Re: [gmx-users] Rupture force definition

[Rakesh Mishra]

Thanks for reply.

Dear Justin

Is it possible to transform .xtc file in the form of .pdb formate
excluding solvent and ion molecules simultaneously.
I am familiar to do this with "trjconv" command. But by using this we can
transform .xtc file in the form of .pdb formate,
where water molecules and ions gets also present in the .pdb formate. How
it is possible to save only system coordinates
rather than solvent ( water molecules ) molecules and ions  at the same
time .





On Wed, Jan 24, 2018 at 6:25 PM, Justin Lemkul  wrote:

>
>
> On 1/24/18 5:02 AM, Rakesh Mishra wrote:
>
>> Dear Justin
>>
>> Thank you very much  for removing the doubts .
>> Let me extend  my query in this respect again. As according to pull code
>> formate which is  discussed in your testing work of umbrella sampling .
>> Please have a rough look.
>>
>> Pull code
>> pull= yes
>> pull_ngroups= 2
>> pull_ncoords= 1
>> pull_group1_name= chain_B
>> pull_group2_name= chain_A
>> pull_coord1_type= umbrella  ; harmonic biasing force
>> pull_coord1_geometry= distance  ; simple distance increase
>> pull_coord1_groups  =  1 2
>> pull_coord1_dim = Y N N
>> pull_coord1_rate= 0.0005  ; 0.0005 nm per ps = 5 nm per 10
>> ns
>> pull_coord1_k   = 400  ; kJ mol^-1 nm^-2
>> pull_coord1_start   = yes   ; define initial COM distance > 0
>>
>> As according to some explanation on the net,  I found  that  in the Pull
>> code written above,
>>
>> "pull_group1_name = chain_B "   gromacs read it as a reference group by
>> default &
>> "pull_group2_name = chain_A"gromacs read it as a pull group by
>> default.
>>
>> But suppose, we want to pull 2 or more groups eg.  B2 & B3 in the same
>> system and which are having
>> two respective reference group A2 & A3 w. r. t. pulled groups  B2 & B3.
>> Then how to define these one in above code.
>>
>> I mean If I have  A1, A2, and A3 three pull group ( which we want to pull)
>> and corresponding to these we have three
>> reference group B1 , B2 and B3. We are pulling all in the same direction
>> (+x  direction ).
>> then how to define these simultaneously in above pull code.
>>
>> will I need to define rate for all these pull group separately ( three
>> times) or if rate value is same then no need to
>>   define three times corresponding to these three pull groups.
>>
>
> You can define any number of groups to be used in any number of biasing
> potentials. Each needs its own complete definition (geometry, dimensions,
> rate, force constant, etc). Get rid of the notion of "reference" and "pull
> group" in this application; groups define the two ends of a reaction
> coordinate, nothing more.
>
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalem...@vt.edu | (540) 231-3129
> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>
> ==
>
> --
> 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.
>



-- 
* Rakesh Kumar Mishra*
*  (RA)CSD  SINP Kolkata, India*

*E-mail - rakesh.mis...@saha.ac.in  *

*Phone n. +91 9473662491, +91877749632*
-- 
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.

Re: [gmx-users] About extracting the non-bonded forces

[Mark Abraham]

Hi,

On Wed, Jan 24, 2018 at 10:05 PM Lovuit CHEN  wrote:

> Hello everyone,
>
>
> I was trying to export non-bonded forces (e.g. LJ, Coulomb) from GROMACS
> during MD simulations, for post-processing of personal projects. But I am
> not sure where to look at. I heard the non-bonded forces are calculated
> with assembly loops, do I have access to them? Which places in the
> installation directory should I look at?
>

First advice: don't, because force fields have not been parametrized such
that they mean anything. But creative use of multiple mdrun -rerun and
choices of energy groups can produce some decompositions of the total force.


> Also, in the case of small non-bonded interactions (like 2 orders of
> magnitude smaller to bonded forces), how much difference it make for my
> simulation if I just remove the [pairs] directive in the topology input
> file?
>

Who can say?

(I am using GROMACS 4.5, BTW, I couldn't upgrade to the latest because the
> research group did heavy customization on this version)
>

Don't, unless you're using those modifications (and then maybe still
don't... there's 7 years of bug fixes you're missing out on...)

Mark


>
> Thank you very much!
>
>
> Lovuit
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
-- 
Gromacs Users mailing list

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

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

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

[gmx-users] About extracting the non-bonded forces

[Lovuit CHEN]

Hello everyone,


I was trying to export non-bonded forces (e.g. LJ, Coulomb) from GROMACS during 
MD simulations, for post-processing of personal projects. But I am not sure 
where to look at. I heard the non-bonded forces are calculated with assembly 
loops, do I have access to them? Which places in the installation directory 
should I look at?


Also, in the case of small non-bonded interactions (like 2 orders of magnitude 
smaller to bonded forces), how much difference it make for my simulation if I 
just remove the [pairs] directive in the topology input file?


(I am using GROMACS 4.5, BTW, I couldn't upgrade to the latest because the 
research group did heavy customization on this version)


Thank you very much!


Lovuit
-- 
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.

Re: [gmx-users] define terminal residue ?

[MD]

On Wed, Jan 24, 2018 at 2:22 PM, Justin Lemkul  wrote:

>
>
> On 1/24/18 2:20 PM, MD wrote:
>
>> Hi Gromacs,
>>
>> Can anyone give me a quick example to define the C-term residue? I have a
>> complaint of OXT not defined in rtp and I think I probably should let
>> gromacs know that is my c-term residue. I searched the tags and found this
>> one "
>>
>> *-[no]ter* (no)
>> Interactive termini selection, instead of charged (default)"
>>
>> But I couldn't find a real example to use this tag. My c-term SER358 is
>> the
>> one that causing this issue. Any help will be appreciated.
>>
>
> There's nothing special about them. If a normal amino acid is causing an
> issue, provide your command line and full screen output (please, in
> general, always do this with pdb2gmx problems - there's lots of output and
> experienced users can find subtle things quite quickly).
>

​sorry, i should have looked more closely. problem solved. ​

>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalem...@vt.edu | (540) 231-3129
> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>
> ==
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/Support
> /Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
-- 
Gromacs Users mailing list

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

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

* 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.

Re: [gmx-users] define terminal residue ?

[Justin Lemkul]

On 1/24/18 2:20 PM, MD wrote:

Hi Gromacs,

Can anyone give me a quick example to define the C-term residue? I have a
complaint of OXT not defined in rtp and I think I probably should let
gromacs know that is my c-term residue. I searched the tags and found this
one "

*-[no]ter* (no)
Interactive termini selection, instead of charged (default)"

But I couldn't find a real example to use this tag. My c-term SER358 is the
one that causing this issue. Any help will be appreciated.


There's nothing special about them. If a normal amino acid is causing an 
issue, provide your command line and full screen output (please, in 
general, always do this with pdb2gmx problems - there's lots of output 
and experienced users can find subtle things quite quickly).


-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==

--
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.

Re: [gmx-users] KALP15 in DPPC

[Justin Lemkul]

On 1/24/18 11:16 AM, negar habibzadeh wrote:

i did it  but when i removed the restraints from water to equilibrate again
,(after new equilibration ) i saw some water molecules  inside the membrane
again. what can i do ?


Let the restrained equilibration run longer. Make sure you're not 
restraining the lipids in any way.


