wouldn't expect to be able to distinguish MWC from KNF in 200 ns but I
>> imagine this could reveal at least part of the underlying communication
>> mechanism. I'm also trying to use MD for this and would be interested in
>> people's views.
>> 
>> Best wishes
>> James
>> 
>>> Hi Qasim,
>>> 
>>> Do you assume MWC or KNF like allostery, and conformational based,
>>> dynamics
>>> based or mixed?
>>> 
>>> Cheers,
>>> 
>>> Tsjerk
>>> 
 On Fri, Jun 3, 2016 at 2:54 AM, Qasim Pars  wrote:
 
 Dear gmx users,
 
 The protein I have simulated over 200 ns with GROMACS is dimer and shows
 positive allostery. Based on experimental data, the second ligand of
 protein has greater binding affinity than the first ligand. I would like
 to
 prove the positive allosteric effect of protein by some analyses. But I
 really don't know which analyses helps me to investigate/look into the
 allosteric effect. Could you please suggest me some useful analyses to
 investigate the allosteric effect (except for RMSD, RMSF)? I have
 simulations for singly liganded, doubly liganded and apo state.
 
 Thanks a lot, in advance.
 --
 Qasim Pars
 --
 Gromacs Users mailing list
 
 * Please search the archive at
 http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
 posting!
 
 * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
 
 * For (un)subscribe requests visit
 https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
 send a mail to gmx-users-requ...@gromacs.org.
>>> 
>>> 
>>> 
>>> --
>>> Tsjerk A. Wassenaar, Ph.D.
>>> --
>>> Gromacs Users mailing list
>>> 
>>> * Please search the archive at
>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>>> posting!
>>> 
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>>> 
>>> * For (un)subscribe requests visit
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>> send
>>> a mail to gmx-users-requ...@gromacs.org.
>> 
>> 
>> --
>> Gromacs Users mailing list
>> 
>> * Please search the archive at
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>> posting!
>> 
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>> send a mail to gmx-users-requ...@gromacs.org.
> 
> 
> 
> -- 
> Qasim Pars
> -- 
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> 
> * Please search the archive at 
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Re: [gmx-users] Cross correlation map of residues

[Qasim Pars]

Hi,

@Tsjerk: I just installed GROMACS-3.3 and implemented g_correlation tool.
Unfortunately this tool generates the colorless correlation matrix (.xpm)
on atoms. Whereas I would like to have the colourful correlation matrix on
residues (not based on atoms). I think there is no way to get the colourful
correlation matrix on residues by g_correlation tool?

@Florent: The R package bio3d is complex :( It would be good if you share
on the user list such a code to generate the correlation matrix?

Cheers,

On 3 June 2016 at 11:27, Florent Hédin  wrote:

> Hi,
>
> In case you really want to produce something similar, I have a solution (
> 2 in fact ;-) )
>
> This plot is easy to produce with the R package bio3d, unfortunately it
> only supports charmm/namd dcd and amber ncdf trajectory types.
>
> The first option : would be to use vmd for converting a gmx trajectory to,
> for example, dcd. Then follow the bio3d tutorials of R.
>
> The second option is : R is really modular, you can write a piece of C
> code reading the gromacs trajectory and returning it (frame by frame) to R.
> This code is compiled as a shared library, and in R you would just easily
> load it. I already have some code doing that, if interested I can share it.
> On long term I plan to put this piece of code directly into a R package.
>
> Regards,
>
> Florent Hédin
>
>
> On 03/06/16 08:02, Tsjerk Wassenaar wrote:
>
>> Hi Qasim,
>>
>> The plot you refer to is the result of NMA on C-alpha only. So g_covar
>> -xpma using only C-alpha atoms should come close. You might also want to
>> try the g_correlation tool mentioned earlier on the list, but again with a
>> selection of only C-alpha atoms.
>>
>> Cheers,
>>
>> Tsjerk
>>
>> On Fri, Jun 3, 2016 at 1:50 AM, Qasim Pars  wrote:
>>
>> Dear gmx users,
>>>
>>> I need to get the cross correlation map of all residues belonging to a
>>> protein (like this figure
>>>
>>> http://thegrantlab.org/bio3d/vignettes/Bio3D_nma/figures/ex1C-dccmplot.png
>>> ).
>>> Is there any tool to get such a plot with GROMACS?
>>>
>>> By the way, gmx covar -xpma gives the cross correlation for each atom
>>> pair
>>> but it is not what I want.
>>>
>>> Any suggestions will be appreciated.
>>>
>>> --
>>> Qasim Pars
>>> --
>>> 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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> posting!
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Re: [gmx-users] allosteric effect

[Qasim Pars]

Hi Tsjerk,

I am interested in the dynamic and conformational effect of allostery on
protein. The RMSD doesn't show those effects clearly. I would appreciate if
someone gives me any example of such analysis that provides the information
about the dynamic and conformational effect of allostery on protein.

