Re: [gmx-users] number of water molecule

[Justin Lemkul]

On 7/15/16 6:37 PM, Alexander Alexander wrote:

Hi,

Sure, but choosing oxygen atom also give the TOTAL number of O atom in the
whole BOX which is not what I want but I want the number of O atom which
are closer than 0.5 nm to the surface.
I also tried your another suggestion below(I hope right usage), but nothing
new, again total number of Oxygen in the box.

gmx select 'water O atom with z < 0.5 + Other_z_value' -f prd.gro -s
prd.tpr -n in.ndx -os size.xvg



That command isn't even syntactically valid and probably should have returned a 
fatal error; if you want help on setting up proper commands, you need to provide 
the exact command you used, copied and pasted.


Let's say your water O are named OW and the surface has a z-coordinate of 2.0 
nm.  Your command would look something like this:


gmx select -f prd.gro -s prd.tpr -n in.ndx -os size.xvg -select 'name OW and z < 
2.5'


I of course haven't tested that, but it should be something simple like that. 
See gmx help selections for additional help and examples.


-Justin


Even reducing the 0.5 to 0.5 also give the same number of Oxygen.

Cheers,
Alex


On Fri, Jul 15, 2016 at 10:26 PM, Justin Lemkul  wrote:




On 7/15/16 3:11 PM, Alexander Alexander wrote:


Thanks for your response.

The first layer of water molecules are in the within of 0.5 nm on top of
the solid surface(Other), and I try to  count the number of water
molecule(SOL) in this region as you suggested by gmx select, I used below
command but it gives me the total number of SOL molecules existing in the
whole box!

gmx select 'Close to Other' resname SOL and within 0.5 of group "Other"
-f
prd.gro -n input/index.ndx -os size.xvg



This will give you the total number of atoms in the selection.  Select by
the oxygen atom name to count the number of waters.

Even more simply, you can define a coordinate value for the selection
instead. If the surface is in the x-y plane, select any water O atom with z
< (0.5 + surface_z_value).

-Justin


Available static index groups:

.
.
Group 16 "Other" (4096 atoms)
.
.
Group 21 "SOL" (8688 atoms)
.
.

Would you please let me know where I am doing wrong?
Thanks,
Alex


On Fri, Jul 15, 2016 at 6:19 PM, Justin Lemkul  wrote:




On 7/15/16 10:19 AM, Alexander Alexander wrote:

Dear gromacs user,


Just suppose a single amino acid is adsorbing to a solid surface in
aqueous
solutions. I was wondering how I can find out the number of water
molecules(immediate to the surface) that are washed away by amino acid
in
such an adsorption?


Count the number of waters in the first solvation layer using, e.g. gmx

select.

-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

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

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

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

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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==

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] number of water molecule

[Alexander Alexander]

Hi,

Sure, but choosing oxygen atom also give the TOTAL number of O atom in the
whole BOX which is not what I want but I want the number of O atom which
are closer than 0.5 nm to the surface.
I also tried your another suggestion below(I hope right usage), but nothing
new, again total number of Oxygen in the box.

gmx select 'water O atom with z < 0.5 + Other_z_value' -f prd.gro -s
prd.tpr -n in.ndx -os size.xvg

Even reducing the 0.5 to 0.5 also give the same number of Oxygen.

Cheers,
Alex


On Fri, Jul 15, 2016 at 10:26 PM, Justin Lemkul  wrote:

>
>
> On 7/15/16 3:11 PM, Alexander Alexander wrote:
>
>> Thanks for your response.
>>
>> The first layer of water molecules are in the within of 0.5 nm on top of
>> the solid surface(Other), and I try to  count the number of water
>> molecule(SOL) in this region as you suggested by gmx select, I used below
>> command but it gives me the total number of SOL molecules existing in the
>> whole box!
>>
>> gmx select 'Close to Other' resname SOL and within 0.5 of group "Other"
>> -f
>> prd.gro -n input/index.ndx -os size.xvg
>>
>>
> This will give you the total number of atoms in the selection.  Select by
> the oxygen atom name to count the number of waters.
>
> Even more simply, you can define a coordinate value for the selection
> instead. If the surface is in the x-y plane, select any water O atom with z
> < (0.5 + surface_z_value).
>
> -Justin
>
>
> Available static index groups:
>> .
>> .
>> Group 16 "Other" (4096 atoms)
>> .
>> .
>> Group 21 "SOL" (8688 atoms)
>> .
>> .
>>
>> Would you please let me know where I am doing wrong?
>> Thanks,
>> Alex
>>
>>
>> On Fri, Jul 15, 2016 at 6:19 PM, Justin Lemkul  wrote:
>>
>>
>>>
>>> On 7/15/16 10:19 AM, Alexander Alexander wrote:
>>>
>>> Dear gromacs user,

 Just suppose a single amino acid is adsorbing to a solid surface in
 aqueous
 solutions. I was wondering how I can find out the number of water
 molecules(immediate to the surface) that are washed away by amino acid
 in
 such an adsorption?


 Count the number of waters in the first solvation layer using, e.g. gmx
>>> select.
>>>
>>> -Justin
>>>
>>> --
>>> ==
>>>
>>> Justin A. Lemkul, Ph.D.
>>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>>
>>> Department of Pharmaceutical Sciences
>>> School of Pharmacy
>>> Health Sciences Facility II, Room 629
>>> University of Maryland, Baltimore
>>> 20 Penn St.
>>> Baltimore, MD 21201
>>>
>>> jalem...@outerbanks.umaryland.edu | (410) 706-7441
>>> http://mackerell.umaryland.edu/~jalemkul
>>>
>>> ==
>>> --
>>> Gromacs Users mailing list
>>>
>>> * Please search the archive at
>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>>> posting!
>>>
>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>
>>> * For (un)subscribe requests visit
>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>>> send a mail to gmx-users-requ...@gromacs.org.
>>>
>>>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==
> --
> Gromacs Users mailing list
>
> * Please search the archive at
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> posting!
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Re: [gmx-users] Question: how fix protein without loops

[Ann Vakhrusheva]

I have complex of protein with DNA. The loops of this protein weren't 
determined, so I've built them. Now I want to minimize system with fixed 
protein and flexible loops, because there could be clashes. How can I do it?
Thank you for response. 