-Justin



On Wed, Jan 24, 2018 at 4:24 PM, Justin Lemkul  wrote:



On 1/24/18 5:02 AM, negar habibzadeh wrote:


hi . i am doing simulation of peptide in DOPC bilayer. i have dopc.itp ,
dopc.pdb, dopc.gro , peptide.itp , sample.top for dopc ,
peptide.pdb,topol.top. i used below commands.

gmx editconf -f peptide.gro -o pep.gro -box 6.35172   6.80701   7.49241 -c
(it corresponds to the x/y/z box vectors of the DOPC unit cell)
i merg peptide and dopc:
cat pep.gro DOPC_323K.gro > tot1.gro
(I remove unnecessary lines)
i add ions :
gmx grompp -f ions.mdp -c tot1.gro -p mem.top -o ions.tpr
gmx genion -s ions.tpr -o tot.gro -p mem.top -pname NA -nname CL -nn 8
i get tpr file  (in mem.mdp i add some line to freeze protein )
gmx grompp -f mem.mdp -c tot.gro -p mem.top -o mem.tpr -n index.ndx
and i use g-membed command:
g_membed -f mem.tpr -dat mem.dat -c final.gro -n index.ndx -xyinit 0.1 (in
mem.dat i include the place of protein in the center of box)
in final.gro there were a few stray water molecules, i deleted them
manually and
i did energy minimization :
gmx grompp -f minim.mdp -c final.gro -p mem.top -o em.tpr
gmx mdrun -v -deffnm em
i checked em.gro , every thing is ok . but when i run nvt
in nvt.gro , A large number of water molecules are inside the membrane.
how can i solve this problem ?


If there's lots of void space around the protein in the membrane, then
you'll either need to prepare the system more carefully to prevent such
voids, or do an equilibration with water molecules restrained in the
z-dimension only, to prevent them from diffusing into the membrane. Then,
remove the restraints and equilibrate again.

-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==

--
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.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==

--
Gromacs Users mailing list

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

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

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

[gmx-users] define terminal residue ?

[MD]

Hi Gromacs,

Can anyone give me a quick example to define the C-term residue? I have a
complaint of OXT not defined in rtp and I think I probably should let
gromacs know that is my c-term residue. I searched the tags and found this
one "

*-[no]ter* (no)
Interactive termini selection, instead of charged (default)"

But I couldn't find a real example to use this tag. My c-term SER358 is the
one that causing this issue. Any help will be appreciated.

Thanks,

Ming
-- 
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.

Re: [gmx-users] KALP15 in DPPC

[negar habibzadeh]

i did it  but when i removed the restraints from water to equilibrate again
,(after new equilibration ) i saw some water molecules  inside the membrane
again. what can i do ?


On Wed, Jan 24, 2018 at 4:24 PM, Justin Lemkul  wrote:

>
>
> On 1/24/18 5:02 AM, negar habibzadeh wrote:
>
>> hi . i am doing simulation of peptide in DOPC bilayer. i have dopc.itp ,
>> dopc.pdb, dopc.gro , peptide.itp , sample.top for dopc ,
>> peptide.pdb,topol.top. i used below commands.
>>
>> gmx editconf -f peptide.gro -o pep.gro -box 6.35172   6.80701   7.49241 -c
>> (it corresponds to the x/y/z box vectors of the DOPC unit cell)
>> i merg peptide and dopc:
>> cat pep.gro DOPC_323K.gro > tot1.gro
>> (I remove unnecessary lines)
>> i add ions :
>> gmx grompp -f ions.mdp -c tot1.gro -p mem.top -o ions.tpr
>> gmx genion -s ions.tpr -o tot.gro -p mem.top -pname NA -nname CL -nn 8
>> i get tpr file  (in mem.mdp i add some line to freeze protein )
>> gmx grompp -f mem.mdp -c tot.gro -p mem.top -o mem.tpr -n index.ndx
>> and i use g-membed command:
>> g_membed -f mem.tpr -dat mem.dat -c final.gro -n index.ndx -xyinit 0.1 (in
>> mem.dat i include the place of protein in the center of box)
>> in final.gro there were a few stray water molecules, i deleted them
>> manually and
>> i did energy minimization :
>> gmx grompp -f minim.mdp -c final.gro -p mem.top -o em.tpr
>> gmx mdrun -v -deffnm em
>> i checked em.gro , every thing is ok . but when i run nvt
>> in nvt.gro , A large number of water molecules are inside the membrane.
>> how can i solve this problem ?
>>
>
> If there's lots of void space around the protein in the membrane, then
> you'll either need to prepare the system more carefully to prevent such
> voids, or do an equilibration with water molecules restrained in the
> z-dimension only, to prevent them from diffusing into the membrane. Then,
> remove the restraints and equilibrate again.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalem...@vt.edu | (540) 231-3129
> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>
> ==
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/Support
> /Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
-- 
Gromacs Users mailing list

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

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

* 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.

Re: [gmx-users] OPLSAA and TOPOLBUILD, regarding

[Ray, Bruce D]

On Jan 24, 2018, at 5:45 AM, RAHUL SURESH  wrote:

> Date: Wed, 24 Jan 2018 16:15:29 +0530
> From: RAHUL SURESH 
> To: gmx-us...@gromacs.org
> Subject: [gmx-users] OPLSAA and TOPOLBUILD, regarding
> Message-ID:
>   
> Content-Type: text/plain; charset="UTF-8"
> 
> I want to perform a Ligand-protein interaction in OPLSAA ff. The
> topolbuild-1.3 package is used to generate lig.gro lig.log lig.top
> fflig.itp and posrelig.itp files.
> 
> In case of fflig.itp it contains
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> *; topolbuild version 1.3; Command line:; ./topolbuild -n chu -dir
> /home/viji/ALZ-PRION-THC/topolbuild1_3/dat/gromacs -ff oplsaa;#define
> _FF_OPLS#define _FF_OPLSAA#define _FF_USER[ defaults ];nbfunc
> comb-rule  gen-pairs fudgeLJ  fudgeQQ  1
> 3   yes 0.5 0.5#include "ffoplsaanb.itp*"
> 
> where #define stats are outdated in latest version of gromacs.
> 
> Now is this .itp file is enough to perform the ligand-protein interaction?
> If not where can I generate or how can I make any most suitable itp file
> for opls ff.
> 
> Any detailed explanation will be most useful in this case. Please
> 
> Thank you
> 
> -- 
> *Regards,*
> *Rahul Suresh*
> *Research Scholar*
> *Bharathiar University*
> *Coimbatore*


Assuming that the command specified a molecule named chu, the file should have 
been
ffchu.itp   This file is basically useless anymore.
The file chu.top is also generated by the topolbuild command and should be 
renamed
chu.itp before editing.  You will need to use a text editor to remove from that 
file
the line near the top of the file that reads

 #include "ffchu.itp"

and all lines near the bottom starting with the line that reads

 ; Include water topology

to the end of the file.  The line removed from the top of the file is 
unnecessary.
The lines near the bottom or some similar appropriate set of lines will need to 
go
into an *.top file in which this file is given in a statement #include chu.itp 
Please see the appropriate Gromacs manual for the version of Gromacs you are
using for proper construction of such a *.top file.