Cheers,

On 3 June 2016 at 11:10,  wrote:

> Hi,
>
> I wouldn't expect to be able to distinguish MWC from KNF in 200 ns but I
> imagine this could reveal at least part of the underlying communication
> mechanism. I'm also trying to use MD for this and would be interested in
> people's views.
>
> Best wishes
> James
>
> > Hi Qasim,
> >
> > Do you assume MWC or KNF like allostery, and conformational based,
> > dynamics
> > based or mixed?
> >
> > Cheers,
> >
> > Tsjerk
> >
> > On Fri, Jun 3, 2016 at 2:54 AM, Qasim Pars  wrote:
> >
> >> Dear gmx users,
> >>
> >> The protein I have simulated over 200 ns with GROMACS is dimer and shows
> >> positive allostery. Based on experimental data, the second ligand of
> >> protein has greater binding affinity than the first ligand. I would like
> >> to
> >> prove the positive allosteric effect of protein by some analyses. But I
> >> really don't know which analyses helps me to investigate/look into the
> >> allosteric effect. Could you please suggest me some useful analyses to
> >> investigate the allosteric effect (except for RMSD, RMSF)? I have
> >> simulations for singly liganded, doubly liganded and apo state.
> >>
> >> Thanks a lot, in advance.
> >> --
> >> Qasim Pars
> >> --
> >> Gromacs Users mailing list
> >>
> >> * Please search the archive at
> >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> >> posting!
> >>
> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >>
> >> * For (un)subscribe requests visit
> >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> >> send a mail to gmx-users-requ...@gromacs.org.
> >>
> >
> >
> >
> > --
> > Tsjerk A. Wassenaar, Ph.D.
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
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> send
> > a mail to gmx-users-requ...@gromacs.org.
> >
>
>
> --
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> posting!
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Re: [gmx-users] Cross correlation map of residues

[Florent Hédin]

Hi,

In case you really want to produce something similar, I have a solution 
( 2 in fact ;-) )


This plot is easy to produce with the R package bio3d, unfortunately it 
only supports charmm/namd dcd and amber ncdf trajectory types.


The first option : would be to use vmd for converting a gmx trajectory 
to, for example, dcd. Then follow the bio3d tutorials of R.


The second option is : R is really modular, you can write a piece of C 
code reading the gromacs trajectory and returning it (frame by frame) to 
R. This code is compiled as a shared library, and in R you would just 
easily load it. I already have some code doing that, if interested I can 
share it. On long term I plan to put this piece of code directly into a 
R package.


Regards,

Florent Hédin

On 03/06/16 08:02, Tsjerk Wassenaar wrote:

Hi Qasim,

The plot you refer to is the result of NMA on C-alpha only. So g_covar
-xpma using only C-alpha atoms should come close. You might also want to
try the g_correlation tool mentioned earlier on the list, but again with a
selection of only C-alpha atoms.

Cheers,

Tsjerk

On Fri, Jun 3, 2016 at 1:50 AM, Qasim Pars  wrote:


Dear gmx users,

I need to get the cross correlation map of all residues belonging to a
protein (like this figure
http://thegrantlab.org/bio3d/vignettes/Bio3D_nma/figures/ex1C-dccmplot.png
).
Is there any tool to get such a plot with GROMACS?

By the way, gmx covar -xpma gives the cross correlation for each atom pair
but it is not what I want.

Any suggestions will be appreciated.

--
Qasim Pars
--
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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] allosteric effect

[jkrieger]

Hi,

I wouldn't expect to be able to distinguish MWC from KNF in 200 ns but I
imagine this could reveal at least part of the underlying communication
mechanism. I'm also trying to use MD for this and would be interested in
people's views.