15.07.2016, 22:46, "Mark Abraham" :
> Hi,
>
> I'm not sure what you're trying to do, or why loops are a concern. Are you
> trying to generate position restraints for multiple molecules when
> assembled together?
>
> Mark
>
> On Fri, Jul 15, 2016 at 2:18 PM Ann Vakhrusheva 
> wrote:
>
>>  Hello!
>>  I would like to restrain my protein but without loops before minimization.
>>  Can anyone advise me something?
>>  I was trying to make ndx file. As I understand, in this format all
>>  residues starts from 1 and don't split into chains by numbers (I mean, for
>>  example, a chain B doesn't start from 1, but continues a chain A). My
>>  protein has 2 chains (+2 chains of DNA), so when I want to exclude loops in
>>  chain B, I get restraints starts not from beginning of chain B, but
>>  subsequent restraints starting in chain A.
>>  So I have the error, that my chain B doesn't correspond to the molecule
>>  and I have to move it to the right molecule (in my file
>>  'topol_Protein_chain_B.itp' the chain B starts from 1 as separate chain).
>>  Maybe I can change numbering in list of residues during make_ndx? Or maybe
>>  here's another way?
>>  Thank you for any help.
>>  --
>>  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
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> --
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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] number of water molecule

[Justin Lemkul]

On 7/15/16 3:11 PM, Alexander Alexander wrote:

Thanks for your response.

The first layer of water molecules are in the within of 0.5 nm on top of
the solid surface(Other), and I try to  count the number of water
molecule(SOL) in this region as you suggested by gmx select, I used below
command but it gives me the total number of SOL molecules existing in the
whole box!

gmx select 'Close to Other' resname SOL and within 0.5 of group "Other"  -f
prd.gro -n input/index.ndx -os size.xvg



This will give you the total number of atoms in the selection.  Select by the 
oxygen atom name to count the number of waters.


Even more simply, you can define a coordinate value for the selection instead. 
If the surface is in the x-y plane, select any water O atom with z < (0.5 + 
surface_z_value).


-Justin


Available static index groups:
.
.
Group 16 "Other" (4096 atoms)
.
.
Group 21 "SOL" (8688 atoms)
.
.

Would you please let me know where I am doing wrong?
Thanks,
Alex


On Fri, Jul 15, 2016 at 6:19 PM, Justin Lemkul  wrote:




On 7/15/16 10:19 AM, Alexander Alexander wrote:


Dear gromacs user,

Just suppose a single amino acid is adsorbing to a solid surface in
aqueous
solutions. I was wondering how I can find out the number of water
molecules(immediate to the surface) that are washed away by amino acid in
such an adsorption?



Count the number of waters in the first solvation layer using, e.g. gmx
select.

-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

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

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
--
Gromacs Users mailing list

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

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

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



--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

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

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
--
Gromacs Users mailing list

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Re: [gmx-users] question about step 3 of kalp-15 in dppc

[Justin Lemkul]

On 7/15/16 3:16 PM, roshanak starlight wrote:

1.in end of topology file , i have sol.it dosen't water?should i remove
that?



Again, topol_dppc.top has absolutely nothing to do with the topol.top that 
should be used for the protein-membrane system.  Ignore it once you have made 
the DPPC whole.  There is no water in the output configuration of InflateGRO, by 
design (the paper regarding this method explains why).  If you were to add 
water, you would have a half million atom system that would probably never 
minimize to anything sensible, as well as distorting your lipids.  Follow the 
tutorial exactly and do not confuse file names.



2.minim.mdp file is not exist for this step


Yes it does.  It is linked from the step 3 page.

http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/Files/minim.mdp

-Justin


On Jul 15, 2016 8:49 PM, "Justin Lemkul"  wrote:




On 7/15/16 12:15 PM, roshanak starlight wrote:


thank you for answers
after this command :grompp -f minim.mdp -c system_inflated.gro -p
topol.top
-o em.tpr
 i receive 2 note :

NOTE 1 [file topol.top, line 927]:
  System has non-zero total charge: 4.00
  Total charge should normally be an integer.

should i add ion ? with ion.itp  that is in gromos53a6_lipid.ff ?



No, because there is no water (nor should there be).



NOTE 2 [file minim.mdp]:
  The optimal PME mesh load for parallel simulations is below 0.5
  and for highly parallel simulations between 0.25 and 0.33,
  for higher performance, increase the cut-off and the PME grid spacing

.what is it's reason and what should i do ?.i used from same minim.mdp
file
that was for dppc( in tutorial.)
should i change cut off ?on what basis? i don't find it in manual



Use the files from the tutorial.  Performance during EM is not anything of
major importance.  There's no way to take a huge, inflated system in vacuo
and make it very efficient.

-Justin




On Fri, Jul 15, 2016 at 6:27 PM, Justin Lemkul  wrote:




On 7/15/16 9:55 AM, roshanak starlight wrote:

excuse me.i don't understand .  should i update [molecule]  just  in

*topol.top* ? how?
my topol.top file in [molecule] has not any number :

[ molecules ]
; Compound#mols
Protein 1


Add a line that says "DPPC 126"


You have to manually account for changes that are being made to the
coordinate file.  Please do some more basic tutorial material if the
content and organization of a topology is unfamiliar to you.