-- 
Bruce D. Ray, Ph.D.
Associate Scientist
IUPUI
Physics Dept.
402 N. Blackford St., Rm. LD-061
Indianapolis, IN  46202


-- 
Gromacs Users mailing list

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

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

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

[gmx-users] citation for amb2gmx.pl, or acpypi.py

[Lara rajam]

Dear Users
Could anyone please let me know the citation for
amb2gmx.pl
,
or acpypi.py

Thank you
-- 
Gromacs Users mailing list

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

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

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] OPLSAA and TOPOLBUILD, regarding

[Justin Lemkul]

On 1/24/18 5:45 AM, RAHUL SURESH wrote:

I want to perform a Ligand-protein interaction in OPLSAA ff. The
topolbuild-1.3 package is used to generate lig.gro lig.log lig.top
fflig.itp and posrelig.itp files.

In case of fflig.itp it contains













*; topolbuild version 1.3; Command line:; ./topolbuild -n chu -dir
/home/viji/ALZ-PRION-THC/topolbuild1_3/dat/gromacs -ff oplsaa;#define
_FF_OPLS#define _FF_OPLSAA#define _FF_USER[ defaults ];nbfunc
comb-rule  gen-pairs fudgeLJ  fudgeQQ  1
3   yes 0.5 0.5#include "ffoplsaanb.itp*"

where #define stats are outdated in latest version of gromacs.

Now is this .itp file is enough to perform the ligand-protein interaction?
If not where can I generate or how can I make any most suitable itp file
for opls ff.

Any detailed explanation will be most useful in this case. Please


You don't want a [defaults] directive in your ligand .itp file, because 
it will clash with the parent force field, anyway. Get rid of that 
section or else you'll get fatal errors from grompp.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==

--
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.

Re: [gmx-users] Rupture force definition

[Justin Lemkul]

On 1/24/18 5:02 AM, Rakesh Mishra wrote:

Dear Justin

Thank you very much  for removing the doubts .
Let me extend  my query in this respect again. As according to pull code
formate which is  discussed in your testing work of umbrella sampling .
Please have a rough look.

Pull code
pull= yes
pull_ngroups= 2
pull_ncoords= 1
pull_group1_name= chain_B
pull_group2_name= chain_A
pull_coord1_type= umbrella  ; harmonic biasing force
pull_coord1_geometry= distance  ; simple distance increase
pull_coord1_groups  =  1 2
pull_coord1_dim = Y N N
pull_coord1_rate= 0.0005  ; 0.0005 nm per ps = 5 nm per 10
ns
pull_coord1_k   = 400  ; kJ mol^-1 nm^-2
pull_coord1_start   = yes   ; define initial COM distance > 0

As according to some explanation on the net,  I found  that  in the Pull
code written above,

"pull_group1_name = chain_B "   gromacs read it as a reference group by
default &
"pull_group2_name = chain_A"gromacs read it as a pull group by default.

But suppose, we want to pull 2 or more groups eg.  B2 & B3 in the same
system and which are having
two respective reference group A2 & A3 w. r. t. pulled groups  B2 & B3.
Then how to define these one in above code.

I mean If I have  A1, A2, and A3 three pull group ( which we want to pull)
and corresponding to these we have three
reference group B1 , B2 and B3. We are pulling all in the same direction
(+x  direction ).
then how to define these simultaneously in above pull code.

will I need to define rate for all these pull group separately ( three
times) or if rate value is same then no need to
  define three times corresponding to these three pull groups.


You can define any number of groups to be used in any number of biasing 
potentials. Each needs its own complete definition (geometry, 
dimensions, rate, force constant, etc). Get rid of the notion of 
"reference" and "pull group" in this application; groups define the two 
ends of a reaction coordinate, nothing more.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==

--
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.

Re: [gmx-users] KALP15 in DPPC

[Justin Lemkul]

On 1/24/18 5:02 AM, negar habibzadeh wrote:

hi . i am doing simulation of peptide in DOPC bilayer. i have dopc.itp ,
dopc.pdb, dopc.gro , peptide.itp , sample.top for dopc ,
peptide.pdb,topol.top. i used below commands.

gmx editconf -f peptide.gro -o pep.gro -box 6.35172   6.80701   7.49241 -c
(it corresponds to the x/y/z box vectors of the DOPC unit cell)
i merg peptide and dopc:
cat pep.gro DOPC_323K.gro > tot1.gro
(I remove unnecessary lines)
i add ions :
gmx grompp -f ions.mdp -c tot1.gro -p mem.top -o ions.tpr
gmx genion -s ions.tpr -o tot.gro -p mem.top -pname NA -nname CL -nn 8
i get tpr file  (in mem.mdp i add some line to freeze protein )
gmx grompp -f mem.mdp -c tot.gro -p mem.top -o mem.tpr -n index.ndx
and i use g-membed command:
g_membed -f mem.tpr -dat mem.dat -c final.gro -n index.ndx -xyinit 0.1 (in
mem.dat i include the place of protein in the center of box)
in final.gro there were a few stray water molecules, i deleted them
manually and
i did energy minimization :
gmx grompp -f minim.mdp -c final.gro -p mem.top -o em.tpr
gmx mdrun -v -deffnm em
i checked em.gro , every thing is ok . but when i run nvt
in nvt.gro , A large number of water molecules are inside the membrane.
how can i solve this problem ?


If there's lots of void space around the protein in the membrane, then 
you'll either need to prepare the system more carefully to prevent such 
voids, or do an equilibration with water molecules restrained in the 
z-dimension only, to prevent them from diffusing into the membrane. 
Then, remove the restraints and equilibrate again.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==

--
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.

Re: [gmx-users] rlist- group scheme

[Faezeh Pousaneh]

>
> Hi again,
>


> Yes. But I thought your comment was referring to "taking the potential to
> zero." Neither the cutoff implementation nor your table was doing that at
> rcutoff, so any particle in the list got computed regardless of rcutoff.
> When you saw a zero-strength interaction, that was because the particles
> weren't being put in the list, and not because it was in the list and
> evaluated as zero strength.
>
> Mark, I thinks there has been misunderstanding. I never saw zero
interactions.

What I mean is: with a LJ table 6,12 given in Gromacs page (even my own
other user tables), when I take rlist=0.6 and rvdw=0.5 in .mdp file, the
resulted potential from simulation shows that instead of potential becomes
zero at rvdW=0.5, it gets zero at rlist=0.6. So many unwanted interactions
are counted.   Which is an important point to know about Gromacs fails
here.