Best wishes
James

> Hi Qasim,
>
> Do you assume MWC or KNF like allostery, and conformational based,
> dynamics
> based or mixed?
>
> Cheers,
>
> Tsjerk
>
> On Fri, Jun 3, 2016 at 2:54 AM, Qasim Pars  wrote:
>
>> Dear gmx users,
>>
>> The protein I have simulated over 200 ns with GROMACS is dimer and shows
>> positive allostery. Based on experimental data, the second ligand of
>> protein has greater binding affinity than the first ligand. I would like
>> to
>> prove the positive allosteric effect of protein by some analyses. But I
>> really don't know which analyses helps me to investigate/look into the
>> allosteric effect. Could you please suggest me some useful analyses to
>> investigate the allosteric effect (except for RMSD, RMSF)? I have
>> simulations for singly liganded, doubly liganded and apo state.
>>
>> Thanks a lot, in advance.
>> --
>> Qasim Pars
>> --
>> 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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>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-requ...@gromacs.org.
>>
>
>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
> --
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> * Please search the archive at
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Re: [gmx-users] Software generating gaff for gromacs with am1bcc charges

[Andrian Saputra]

Thanks hannes, in my qmmm system, qm parts consist of 100 atoms...
Pada tanggal 3 Jun 2016 13.30, "Hannes Loeffler" 
menulis:

> On Fri, 3 Jun 2016 12:47:34 +0700
> Andrian Saputra  wrote:
>
> > Hi all, can anyone suggest me whats softwares can produce gaff
> > topology for gromacs with am1bcc charges automatically for 100-200
> > atoms ?
>
> All the software I'm aware of wraps around antechamber and so won't do
> any magic to fix problems with the input structure.  With that number
> of atoms I also wonder what that particular molecule is and whether
> you better split that into smaller pieces.
>
>
> > I tried antechamber and always found error...
>
> That's an entirely useless statement and nobody will be able to help
> you with that.  You may want to go through the relevant AMBER tutorial
> to learn how to use the tool and ask antechamber specific questions on
> the AMBER mailing list.
>
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Re: [gmx-users] Software generating gaff for gromacs with am1bcc charges

[Hannes Loeffler]

On Fri, 3 Jun 2016 12:47:34 +0700
Andrian Saputra  wrote:

> Hi all, can anyone suggest me whats softwares can produce gaff
> topology for gromacs with am1bcc charges automatically for 100-200
> atoms ?

All the software I'm aware of wraps around antechamber and so won't do
any magic to fix problems with the input structure.  With that number
of atoms I also wonder what that particular molecule is and whether
you better split that into smaller pieces.


> I tried antechamber and always found error...

That's an entirely useless statement and nobody will be able to help
you with that.  You may want to go through the relevant AMBER tutorial
to learn how to use the tool and ask antechamber specific questions on
the AMBER mailing list.

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Re: [gmx-users] allosteric effect

[Tsjerk Wassenaar]

Hi Qasim,

Do you assume MWC or KNF like allostery, and conformational based, dynamics
based or mixed?

Cheers,

Tsjerk

On Fri, Jun 3, 2016 at 2:54 AM, Qasim Pars  wrote:

> Dear gmx users,
>
> The protein I have simulated over 200 ns with GROMACS is dimer and shows
> positive allostery. Based on experimental data, the second ligand of
> protein has greater binding affinity than the first ligand. I would like to
> prove the positive allosteric effect of protein by some analyses. But I
> really don't know which analyses helps me to investigate/look into the
> allosteric effect. Could you please suggest me some useful analyses to
> investigate the allosteric effect (except for RMSD, RMSF)? I have
> simulations for singly liganded, doubly liganded and apo state.
>
> Thanks a lot, in advance.
> --
> Qasim Pars
> --
> 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] Cross correlation map of residues

[Tsjerk Wassenaar]

Hi Qasim,

The plot you refer to is the result of NMA on C-alpha only. So g_covar
-xpma using only C-alpha atoms should come close. You might also want to
try the g_correlation tool mentioned earlier on the list, but again with a
selection of only C-alpha atoms.

Cheers,

Tsjerk

On Fri, Jun 3, 2016 at 1:50 AM, Qasim Pars  wrote:

> Dear gmx users,
>
> I need to get the cross correlation map of all residues belonging to a
> protein (like this figure
> http://thegrantlab.org/bio3d/vignettes/Bio3D_nma/figures/ex1C-dccmplot.png
> ).
> Is there any tool to get such a plot with GROMACS?
>
> By the way, gmx covar -xpma gives the cross correlation for each atom pair
> but it is not what I want.
>
> Any suggestions will be appreciated.
>
> --
> Qasim Pars
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>



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