-Justin


in my topol_dppc.top is this:



[ molecules ]
; molecule name nr.
DPPC 128
SOL 3655



On Fri, Jul 15, 2016 at 6:12 PM, Justin Lemkul  wrote:




On 7/15/16 9:40 AM, roshanak starlight wrote:

should i do this ? :


 i should change dppc from  128lipid (topol_dppc.top) to 6300atom and


topol_dppc.top is only ever used for making molecules whole, and never

again.

system_inflated.gro from 6348 t0 6300 ?




Do not change the .gro file at all.


but why is number of system.gro 6538 ? (6400 + 138)




In system.gro (and the corresponding topol.top) you have 128 lipids

and
the peptide.  Then InflateGRO removes two of those lipids, so you have
to
account for this in topol.top, which now has the peptide and 126
lipids.

-Justin


50 is atom per lipid




On Fri, Jul 15, 2016 at 5:58 PM, Justin Lemkul 
wrote:



On 7/15/16 9:26 AM, roshanak starlight wrote:


hello . when i want to do energy minimizationin step 3 , with this

 command: grompp -f minim.mdp -c system_inflated.gro -p topol.top -o

em.tpr
 (or confout.gro replace em.tpr) i face with this error:

Fatal error:
number of coordinates in coordinate file (system_inflated.gro, 6438)
 does not match topology (topol.top, 138)

Earlier, right after this command : perl inflategro.pl system.gro 4
DPPC
14
system_inflated.gro 5 area.dat
, i updated [molecules] in topol-dppc.top from 128 to 126 dppc
(because
of
this sentence in terminal:
There are 2 lipids within cut-off range...
1 will be removed from the upper leaflet...
1 will be removed from the lower leaflet...)

where is the problem from ?


Apparently you didn't actually update the topology.



126 * 50 = 6300
6438 - 138 = 6300

So your topology specifies no lipids.

-Justin


On Fri, Jul 15, 2016 at 2:16 PM, Justin Lemkul 
wrote:





On 7/15/16 4:56 AM, roshanak starlight wrote:



excuse me i forgot that  write subject.


On Fri, Jul 15, 2016 at 1:20 PM, roshanak starlight <

starlight@gmail.com

wrote:




hello



i use kalp-15 in dppc tutorial  that there is in this website :

http://www.bevanlab.biochem.vt.edu

i have 2 question about step 3 :
1.after this command : genrestr -f KALP_newbox.gro -o
strong_posre.itp
-fc 10 10 10 which shoud i choose ?( i choose
1:protein .
is it right ?)


From the tutorial:




"The authors of the InflateGRO script recommend using a very

strong
position-restraining force on protein heavy atoms to ensure 

Re: [gmx-users] question about step 3 of kalp-15 in dppc

[roshanak starlight]

1.in end of topology file , i have sol.it dosen't water?should i remove
that?

2.minim.mdp file is not exist for this step
On Jul 15, 2016 8:49 PM, "Justin Lemkul"  wrote:

>
>
> On 7/15/16 12:15 PM, roshanak starlight wrote:
>
>> thank you for answers
>> after this command :grompp -f minim.mdp -c system_inflated.gro -p
>> topol.top
>> -o em.tpr
>>  i receive 2 note :
>>
>> NOTE 1 [file topol.top, line 927]:
>>   System has non-zero total charge: 4.00
>>   Total charge should normally be an integer.
>>
>> should i add ion ? with ion.itp  that is in gromos53a6_lipid.ff ?
>>
>>
> No, because there is no water (nor should there be).
>
>
>> NOTE 2 [file minim.mdp]:
>>   The optimal PME mesh load for parallel simulations is below 0.5
>>   and for highly parallel simulations between 0.25 and 0.33,
>>   for higher performance, increase the cut-off and the PME grid spacing
>>
>> .what is it's reason and what should i do ?.i used from same minim.mdp
>> file
>> that was for dppc( in tutorial.)
>> should i change cut off ?on what basis? i don't find it in manual
>>
>>
> Use the files from the tutorial.  Performance during EM is not anything of
> major importance.  There's no way to take a huge, inflated system in vacuo
> and make it very efficient.
>
> -Justin
>
>
>>
>> On Fri, Jul 15, 2016 at 6:27 PM, Justin Lemkul  wrote:
>>
>>
>>>
>>> On 7/15/16 9:55 AM, roshanak starlight wrote:
>>>
>>> excuse me.i don't understand .  should i update [molecule]  just  in
 *topol.top* ? how?
 my topol.top file in [molecule] has not any number :

 [ molecules ]
 ; Compound#mols
 Protein 1


 Add a line that says "DPPC 126"
>>>
>>> You have to manually account for changes that are being made to the
>>> coordinate file.  Please do some more basic tutorial material if the
>>> content and organization of a topology is unfamiliar to you.
>>>
>>> -Justin
>>>
>>>
>>> in my topol_dppc.top is this:
>>>

 [ molecules ]
 ; molecule name nr.
 DPPC 128
 SOL 3655



 On Fri, Jul 15, 2016 at 6:12 PM, Justin Lemkul  wrote:



> On 7/15/16 9:40 AM, roshanak starlight wrote:
>
> should i do this ? :
>
>>  i should change dppc from  128lipid (topol_dppc.top) to 6300atom and
>>
>>
>> topol_dppc.top is only ever used for making molecules whole, and never
> again.
>
> system_inflated.gro from 6348 t0 6300 ?
>
>
>>
>> Do not change the .gro file at all.
>
> but why is number of system.gro 6538 ? (6400 + 138)
>
>
>>
>> In system.gro (and the corresponding topol.top) you have 128 lipids
> and
> the peptide.  Then InflateGRO removes two of those lipids, so you have
> to
> account for this in topol.top, which now has the peptide and 126
> lipids.
>
> -Justin
>
>
> 50 is atom per lipid
>
>
>>
>> On Fri, Jul 15, 2016 at 5:58 PM, Justin Lemkul 
>> wrote:
>>
>>
>>
>> On 7/15/16 9:26 AM, roshanak starlight wrote:
>>>
>>> hello . when i want to do energy minimizationin step 3 , with this
>>>
>>>  command: grompp -f minim.mdp -c system_inflated.gro -p topol.top -o
 em.tpr
  (or confout.gro replace em.tpr) i face with this error:

 Fatal error:
 number of coordinates in coordinate file (system_inflated.gro, 6438)
  does not match topology (topol.top, 138)

 Earlier, right after this command : perl inflategro.pl system.gro 4
 DPPC
 14
 system_inflated.gro 5 area.dat
 , i updated [molecules] in topol-dppc.top from 128 to 126 dppc
 (because
 of
 this sentence in terminal:
 There are 2 lipids within cut-off range...
 1 will be removed from the upper leaflet...
 1 will be removed from the lower leaflet...)

 where is the problem from ?


 Apparently you didn't actually update the topology.


>>> 126 * 50 = 6300
>>> 6438 - 138 = 6300
>>>
>>> So your topology specifies no lipids.
>>>
>>> -Justin
>>>
>>>
>>> On Fri, Jul 15, 2016 at 2:16 PM, Justin Lemkul 
>>> wrote:
>>>
>>>
>>>

 On 7/15/16 4:56 AM, roshanak starlight wrote:

>
> excuse me i forgot that  write subject.
>
>
> On Fri, Jul 15, 2016 at 1:20 PM, roshanak starlight <
>> starlight@gmail.com
>>
>> wrote:
>>
>>
>>
>>> hello
>>>
>>>
>> i use kalp-15 in dppc tutorial  that there is in this website :
>>
>> http://www.bevanlab.biochem.vt.edu
>>> i have 2 question about step 3 :
>>> 1.after this command : genrestr -f 

Re: [gmx-users] number of water molecule

[Alexander Alexander]

Thanks for your response.

The first layer of water molecules are in the within of 0.5 nm on top of
the solid surface(Other), and I try to  count the number of water
molecule(SOL) in this region as you suggested by gmx select, I used below
command but it gives me the total number of SOL molecules existing in the
whole box!

gmx select 'Close to Other' resname SOL and within 0.5 of group "Other"  -f
prd.gro -n input/index.ndx -os size.xvg

Available static index groups:
.
.
Group 16 "Other" (4096 atoms)
.
.
Group 21 "SOL" (8688 atoms)
.
.

Would you please let me know where I am doing wrong?
Thanks,
Alex


On Fri, Jul 15, 2016 at 6:19 PM, Justin Lemkul  wrote:

>
>
> On 7/15/16 10:19 AM, Alexander Alexander wrote:
>
>> Dear gromacs user,
>>
>> Just suppose a single amino acid is adsorbing to a solid surface in
>> aqueous
>> solutions. I was wondering how I can find out the number of water
>> molecules(immediate to the surface) that are washed away by amino acid in
>> such an adsorption?
>>
>>
> Count the number of waters in the first solvation layer using, e.g. gmx
> select.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
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Re: [gmx-users] GPU Not Being Utilized during mdrun

[Vito Spadavecchio]

My apologies! I meant to include the logfile as well. You can view it here:

https://www.dropbox.com/s/8ddm226gpgs5kpr/md_0_2.log?dl=0

Thanks!

On Fri, Jul 15, 2016 at 2:45 AM, Justin Lemkul  wrote:

>
>
> On 7/14/16 10:35 PM, Vito Spadavecchio wrote:
>
>> Szilard
>>
>> You are correct; I misspoke. It appears that the GPU is doing *something*,
>> but I it would seem it is severely under performing (near the point where
>> its basically doing nothing).
>>
>> the entire log, not just parts, in particular we want to see the
>>
>>> header, perf table
>>>
>>>
>> xyz@Turing:~/Desktop/xyz_MD/APO_xyz$ gmx mdrun -deffnm md_0_2 -nb gpu
>>:-) GROMACS - gmx mdrun, VERSION 5.1.2 (-:
>>
>> GROMACS is written by:
>>  Emile Apol  Rossen Apostolov  Herman J.C. BerendsenPar
>> Bjelkmar
>>  Aldert van Buuren   Rudi van Drunen Anton Feenstra   Sebastian
>> Fritsch
>>   Gerrit Groenhof   Christoph Junghans   Anca HamuraruVincent
>> Hindriksen
>>  Dimitrios KarkoulisPeter KassonJiri Kraus  Carsten
>> Kutzner
>>
>> Per Larsson  Justin A. Lemkul   Magnus Lundborg   Pieter
>> Meulenhoff
>>Erik Marklund  Teemu Murtola   Szilard Pall   Sander Pronk
>>Roland Schulz Alexey Shvetsov Michael Shirts Alfons Sijbers
>>Peter TielemanTeemu Virolainen  Christian WennbergMaarten 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) 2001-2015, 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 mdrun, VERSION 5.1.2
>> Executable:   /usr/local/gromacs/bin/gmx
>> Data prefix:  /usr/local/gromacs
>> Command line:
>>   gmx mdrun -deffnm md_0_2 -nb gpu
>>
>>
>> Back Off! I just backed up md_0_2.log to ./#md_0_2.log.1#
>>
>> Running on 1 node with total 4 cores, 8 logical cores, 1 compatible GPU
>> Hardware detected:
>>   CPU info:
>> Vendor: GenuineIntel
>> Brand:  Intel(R) Core(TM) i7-6700K CPU @ 4.00GHz
>> SIMD instructions most likely to fit this hardware: AVX2_256
>> SIMD instructions selected at GROMACS compile time: AVX2_256
>>   GPU info:
>> Number of GPUs detected: 1
>> #0: NVIDIA GeForce GTX 1080, compute cap.: 6.1, ECC:  no, stat:
>> compatible
>>
>> Reading file md_0_2.tpr, VERSION 5.1.2 (single precision)
>> Changing nstlist from 10 to 40, rlist from 1 to 1.099
>>
>> Using 1 MPI thread
>> Using 8 OpenMP threads
>>
>> 1 compatible GPU is present, with ID 0
>> 1 GPU auto-selected for this run.
>> Mapping of GPU ID to the 1 PP rank in this node: 0
>>
>>
>> Back Off! I just backed up md_0_2.trr to ./#md_0_2.trr.1#
>>
>> Back Off! I just backed up md_0_2.xtc to ./#md_0_2.xtc.1#
>>
>> Back Off! I just backed up md_0_2.edr to ./#md_0_2.edr.1#
>> starting mdrun 'Protein in water'
>> 50 steps,   1000.0 ps.
>>
>>
>> - the output of nvidia-smi dmon executing *during* mdrun's execution
>>
>>
>> heres a snapshot:
>>
>> # gpu   pwr  tempsm   mem   enc   dec  mclk  pclk
>>
>>> # Idx W C % % % %   MHz   MHz
>>>  0   1175156 3 0 0  4513  1847
>>> 0   1155254 3 0 0  4513  1847
>>> 0   1175247 3 0 0  4513  1847
>>> 0   1015252 3 0 0  4513  1848
>>> 0   1195354 3 0 0  4513  1847
>>> 0   1155354 3 0 0  4513  1848
>>> 0   1065454 3 0 0  4513  1848
>>> 0   1185454 3 0 0  4513  1849
>>> 0945452 3 0 0  4513  1848
>>> 0   1105552 3 0 0  4513  1849
>>> 0   1165553 3 0 0  4513  1854
>>> 0   1265551 3 0 0  4513  1854
>>> 0   1195651 3 0 0  4513  1855
>>> 0   1165652 3 0 0  4513  1855
>>> 0   1165653 3 0 0  4513  1855
>>> 0   1205753 3 0 0  4513  1855
>>> 0   1135754 3 0 0  4513  1855
>>>
>>>
>> and here's the tail of the performance in .log
>>
>> Reading file md_0_2.tpr, VERSION 5.1.2 (single precision)
>>
>>> Changing nstlist from 10 to 40, rlist from 1 to 1.099
>>> Using 1 MPI thread
>>> Using 8 OpenMP threads
>>> 1 compatible GPU is present, with ID 0
>>> 1 GPU auto-selected for this run.
>>> Mapping of GPU ID to the 1 PP rank in this node: 0
>>>
>>> Back Off! I just backed up 

Re: [gmx-users] g_select, only 'one' water within z>=10 and z<=10.1

[Mark Abraham]

Hi,

If your criterion could satisfy more than one molecule but you for example
only want the first one, then you can likely create a second selection
where you filter out from the first selection the molecule or atom indices
that suit you. I assume that can be done in one call to gmx select, but the
details are an exercise for the reader :-P

Mark

On Fri, 15 Jul 2016 15:52 Faezeh Pousaneh  wrote:

> I undrestand my command is not correct for having one water. So it is my
> question how to change the command to have a single molecule?
>
>
>
> Best regards
>
>
> On Fri, Jul 15, 2016 at 3:35 PM, Justin Lemkul  wrote:
>
> >
> >
> > On 7/15/16 9:28 AM, Faezeh Pousaneh wrote:
> >
> >> Hi,
> >>
> >> I want to select only a 'single' water molecule at specific part of my
> >> simulation box.
> >> So I try:
> >>
> >> g_select-selrpos whole_mol_com
> >>
> >> and select
> >>
> >> resname SOL and z >= 10 and z <= 10.1
> >>
> >> But depending on time frame I get more than one molecules or sometimes
> no
> >> molecules. How can I fix it?
> >>
> >>
> > Why do you think that the selection criteria should always return exactly
> > one water?  I see no reason to think that based on what your syntax
> > specifies.
> >
> > -Justin
> >
> > --
> > ==
> >
> > Justin A. Lemkul, Ph.D.
> > Ruth L. Kirschstein NRSA Postdoctoral Fellow
> >
> > Department of Pharmaceutical Sciences
> > School of Pharmacy
> > Health Sciences Facility II, Room 629
> > University of Maryland, Baltimore
> > 20 Penn St.
> > Baltimore, MD 21201
> >
> > jalem...@outerbanks.umaryland.edu | (410) 706-7441
> > http://mackerell.umaryland.edu/~jalemkul
> >
> > ==
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
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> >
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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] question about step 3 of kalp-15 in dppc

[Justin Lemkul]

On 7/15/16 12:15 PM, roshanak starlight wrote:

thank you for answers
after this command :grompp -f minim.mdp -c system_inflated.gro -p topol.top
-o em.tpr
 i receive 2 note :

NOTE 1 [file topol.top, line 927]:
  System has non-zero total charge: 4.00
  Total charge should normally be an integer.

should i add ion ? with ion.itp  that is in gromos53a6_lipid.ff ?