It is OK as long as rvdw-off=rcoulmb=rlist. But if we have a case with
rvdW Mark
>
> > So the solution for me now is to put the potential in the table file to
> > > > zero manually for x>cut-off.
> > >
> > >
> > > Glancing at the kernels that implement user tables, that's what you
> > should
> > > do. That means the forces are strange and you would wish to consider a
> > form
> > > where the potential smoothly reaches zero at the cutoff.
> > >
> > > But it is better to solve the problem in
> > > > Gromacs.
> > > >
> > >
> > > It looks like the group scheme with user tables doesn't have support
> for
> > > buffered lists with a correct cutoff. That correct cutoff is only
> > available
> > > in the group scheme for potentials that do go to zero. Likely we
> > concluded
> > > that because you have the ability to express your wishes entirely in
> your
> > > table, you should do so. Or use rlist == rvdw == rcoulomb.
> > >
> > > Mark
> > >
> > > > Mark
> > > > >
> > > > >
> > > > > >
> > > > > >
> > > > > > Best regards
> > > > > >
> > > > > >
> > > > > > On Sun, Jan 21, 2018 at 12:57 AM, Mark Abraham <
> > > > mark.j.abra...@gmail.com
> > > > > >
> > > > > > wrote:
> > > > > >
> > > > > > > Hi,
> > > > > > >
> > > > > > > Yes, you said that before. But I asked what range it worked
> over,
> > > ie
> > > > > what
> > > > > > > range of cutoff.
> > > > > > >
> > > > > > > Mark
> > > > > > >
> > > > > > > On Sat, Jan 20, 2018, 17:15 Faezeh Pousaneh <
> fpoosa...@gmail.com
> > >
> > > > > wrote:
> > > > > > >
> > > > > > > > Hi Mark,
> > > > > > > >
> > > > > > > > For rlist=rcut-off (max one) it works correctly, but as soon
> as
> > > > > rlist>
> > > > > > > > rcut-off it fails and gives different energies. Which I do
> not
> > > > > > understand
> > > > > > > > why. In principle, there is nothing going on after cut-off in
> > > > > > potentials.
> > > > > > > >
> > > > > > > >
> > > > > > > >
> > > > > > > >
> > > > > > > > Best regards
> > > > > > > >
> > > > > > > >
> > > > > > > > On Sat, Jan 20, 2018 at 1:13 AM, Mark Abraham <
> > > > > > mark.j.abra...@gmail.com>
> > > > > > > > wrote:
> > > > > > > >
> > > > > > > > > Hi,
> > > > > > > > >
> > > > > > > > > There could be. But over what range does your table work
> > > > correctly?
> > > > > > > What
> > > > > > > > do
> > > > > > > > > you get when you have a two particle system at various
> > > > > displacements?
> > > > > > > > >
> > > > > > > > > Mark
> > > > > > > > >
> > > > > > > > > On Fri, Jan 19, 2018, 23:59 Faezeh Pousaneh <
> > > fpoosa...@gmail.com
> > > > >
> > > > > > > wrote:
> > > > > > > > >
> > > > > > > > > > Dear Mark,
> > > > > > > > > >
> > > > > > > > > > Thank you, however, the problem occurs when 'table' is
> > used.
> > > > For
> > > > > > > > > > vdWtype=not-user the energies are OK and the same for
> both
> > > > cases,
> > > > > > as
> > > > > > > I
> > > > > > > > > > mentioned. So I guess there should be something wrong in
> > the
> > > > way
> > > > > > > > Gromacs
> > > > > > > > > > interpolates the table with cutoffs and rlist.
> > > > > > > > > >
> > > > > > > > > > Best regards
> > > > > > > > > >
> > > > > > > > > >
> > > > > > > > > >
> > > > > > > > > > Best regards
> > > > > > > > > >
> > > > > > > > > >
> > > > > > > > > > On Fri, Jan 19, 2018 at 8:09 PM, Mark Abraham <
> > > > > > > > mark.j.abra...@gmail.com>
> > > > > > > > > > wrote:
> > > > > > > > > >
> > > > > > > > > > > Hi,
> > > > > > > > > > >
> > > > > > > > > > > With the group scheme, when you choose nstlist > 1 then
> > you
> > > > > get a
> > > > > > > > list
> > > > > > > > > of
> > > > > > > > > > > all the groups that satisfy rlist, whatever it is, and
> > > > continue
> > > > > > to
> > > > > > > > use
> > > > > > > > > > that
> > > > > > > > > > > list for the whole lifetime. If you chose
> > rlist==rcoulomb,
> > > > then
> > > > > > > > > rcoulomb
> > > > > > > > > > is
> > > > > > > > > > > never considered again, because you chose to use an
> > > > unbuffered
> > > > > > > list.
> > > > > > > > > But
> > > > > > > > > > > with rlist > rcoulomb, you chose the list to have
> > > >

Re: [gmx-users] Acetylation of lysine

[Justin Lemkul]

On 1/23/18 10:03 PM, Shraddha Parate wrote:

On Wed, Jan 24, 2018 at 11:58 AM, Shraddha Parate 
wrote:


[sp@atp 2RTU_Gromos45a3]$ gmx pdb2gmx -f 2RTU_1.pdb -o 2RTU.gro -water
spce
GROMACS:gmx pdb2gmx, VERSION 5.0.6

GROMACS is written by:
Emile Apol Rossen Apostolov   Herman J.C. Berendsen Par Bjelkmar
Aldert van Buuren  Rudi van DrunenAnton Feenstra Sebastian Fritsch
Gerrit GroenhofChristoph Junghans Peter Kasson   Carsten Kutzner
Per LarssonJustin A. Lemkul   Magnus LundborgPieter Meulenhoff
Erik Marklund  Teemu Murtola  Szilard Pall   Sander Pronk
Roland Schulz  Alexey ShvetsovMichael Shirts Alfons Sijbers
Peter Tieleman Christian Wennberg Maarten Wolf
and the project leaders:
Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel

Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2014, The GROMACS development team at
Uppsala University, Stockholm University and
the Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.

GROMACS is free software; you can redistribute it and/or modify it
under the terms of the GNU Lesser General Public License
as published by the Free Software Foundation; either version 2.1
of the License, or (at your option) any later version.

GROMACS:  gmx pdb2gmx, VERSION 5.0.6
Executable:   /usr/local/gromacs_5.0.6/bin/gmx
Library dir:  /usr/local/gromacs_5.0.6/share/gromacs/top
Command line:
   gmx pdb2gmx -f 2RTU_1.pdb -o 2RTU.gro -water spce


Select the Force Field:
 From current directory:
  1: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205)
 From '/usr/local/gromacs_5.0.6/share/gromacs/top':
  2: AMBER03 protein, nucleic AMBER94 (Duan et al., J. Comp. Chem. 24,
1999-2012, 2003)
  3: AMBER94 force field (Cornell et al., JACS 117, 5179-5197, 1995)
  4: AMBER96 protein, nucleic AMBER94 (Kollman et al., Acc. Chem. Res. 29,
461-469, 1996)
  5: AMBER99 protein, nucleic AMBER94 (Wang et al., J. Comp. Chem. 21,
1049-1074, 2000)
  6: AMBER99SB protein, nucleic AMBER94 (Hornak et al., Proteins 65,
712-725, 2006)
  7: AMBER99SB-ILDN protein, nucleic AMBER94 (Lindorff-Larsen et al.,
Proteins 78, 1950-58, 2010)
  8: AMBERGS force field (Garcia & Sanbonmatsu, PNAS 99, 2782-2787, 2002)
  9: CHARMM27 all-atom force field (CHARM22 plus CMAP for proteins)
10: GROMOS96 43a1 force field
11: GROMOS96 43a2 force field (improved alkane dihedrals)
12: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205)
13: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656)
14: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656)
15: GROMOS96 53A6 force field, extended to include Berger lipid parameters
16: GROMOS96 54a7 force field (Eur. Biophys. J. (2011), 40,, 843-856, DOI:
10.1007/s00249-011-0700-9)
17: gromos_lipid
18: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
1

Using the Gromos45a3 force field in directory ./gromos45a3.ff

Warning: file does not end with a newline, last line:
KAC  Protein


There is still the likelihood of something being misinterpreted here, or 
in any other file you've modified, if you're not using a proper 
plain-text editor. Never ignore formatting warnings.