No, because there is no water (nor should there be).



NOTE 2 [file minim.mdp]:
  The optimal PME mesh load for parallel simulations is below 0.5
  and for highly parallel simulations between 0.25 and 0.33,
  for higher performance, increase the cut-off and the PME grid spacing

.what is it's reason and what should i do ?.i used from same minim.mdp file
that was for dppc( in tutorial.)
should i change cut off ?on what basis? i don't find it in manual



Use the files from the tutorial.  Performance during EM is not anything of major 
importance.  There's no way to take a huge, inflated system in vacuo and make it 
very efficient.


-Justin




On Fri, Jul 15, 2016 at 6:27 PM, Justin Lemkul  wrote:




On 7/15/16 9:55 AM, roshanak starlight wrote:


excuse me.i don't understand .  should i update [molecule]  just  in
*topol.top* ? how?
my topol.top file in [molecule] has not any number :

[ molecules ]
; Compound#mols
Protein 1



Add a line that says "DPPC 126"

You have to manually account for changes that are being made to the
coordinate file.  Please do some more basic tutorial material if the
content and organization of a topology is unfamiliar to you.

-Justin


in my topol_dppc.top is this:


[ molecules ]
; molecule name nr.
DPPC 128
SOL 3655



On Fri, Jul 15, 2016 at 6:12 PM, Justin Lemkul  wrote:




On 7/15/16 9:40 AM, roshanak starlight wrote:

should i do this ? :

 i should change dppc from  128lipid (topol_dppc.top) to 6300atom and



topol_dppc.top is only ever used for making molecules whole, and never
again.

system_inflated.gro from 6348 t0 6300 ?





Do not change the .gro file at all.

but why is number of system.gro 6538 ? (6400 + 138)





In system.gro (and the corresponding topol.top) you have 128 lipids and
the peptide.  Then InflateGRO removes two of those lipids, so you have to
account for this in topol.top, which now has the peptide and 126 lipids.

-Justin


50 is atom per lipid




On Fri, Jul 15, 2016 at 5:58 PM, Justin Lemkul  wrote:




On 7/15/16 9:26 AM, roshanak starlight wrote:

hello . when i want to do energy minimizationin step 3 , with this


 command: grompp -f minim.mdp -c system_inflated.gro -p topol.top -o
em.tpr
 (or confout.gro replace em.tpr) i face with this error:

Fatal error:
number of coordinates in coordinate file (system_inflated.gro, 6438)
 does not match topology (topol.top, 138)

Earlier, right after this command : perl inflategro.pl system.gro 4
DPPC
14
system_inflated.gro 5 area.dat
, i updated [molecules] in topol-dppc.top from 128 to 126 dppc
(because
of
this sentence in terminal:
There are 2 lipids within cut-off range...
1 will be removed from the upper leaflet...
1 will be removed from the lower leaflet...)

where is the problem from ?


Apparently you didn't actually update the topology.



126 * 50 = 6300
6438 - 138 = 6300

So your topology specifies no lipids.

-Justin


On Fri, Jul 15, 2016 at 2:16 PM, Justin Lemkul 
wrote:





On 7/15/16 4:56 AM, roshanak starlight wrote:


excuse me i forgot that  write subject.



On Fri, Jul 15, 2016 at 1:20 PM, roshanak starlight <
starlight@gmail.com

wrote:




hello



i use kalp-15 in dppc tutorial  that there is in this website :


http://www.bevanlab.biochem.vt.edu
i have 2 question about step 3 :
1.after this command : genrestr -f KALP_newbox.gro -o
strong_posre.itp
-fc 10 10 10 which shoud i choose ?( i choose
1:protein .
is it right ?)


From the tutorial:





"The authors of the InflateGRO script recommend using a very strong
position-restraining force on protein heavy atoms to ensure that the
position of the protein does not change during EM."

So choose the protein heavy atoms (Protein-H).

2.where should i add a line "define = -DSTRONG_POSRES"  in minim.mdp
?
i

add it (define = -DSTRONG_POSRES ) to end of my file . is it true?



thank you



It doesn't matter.



-Justin


--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

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

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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posting!

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Re: [gmx-users] question about step 3 of kalp-15 in dppc

[roshanak starlight]

thank you for answers
after this command :grompp -f minim.mdp -c system_inflated.gro -p topol.top
-o em.tpr
 i receive 2 note :

NOTE 1 [file topol.top, line 927]:
  System has non-zero total charge: 4.00
  Total charge should normally be an integer.

should i add ion ? with ion.itp  that is in gromos53a6_lipid.ff ?


NOTE 2 [file minim.mdp]:
  The optimal PME mesh load for parallel simulations is below 0.5
  and for highly parallel simulations between 0.25 and 0.33,
  for higher performance, increase the cut-off and the PME grid spacing

.what is it's reason and what should i do ?.i used from same minim.mdp file
that was for dppc( in tutorial.)
should i change cut off ?on what basis? i don't find it in manual



On Fri, Jul 15, 2016 at 6:27 PM, Justin Lemkul  wrote:

>
>
> On 7/15/16 9:55 AM, roshanak starlight wrote:
>
>> excuse me.i don't understand .  should i update [molecule]  just  in
>> *topol.top* ? how?
>> my topol.top file in [molecule] has not any number :
>>
>> [ molecules ]
>> ; Compound#mols
>> Protein 1
>>
>>
> Add a line that says "DPPC 126"
>
> You have to manually account for changes that are being made to the
> coordinate file.  Please do some more basic tutorial material if the
> content and organization of a topology is unfamiliar to you.
>
> -Justin
>
>
> in my topol_dppc.top is this:
>>
>> [ molecules ]
>> ; molecule name nr.
>> DPPC 128
>> SOL 3655
>>
>>
>>
>> On Fri, Jul 15, 2016 at 6:12 PM, Justin Lemkul  wrote:
>>
>>
>>>
>>> On 7/15/16 9:40 AM, roshanak starlight wrote:
>>>
>>> should i do this ? :
  i should change dppc from  128lipid (topol_dppc.top) to 6300atom and


>>> topol_dppc.top is only ever used for making molecules whole, and never
>>> again.
>>>
>>> system_inflated.gro from 6348 t0 6300 ?
>>>


>>> Do not change the .gro file at all.
>>>
>>> but why is number of system.gro 6538 ? (6400 + 138)
>>>


>>> In system.gro (and the corresponding topol.top) you have 128 lipids and
>>> the peptide.  Then InflateGRO removes two of those lipids, so you have to
>>> account for this in topol.top, which now has the peptide and 126 lipids.
>>>
>>> -Justin
>>>
>>>
>>> 50 is atom per lipid
>>>


 On Fri, Jul 15, 2016 at 5:58 PM, Justin Lemkul  wrote:



> On 7/15/16 9:26 AM, roshanak starlight wrote:
>
> hello . when i want to do energy minimizationin step 3 , with this
>
>>  command: grompp -f minim.mdp -c system_inflated.gro -p topol.top -o
>> em.tpr
>>  (or confout.gro replace em.tpr) i face with this error:
>>
>> Fatal error:
>> number of coordinates in coordinate file (system_inflated.gro, 6438)
>>  does not match topology (topol.top, 138)
>>
>> Earlier, right after this command : perl inflategro.pl system.gro 4
>> DPPC
>> 14
>> system_inflated.gro 5 area.dat
>> , i updated [molecules] in topol-dppc.top from 128 to 126 dppc
>> (because
>> of
>> this sentence in terminal:
>> There are 2 lipids within cut-off range...
>> 1 will be removed from the upper leaflet...
>> 1 will be removed from the lower leaflet...)
>>
>> where is the problem from ?
>>
>>
>> Apparently you didn't actually update the topology.
>>
>
> 126 * 50 = 6300
> 6438 - 138 = 6300
>
> So your topology specifies no lipids.
>
> -Justin
>
>
> On Fri, Jul 15, 2016 at 2:16 PM, Justin Lemkul 
> wrote:
>
>
>>
>>
>> On 7/15/16 4:56 AM, roshanak starlight wrote:
>>>
>>> excuse me i forgot that  write subject.
>>>
>>>
 On Fri, Jul 15, 2016 at 1:20 PM, roshanak starlight <
 starlight@gmail.com

 wrote:


>
> hello
>

 i use kalp-15 in dppc tutorial  that there is in this website :

> http://www.bevanlab.biochem.vt.edu
> i have 2 question about step 3 :
> 1.after this command : genrestr -f KALP_newbox.gro -o
> strong_posre.itp
> -fc 10 10 10 which shoud i choose ?( i choose
> 1:protein .
> is it right ?)
>
>
> From the tutorial:
>


>>> "The authors of the InflateGRO script recommend using a very strong
>>> position-restraining force on protein heavy atoms to ensure that the
>>> position of the protein does not change during EM."
>>>
>>> So choose the protein heavy atoms (Protein-H).
>>>
>>> 2.where should i add a line "define = -DSTRONG_POSRES"  in minim.mdp
>>> ?
>>> i
>>>
>>> add it (define = -DSTRONG_POSRES ) to end of my file . is it true?
>>>

 thank you
>
>
> It doesn't matter.
>
>
 -Justin
>>>
>>> --
>>> 

[gmx-users] number of water molecule

[Alexander Alexander]

Dear gromacs user,

Just suppose a single amino acid is adsorbing to a solid surface in aqueous
solutions. I was wondering how I can find out the number of water
molecules(immediate to the surface) that are washed away by amino acid in
such an adsorption?

Thanks,
Alex
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[gmx-users] mdrun bailing out on mpi cluster

[Gregory, Andrew J.]

We have run into two issues using a high performance cluster with gromacs that 
we have not had when using our own machines.

1)  Jobs stop writing to file after 2-3 days
We have seen the "Simulation running but no output" 
http://www.gromacs.org/Documentation/Errors?highlight=stops+writing#Simulation_running_but_no_output
 on gromacs error but none of those options seem to apply-
-It writes out for two days at full speed so it is not the speed of the 
simulation
-These simulations on our machines never run into this so it's unlikely they 
are producing extraneous NAN and the cluster doesn't report high system cpu 
usage but actually lower usage when output stops
-.mdp file works on our other machine and there is full output for the first 
couple days
- the disk is not full, it is very large
- WE are using MPI but it works for the first couple days so it is unlikely LAM 
id not started
There is no warning or error output by this and the jobs will 
continue running for days in this state. We only know of this error because we 
were monitoring the cluster nodes running our jobs.

2)  Nodes stop communicating with the error:
[dnode28]  ud_channel.c:768  Fatal: UD timeout sending to dnode05 (after 600.16 
seconds)
(full back trace following it attached, all from the .out file we pipe the 
output into)
-The cluster IT department has looked into it and assured us it is not their 
error but a software error
-Their only suggestion was running on one 16 core node to avoid the 
communication errors but the slow down would be too much and with error 1 still 
occurring it wouldn't be worth it.