Opening force field file ./gromos45a3.ff/aminoacids.r2b
Warning: file does not end with a newline, last line:
KAC  Protein
Reading 2RTU_1.pdb...
WARNING: all CONECT records are ignored
Read 715 atoms
Analyzing pdb file
Splitting chemical chains based on TER records or chain id changing.
There are 1 chains and 0 blocks of water and 87 residues with 715 atoms

   chain  #res #atoms
   1 'A'87715

All occupancies are one
Opening force field file ./gromos45a3.ff/atomtypes.atp
Atomtype 49
Reading residue database... (gromos45a3)
Opening force field file ./gromos45a3.ff/aminoacids.rtp
Using default: not generating all possible dihedrals
Using default: excluding 3 bonded neighbors
Using default: generating 1,4 H--H interactions
Using default: removing proper dihedrals found on the same bond as a
proper dihedral
Residue 97
Sorting it all out...
Opening force field file ./gromos45a3.ff/aminoacids.hdb
Error in hdb file: nah = 44
line = ''


This error suggests your modifications to the .hdb file are incorrect, 
and are therefore not being used, so you get missing H atoms in KAC. 
Check your work, and again, always use a plain text editor.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==

--
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

Re: [gmx-users] gangle for a plane and z axis

[Justin Lemkul]

On 1/23/18 7:20 PM, Mohsen Ramezanpour wrote:

Hi Gromacs users,

I would like to calculate the angle distribution between a plane and z
axis using gangle.

In a 5-member ring, there are three atoms of O1-C-O2 which form an angle.
So, I will choose these three atom names to define the plane.

I am not sure how the g_angle makes the vector normal for this plane,
though. I know that it first make two vectors, and then does a cross
product of these two initial vectors to make the normal vector to the
plane. But, what is the direction of the vector normal to this plane?

Looking at the calc_vec function (lines 652 to 690) code from:
https://github.com/gromacs/gromacs/blob/master/src/gromacs/trajectoryanalysis/modules/angle.cpp
It is using functions cprod and rvec_sub.

I found cprod definition here:
http://manual.gromacs.org/documentation/2018-beta3/doxygen/html-lib/group__module__simd.xhtml#ga54124af0ff118d3f171b0eef07105c76

cprod (v1,v2,xout) means C = v1 * v2 (so the Right Hand Rule can be used to
get the direction)

I could not find rvec_sub function, though. However, I think:
rvec_sub(x[1], x[0], v1) gives the v1 as v1= x[1]-x[0]. i.e. a vector
starting from x[0] and ending on x[1].

Are these correct?


Yes. rvec_sub() is in src/gromacs/math/vec.h

-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==

--
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.

Re: [gmx-users] rlist- group scheme

[Mark Abraham]

Hi,

On Tue, Jan 23, 2018 at 6:27 PM Faezeh Pousaneh  wrote:

> Hi Mark,
> thanks for remarks, just one point:
>
>
> > > But what I see from resulted potential vs
> > > displacement of two molecules, is that Gromacs has taken the potential
> to
> > > zero at rlist not *''rcut-off''*. That is why for rcut-off > rlist the
> > > result is not correct.
> > >
> >
> > You're seeing the consequence of the particles at displacement > rlist
> not
> > being put into the list, so not making a contribution.
> >
>
> no, I see the particles between rcut-off and rlist  which should have no
> contribution to the potential (since potential should be zero after cut-off
> and rlist is bigger than rcutoff) *have* contributions, and that is what
> makes the wrong results.
>

Yes. But I thought your comment was referring to "taking the potential to
zero." Neither the cutoff implementation nor your table was doing that at
rcutoff, so any particle in the list got computed regardless of rcutoff.
When you saw a zero-strength interaction, that was because the particles
weren't being put in the list, and not because it was in the list and
evaluated as zero strength.

Mark

> So the solution for me now is to put the potential in the table file to
> > > zero manually for x>cut-off.
> >
> >
> > Glancing at the kernels that implement user tables, that's what you
> should
> > do. That means the forces are strange and you would wish to consider a
> form
> > where the potential smoothly reaches zero at the cutoff.
> >
> > But it is better to solve the problem in
> > > Gromacs.
> > >
> >
> > It looks like the group scheme with user tables doesn't have support for
> > buffered lists with a correct cutoff. That correct cutoff is only
> available
> > in the group scheme for potentials that do go to zero. Likely we
> concluded
> > that because you have the ability to express your wishes entirely in your
> > table, you should do so. Or use rlist == rvdw == rcoulomb.
> >
> > Mark
> >
> > > Mark
> > > >
> > > >
> > > > >
> > > > >
> > > > > Best regards
> > > > >
> > > > >
> > > > > On Sun, Jan 21, 2018 at 12:57 AM, Mark Abraham <
> > > mark.j.abra...@gmail.com
> > > > >
> > > > > wrote:
> > > > >
> > > > > > Hi,
> > > > > >
> > > > > > Yes, you said that before. But I asked what range it worked over,
> > ie
> > > > what
> > > > > > range of cutoff.
> > > > > >
> > > > > > Mark
> > > > > >
> > > > > > On Sat, Jan 20, 2018, 17:15 Faezeh Pousaneh  >
> > > > wrote:
> > > > > >
> > > > > > > Hi Mark,
> > > > > > >
> > > > > > > For rlist=rcut-off (max one) it works correctly, but as soon as
> > > > rlist>
> > > > > > > rcut-off it fails and gives different energies. Which I do not
> > > > > understand
> > > > > > > why. In principle, there is nothing going on after cut-off in
> > > > > potentials.
> > > > > > >
> > > > > > >
> > > > > > >
> > > > > > >
> > > > > > > Best regards
> > > > > > >
> > > > > > >
> > > > > > > On Sat, Jan 20, 2018 at 1:13 AM, Mark Abraham <
> > > > > mark.j.abra...@gmail.com>
> > > > > > > wrote:
> > > > > > >
> > > > > > > > Hi,
> > > > > > > >
> > > > > > > > There could be. But over what range does your table work
> > > correctly?
> > > > > > What
> > > > > > > do
> > > > > > > > you get when you have a two particle system at various
> > > > displacements?
> > > > > > > >
> > > > > > > > Mark
> > > > > > > >
> > > > > > > > On Fri, Jan 19, 2018, 23:59 Faezeh Pousaneh <
> > fpoosa...@gmail.com
> > > >
> > > > > > wrote:
> > > > > > > >
> > > > > > > > > Dear Mark,
> > > > > > > > >
> > > > > > > > > Thank you, however, the problem occurs when 'table' is
> used.
> > > For
> > > > > > > > > vdWtype=not-user the energies are OK and the same for both
> > > cases,
> > > > > as
> > > > > > I
> > > > > > > > > mentioned. So I guess there should be something wrong in
> the
> > > way
> > > > > > > Gromacs
> > > > > > > > > interpolates the table with cutoffs and rlist.
> > > > > > > > >
> > > > > > > > > Best regards
> > > > > > > > >
> > > > > > > > >
> > > > > > > > >
> > > > > > > > > Best regards
> > > > > > > > >
> > > > > > > > >
> > > > > > > > > On Fri, Jan 19, 2018 at 8:09 PM, Mark Abraham <
> > > > > > > mark.j.abra...@gmail.com>
> > > > > > > > > wrote:
> > > > > > > > >
> > > > > > > > > > Hi,
> > > > > > > > > >
> > > > > > > > > > With the group scheme, when you choose nstlist > 1 then
> you
> > > > get a
> > > > > > > list
> > > > > > > > of
> > > > > > > > > > all the groups that satisfy rlist, whatever it is, and
> > > continue
> > > > > to
> > > > > > > use
> > > > > > > > > that
> > > > > > > > > > list for the whole lifetime. If you chose
> rlist==rcoulomb,
> > > then
> > > > > > > > rcoulomb
> > > > > > > > > is
> > > > > > > > > > never considered again, because you chose to use an
> > > unbuffered
> > > > > > list.
> > > > > > > > But
> > > > > > > > > > with rlist > rcoulomb, you chose the list to have
> > > interactions
> > > > > that
> > > > > > > are
> > > > > > > > > not
> > > > > > > > > > within rcoulom

Re: [gmx-users] (no subject)

[Mark Abraham]

Hi,

Either your topology components are in the wrong order (like the message
says) or you're doing something strange. Notice how your water won't have
any atoms unless _FF_CHARMM is defined, which will only be defined if
you've got a charmm force field involved. But nobody's got enough
information to help you.

And please do yourself a favour and get a more recent GROMACS version
installed. It's been more than 7 years since 4.5.5...

Mark

‪On Wed, Jan 24, 2018 at 10:45 AM ‫حلیمه میرسالاری‬‎ <
h.mirsalar...@gmail.com> wrote:‬

> Dear all
>
> l am using gromacs 4.5.5 version for simulation carbon nanotubes  with
> charmm27 force feild ,there was no error grompp stage,but when l do
> simulation of carbon nanotube in tip3p  water encountered with
>  fatal error:
>
>   [ file tip3p.itp, line 40]:
> Atom index (1) in settles out of bounds (1-0).
> This probably means that you have inserted topology section "settles"
> in a part belonging to a different molecule than you intended to.
> In that case move the "settles" section to the right molecule.
>
> Please guide me
>
> File:tip3p.itp
>
> Thanks
>
> Halimeh
>
>
>  1
>  2
>  3
>  4
>  5
>  6
>  7
>  8
>  9
> 10
> 11
> 12
> 13
> 14
> 15
> 16
> 17
> 18
> 19
> 20
> 21
> 22
> 23
> 24
> 25
> 26
> 27
> 28
> 29
> 30
> 31
> 32
> 33
> 34
> 35
> 36
> 37
> 38
> 39
> 40
> 41
> 42
> 43
> 44
> 45
> 46
>
> [ moleculetype ]
> ; molname  nrexcl
> SOL 2
>
> [ atoms ]
> ; id   at type  res nr  residu name at name cg nr   charge
> #ifdef _FF_CHARMM
> 1   OWT31   SOL  OW 1   -0.834
> 2   HWT31   SOL HW1 10.417
> 3   HWT31   SOL HW2 10.417
> #endif
>
>
> #ifdef FLEXIBLE
>
> #ifdef CHARMM_TIP3P
> [ bonds ]
> ; i j   funct   length  force.c.
> 1   2   1   0.09572 376560.0 0.09572376560.0
> 1   3   1   0.09572 376560.0 0.09572376560.0
>
> [ angles ]
> ; i  j  k   funct   angle   force.c.
> 21  3   1   104.52  460.24  104.52  460.24
> #else
> [ bonds ]
> ; i j   funct   length  force.c.
> 1   2   1   0.09572 502416.0 0.09572502416.0
> 1   3   1   0.09572 502416.0 0.09572502416.0
>
> [ angles ]
> ; i  j  k   funct   angle   force.c.
> 21  3   1   104.52  628.02  104.52  628.02
> #endif
>
>
> #else
> [ settles ]
> ; i   j funct   length
> 1 1 0.09572 0.15139
>
> [ exclusions ]
> 1 2 3
> 2 1 3
> 3 1 2
> #endif
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
-- 
Gromacs Users mailing list

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

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

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

[gmx-users] OPLSAA and TOPOLBUILD, regarding

[RAHUL SURESH]

I want to perform a Ligand-protein interaction in OPLSAA ff. The
topolbuild-1.3 package is used to generate lig.gro lig.log lig.top
fflig.itp and posrelig.itp files.

In case of fflig.itp it contains













*; topolbuild version 1.3; Command line:; ./topolbuild -n chu -dir
/home/viji/ALZ-PRION-THC/topolbuild1_3/dat/gromacs -ff oplsaa;#define
_FF_OPLS#define _FF_OPLSAA#define _FF_USER[ defaults ];nbfunc
comb-rule  gen-pairs fudgeLJ  fudgeQQ  1
3   yes 0.5 0.5#include "ffoplsaanb.itp*"

where #define stats are outdated in latest version of gromacs.

Now is this .itp file is enough to perform the ligand-protein interaction?
If not where can I generate or how can I make any most suitable itp file
for opls ff.

Any detailed explanation will be most useful in this case. Please

Thank you

-- 
*Regards,*
*Rahul Suresh*
*Research Scholar*
*Bharathiar University*
*Coimbatore*
-- 
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.

Re: [gmx-users] Rupture force definition

[Rakesh Mishra]

Dear Justin

Thank you very much  for removing the doubts .
Let me extend  my query in this respect again. As according to pull code
formate which is  discussed in your testing work of umbrella sampling .
Please have a rough look.

Pull code
pull= yes
pull_ngroups= 2
pull_ncoords= 1
pull_group1_name= chain_B
pull_group2_name= chain_A
pull_coord1_type= umbrella  ; harmonic biasing force
pull_coord1_geometry= distance  ; simple distance increase
pull_coord1_groups  =  1 2
pull_coord1_dim = Y N N
pull_coord1_rate= 0.0005  ; 0.0005 nm per ps = 5 nm per 10
ns
pull_coord1_k   = 400  ; kJ mol^-1 nm^-2
pull_coord1_start   = yes   ; define initial COM distance > 0

As according to some explanation on the net,  I found  that  in the Pull
code written above,

"pull_group1_name = chain_B "   gromacs read it as a reference group by
default &
"pull_group2_name = chain_A"gromacs read it as a pull group by default.

But suppose, we want to pull 2 or more groups eg.  B2 & B3 in the same
system and which are having
two respective reference group A2 & A3 w. r. t. pulled groups  B2 & B3.
Then how to define these one in above code.

I mean If I have  A1, A2, and A3 three pull group ( which we want to pull)
and corresponding to these we have three
reference group B1 , B2 and B3. We are pulling all in the same direction
(+x  direction ).
then how to define these simultaneously in above pull code.

will I need to define rate for all these pull group separately ( three
times) or if rate value is same then no need to
 define three times corresponding to these three pull groups.


thanks



On Tue, Jan 23, 2018 at 5:17 PM, Justin Lemkul  wrote:

>
>
> On 1/23/18 3:01 AM, Rakesh Mishra wrote:
>
>> Ok, thanks for learifivcation.
>> Dear Justin I have one  another query regarding
>> pulling using umbrella sampling. See these two lines below.
>>
>> Eg.Pull group   natomspbc atom  distance at startreference at
>> t=0
>>   131   1387
>>   231   6867.424 nm
>> 7.424 nm
>>
>> When we use grompp for obtaining .tpr file before mdrun of pulling. We see
>> 2 lines which are shown just above .
>>
>> My query is that why it is written 7.424 nm in the second line below the
>> distance at start (written in the first line).
>> I am asking because, in my thinking my object( reference group ) is very
>> close to wall ( nearly 2 nm away from the wall of yz. here I am
>> pulling in + x direction), which I can see in VMD.  Does this distance is
>> distance from the pull group to the reference group or
>> distance between pulled group to the wall near the reference group.
>>
>>
> grompp is reporting the distance that it finds along the reaction
> coordinate (first value) and the expected reference value from your .mdp
> settings (second value). However you have your groups and pull settings
> defined leads grompp to tell you that this coordinate file has a 7.4-nm
> separation between your two groups.
>
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalem...@vt.edu | (540) 231-3129
> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>
> ==
>
> --
> 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.
>



-- 
* Rakesh Kumar Mishra*
*  (RA)CSD  SINP Kolkata, India*

*E-mail - rakesh.mis...@saha.ac.in  *

*Phone n. +91 9473662491, +91877749632*
-- 
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.

Re: [gmx-users] KALP15 in DPPC

[negar habibzadeh]

hi . i am doing simulation of peptide in DOPC bilayer. i have dopc.itp ,
dopc.pdb, dopc.gro , peptide.itp , sample.top for dopc ,
peptide.pdb,topol.top. i used below commands.

gmx editconf -f peptide.gro -o pep.gro -box 6.35172   6.80701   7.49241 -c
(it corresponds to the x/y/z box vectors of the DOPC unit cell)
i merg peptide and dopc:
cat pep.gro DOPC_323K.gro > tot1.gro
(I remove unnecessary lines)
i add ions :
gmx grompp -f ions.mdp -c tot1.gro -p mem.top -o ions.tpr
gmx genion -s ions.tpr -o tot.gro -p mem.top -pname NA -nname CL -nn 8
i get tpr file  (in mem.mdp i add some line to freeze protein )
gmx grompp -f mem.mdp -c tot.gro -p mem.top -o mem.tpr -n index.ndx
and i use g-membed command:
g_membed -f mem.tpr -dat mem.dat -c final.gro -n index.ndx -xyinit 0.1 (in
mem.dat i include the place of protein in the center of box)
in final.gro there were a few stray water molecules, i deleted them
manually and
i did energy minimization :
gmx grompp -f minim.mdp -c final.gro -p mem.top -o em.tpr
gmx mdrun -v -deffnm em
i checked em.gro , every thing is ok . but when i run nvt
in nvt.gro , A large number of water molecules are inside the membrane.
how can i solve this problem ?

On Mon, Jan 22, 2018 at 4:19 PM, Justin Lemkul  wrote:

>
>
> On 1/21/18 1:23 PM, negar habibzadeh wrote:
>
>> hi . in vmd how can i find special number for each atom? i want to delete
>> those atoms from my gro file.
>>
>
> You can label atoms by clicking on them in label mode. If you have further
> questions about VMD, post to their mailing list.
>
> -Justin
>
>
> tnx
>>
>>
>> On Mon, Jan 15, 2018 at 9:12 PM, Justin Lemkul  wrote:
>>
>>
>>> On 1/15/18 10:56 AM, negar habibzadeh wrote:
>>>
>>> tnx so much
i got nvt.tpr and now i want to run it but i am getting this error :
 Fatal error:
 Too many LINCS warnings (5258)
 If you know what you are doing you can adjust the lincs warning
 threshold
 in your mdp file
 or set the environment variable GMX_MAXCONSTRWARN to -1,
 but normally it is better to fix the problem

 I use position restraints on the lipid headgroups for P of DOPC . i add
 the
 following lines to the system topology after the #include "dopc.itp"
 line.

 #include "DOPC.itp"

 #ifdef POSRES_LIPID
 #include "lipid_posre.itp"
 #endif

 and i add the following line in nvt.mdp :
 define  = -DPOSRES_protein  -DPOSRES_LIPID  ; Position restraint
 for each protein and for DOPC P

 i created lipid_posre.itp :

 ; position restraint file for DOPC P

 [ position_restraints ]
 ;  i funct   fcxfcyfcz
  201   0   0   1000
 ~

 i used position restraints for lipids but again when i want to run nvt
 ,i
 get this error :

 Fatal error:
 Too many LINCS warnings (5258)
 If you know what you are doing you can adjust the lincs warning
 threshold
 in your mdp file
 or set the environment variable GMX_MAXCONSTRWARN to -1,
 but normally it is better to fix the problem

 how can i solve this problem ?

 http://www.gromacs.org/Documentation/Terminology/Blowing_Up#
>>> Diagnosing_an_Unstable_System
>>>
>>> -Justin
>>>
>>>
>>> --
>>> ==
>>>
>>> Justin A. Lemkul, Ph.D.
>>> Assistant Professor
>>> Virginia Tech Department of Biochemistry
>>>
>>> 303 Engel Hall
>>> 340 West Campus Dr.
>>> Blacksburg, VA 24061
>>>
>>> jalem...@vt.edu | (540) 231-3129
>>> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>>>
>>> ==
>>>
>>> --
>>> 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.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalem...@vt.edu | (540) 231-3129
> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>
> ==
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/Support
> /Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
-- 
Gromacs Users mailing list

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

* Can't post? Read ht

[gmx-users] (no subject)

[حلیمه میرسالاری]

Dear all

l am using gromacs 4.5.5 version for simulation carbon nanotubes  with
charmm27 force feild ,there was no error grompp stage,but when l do
simulation of carbon nanotube in tip3p  water encountered with
 fatal error:

  [ file tip3p.itp, line 40]:
Atom index (1) in settles out of bounds (1-0).
This probably means that you have inserted topology section "settles"
in a part belonging to a different molecule than you intended to.
In that case move the "settles" section to the right molecule.

Please guide me

File:tip3p.itp

Thanks

Halimeh


 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46

[ moleculetype ]
; molname  nrexcl
SOL 2

[ atoms ]
; id   at type  res nr  residu name at name cg nr   charge
#ifdef _FF_CHARMM
1   OWT31   SOL  OW 1   -0.834
2   HWT31   SOL HW1 10.417
3   HWT31   SOL HW2 10.417
#endif


#ifdef FLEXIBLE

#ifdef CHARMM_TIP3P
[ bonds ]
; i j   funct   length  force.c.
1   2   1   0.09572 376560.0 0.09572376560.0
1   3   1   0.09572 376560.0 0.09572376560.0

[ angles ]
; i  j  k   funct   angle   force.c.
21  3   1   104.52  460.24  104.52  460.24  
#else
[ bonds ]
; i j   funct   length  force.c.
1   2   1   0.09572 502416.0 0.09572502416.0
1   3   1   0.09572 502416.0 0.09572502416.0

[ angles ]
; i  j  k   funct   angle   force.c.
21  3   1   104.52  628.02  104.52  628.02  
#endif


#else
[ settles ]
; i   j funct   length
1 1 0.09572 0.15139

[ exclusions ]
1 2 3
2 1 3
3 1 2
#endif
-- 
Gromacs Users mailing list

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

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

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

[gmx-users] (no subject)

[negar habibzadeh]

hi . i am doing simulation of peptide in DOPC bilayer. i have dopc.itp ,
dopc.pdb, dopc.gro , peptide.itp , sample.top for dopc ,
peptide.pdb,topol.top. i used below commands.

gmx editconf -f peptide.gro -o pep.gro -box 6.35172   6.80701   7.49241 -c
(it corresponds to the x/y/z box vectors of the DOPC unit cell)
i merg peptide and dopc:
cat pep.gro DOPC_323K.gro > tot1.gro
(I remove unnecessary lines)
i add ions :
gmx grompp -f ions.mdp -c tot1.gro -p mem.top -o ions.tpr
gmx genion -s ions.tpr -o tot.gro -p mem.top -pname NA -nname CL -nn 8
i get tpr file  (in mem.mdp i add some line to freeze protein )
gmx grompp -f mem.mdp -c tot.gro -p mem.top -o mem.tpr -n index.ndx
and i use g-membed command:
g_membed -f mem.tpr -dat mem.dat -c final.gro -n index.ndx -xyinit 0.1 (in
mem.dat i include the place of protein in the center of box)
in final.gro there were a few stray water molecules, i deleted them
manually and
i did energy minimization :
gmx grompp -f minim.mdp -c final.gro -p mem.top -o em.tpr
gmx mdrun -v -deffnm em
i checked em.gro , every thing is ok . but when i run nvt
in nvt.gro , A large number of water molecules are inside the membrane.
how can i solve this problem ?
-- 
Gromacs Users mailing list

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

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

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

[gmx-users] Tests with Threadripper and dual gpu setup

[Harry Mark Greenblatt]

BS”D

In case anybody is interested we have tested Gromacs on a Threadripper machine 
with two GPU’s.

Hardware:

Ryzen Threadripper 1950X 16 core CPU (multithreading on), with Corsair H100i V2 
Liquid cooling
Asus Prime X399-A M/B
2 X Geforce GTX 1080 GPU’s
32 GB of 3200MHz memory
Samsung 850 Pro 512GB SSD

OS, software:

Centos 7.4, with 4.14 Kernel from ElRepo
gcc 4.8.5 and gcc 5.5.0
fftw 3.3.7 (AVX2 enabled)
Cuda 8
Gromacs 2016.4
Gromacs 2018-rc1 and final 2018.
Using thread-MPI


I managed to compile gcc 5.5.0, but when I went to use it to compile Gromacs, 
the compiler could not recognise the hardware, although the native gcc 4.8.5 
had no problem.
In 2016.4, I was able to specify which SIMD set to use, so this was not an 
issue.   In any case there was very little difference between gcc 5.5.0 and 
4.8.5.  So I used 4.8.5 for 2018.
Any ideas how to overcome this problem with 5.5.0?


Gromacs 2016.4


System: Protein/DNA complex, with 438,397 atoms (including waters/ions), 100 ps 
npt equilibration.

Allowing Gromacs to choose how it wanted to allocate the hardware gave

8 tMPI ranks, 4 thread per rank, both GPU’s

12.4 ns/day

When I told it to use 4 tMPI ranks, 8 threads per rank, both GPU’s

12.2 ns/day


Running on “real” cores only

4 tMPI ranks, 4 threads per rank, 2 GPU’s

10.2 ns/day

1 tMPI rank, 16 threads per rank, *one* GPU (“half” the machine; pin on, but 
pinstride and pinoffset automatic)

10.6 ns/day

1 tMP rank, 16 threads per rank, one gpu, and manually set all pinning options:

gmx mdrun -v -deffnm test.npt -s test.npt.tpr -pin on -ntomp 16 -ntmpi 1 
-gpu_id 0 -pinoffset 0 -pinstride 2

12.3 ns/day

Presumably, the gain here is because “pintstride 2” caused the job to run on 
the “real” (1,2,3…15) cores, and not on virtual cores.  The automatic pinstride 
above used cores [0,16], [1,17], [2,18]…[7,23], half of which are virtual and 
so gave only 10.6ns/day.

** So there very little gain from the second GPU, and very little gain from 
multithreading. **

Using AVX_256 and not AVX2_256 with above command gave a small speed up 
(although using AVX instead of AVX2 for FFTW made things worse).

12.5 ns/day


To compare with an Intel Xeon Silver system:
2 x Xeon Silver 4116 (2.1GHz base clock, 12 cores each, no Hyperthreading), 
64GB memory
2 x Geforce 1080’s (as used in the above tests)

gcc 4.8.5
Gromacs 2016.4, with MPI, AVX_256 (compiled on an older GPU machine, and not by 
me).


2 MPI ranks, 12 threads each rank, 2 GPU’s

11.7 ns/day

4 MPI ranks, 6 threads each rank, 2 GPU’s

13.0 ns/day

6 MPI ranks, 4 threads each rank, 2 GPU’s

14.0 ns/day

To compare with the AMD machine, same number of cores

1 MPI rank, 16 threads, 1 GPU

11.2 ns/day

—
Gromacs 2018 rc1 (using gcc 4.8.5)
—

Using AVX_256

In ‘classic’ mode, not using gpu for PME

8 tMPI ranks, 4 threads per rank, 2 GPU’s

12.7 ns/day (modest speed up from 12.4 ns/day with 2016.4)

Now use a gpu for PME

gmx mdrun -v -deffnm test.npt -s test.npt.tpr -pme gpu -pin on

used 1 tMPI rank, 32 OpenMP threads, 1 GPU

14.9 ns/day

Forcing the program to use both GPU’s

gmx mdrun -v -deffnm test.npt -s test.npt.tpr -pme gpu -pin on -ntmpi 4 -npme 1 
-gputasks 0011 -nb gpu

18.5 ns/day

Now with AVX2_128

19.0 ns/day

Now force Dynamic Load Balancing

gmx mdrun -v -deffnm test.npt -s test.npt.tpr -pme gpu -pin on -ntmpi 4 -npme 1 
-gputasks 0011 -nb gpu -dlb yes

20.1 ns/day

Now use more (8) tMPI ranks

gmx mdrun -v -deffnm test.npt -s test.npt.tpr -pme gpu -pin on -ntmpi 8 -npme 1 
-gputasks  -nb gpu -dlb yes

20.7 ns/day

And finally, using 2018 (AVX2_128) with the above command line

20.9 ns/day

Here are the final lines from the log file

Dynamic load balancing report:
 DLB was permanently on during the run per user request.
 Average load imbalance: 7.7%.
 The balanceable part of the MD step is 51%, load imbalance is computed from 
this.
 Part of the total run time spent waiting due to load imbalance: 3.9%.
 Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 %
 Average PME mesh/force load: 1.275
 Part of the total run time spent waiting due to PP/PME imbalance: 9.4 %

NOTE: 9.4 % performance was lost because the PME ranks
  had more work to do than the PP ranks.
  You might want to increase the number of PME ranks
  or increase the cut-off and the grid spacing.


 R E A L   C Y C L E   A N D   T I M E   A C C O U N T I N G

On 7 MPI ranks doing PP, each using 4 OpenMP threads, and
on 1 MPI rank doing PME, using 4 OpenMP threads

 Computing:  Num   Num  CallWall time Giga-Cycles
 Ranks Threads  Count  (s) total sum%
-
 Domain decomp. 74500  13.721   1306.196   2.9
 DD comm. load  74500   0.366 34.875   0.1
 DD comm. bounds74