In our sbatch submission we use the command:

mpirun -np $NSLOTS gmx_mpi mdrun  -deffnm md >md.out

We are running gromacs 5.1.1, and openmpi 1.8.1

Is there anything else that could be stopping our jobs from writing out?
Could Gromacs cause a communication issue between nodes?
Is the node communication error connected to the writing out issue?

Thank you

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Re: [gmx-users] question about step 3 of kalp-15 in dppc

[Justin Lemkul]

On 7/15/16 9:55 AM, roshanak starlight wrote:

excuse me.i don't understand .  should i update [molecule]  just  in
*topol.top* ? how?
my topol.top file in [molecule] has not any number :

[ molecules ]
; Compound#mols
Protein 1



Add a line that says "DPPC 126"

You have to manually account for changes that are being made to the coordinate 
file.  Please do some more basic tutorial material if the content and 
organization of a topology is unfamiliar to you.


-Justin


in my topol_dppc.top is this:

[ molecules ]
; molecule name nr.
DPPC 128
SOL 3655



On Fri, Jul 15, 2016 at 6:12 PM, Justin Lemkul  wrote:




On 7/15/16 9:40 AM, roshanak starlight wrote:


should i do this ? :
 i should change dppc from  128lipid (topol_dppc.top) to 6300atom and



topol_dppc.top is only ever used for making molecules whole, and never
again.

system_inflated.gro from 6348 t0 6300 ?




Do not change the .gro file at all.

but why is number of system.gro 6538 ? (6400 + 138)




In system.gro (and the corresponding topol.top) you have 128 lipids and
the peptide.  Then InflateGRO removes two of those lipids, so you have to
account for this in topol.top, which now has the peptide and 126 lipids.

-Justin


50 is atom per lipid



On Fri, Jul 15, 2016 at 5:58 PM, Justin Lemkul  wrote:




On 7/15/16 9:26 AM, roshanak starlight wrote:

hello . when i want to do energy minimizationin step 3 , with this

 command: grompp -f minim.mdp -c system_inflated.gro -p topol.top -o
em.tpr
 (or confout.gro replace em.tpr) i face with this error:

Fatal error:
number of coordinates in coordinate file (system_inflated.gro, 6438)
 does not match topology (topol.top, 138)

Earlier, right after this command : perl inflategro.pl system.gro 4
DPPC
14
system_inflated.gro 5 area.dat
, i updated [molecules] in topol-dppc.top from 128 to 126 dppc (because
of
this sentence in terminal:
There are 2 lipids within cut-off range...
1 will be removed from the upper leaflet...
1 will be removed from the lower leaflet...)

where is the problem from ?


Apparently you didn't actually update the topology.


126 * 50 = 6300
6438 - 138 = 6300

So your topology specifies no lipids.

-Justin


On Fri, Jul 15, 2016 at 2:16 PM, Justin Lemkul  wrote:






On 7/15/16 4:56 AM, roshanak starlight wrote:

excuse me i forgot that  write subject.



On Fri, Jul 15, 2016 at 1:20 PM, roshanak starlight <
starlight@gmail.com

wrote:




hello


i use kalp-15 in dppc tutorial  that there is in this website :

http://www.bevanlab.biochem.vt.edu
i have 2 question about step 3 :
1.after this command : genrestr -f KALP_newbox.gro -o
strong_posre.itp
-fc 10 10 10 which shoud i choose ?( i choose
1:protein .
is it right ?)


From the tutorial:




"The authors of the InflateGRO script recommend using a very strong
position-restraining force on protein heavy atoms to ensure that the
position of the protein does not change during EM."

So choose the protein heavy atoms (Protein-H).

2.where should i add a line "define = -DSTRONG_POSRES"  in minim.mdp ?
i

add it (define = -DSTRONG_POSRES ) to end of my file . is it true?



thank you


It doesn't matter.




-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

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

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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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

Re: [gmx-users] question about step 3 of kalp-15 in dppc

[roshanak starlight]

excuse me.i don't understand .  should i update [molecule]  just  in
*topol.top* ? how?
my topol.top file in [molecule] has not any number :

[ molecules ]
; Compound#mols
Protein 1

in my topol_dppc.top is this:

[ molecules ]
; molecule name nr.
DPPC 128
SOL 3655



On Fri, Jul 15, 2016 at 6:12 PM, Justin Lemkul  wrote:

>
>
> On 7/15/16 9:40 AM, roshanak starlight wrote:
>
>> should i do this ? :
>>  i should change dppc from  128lipid (topol_dppc.top) to 6300atom and
>>
>
> topol_dppc.top is only ever used for making molecules whole, and never
> again.
>
> system_inflated.gro from 6348 t0 6300 ?
>>
>
> Do not change the .gro file at all.
>
> but why is number of system.gro 6538 ? (6400 + 138)
>>
>
> In system.gro (and the corresponding topol.top) you have 128 lipids and
> the peptide.  Then InflateGRO removes two of those lipids, so you have to
> account for this in topol.top, which now has the peptide and 126 lipids.
>
> -Justin
>
>
> 50 is atom per lipid
>>
>>
>> On Fri, Jul 15, 2016 at 5:58 PM, Justin Lemkul  wrote:
>>
>>
>>>
>>> On 7/15/16 9:26 AM, roshanak starlight wrote:
>>>
>>> hello . when i want to do energy minimizationin step 3 , with this
  command: grompp -f minim.mdp -c system_inflated.gro -p topol.top -o
 em.tpr
  (or confout.gro replace em.tpr) i face with this error:

 Fatal error:
 number of coordinates in coordinate file (system_inflated.gro, 6438)
  does not match topology (topol.top, 138)

 Earlier, right after this command : perl inflategro.pl system.gro 4
 DPPC
 14
 system_inflated.gro 5 area.dat
 , i updated [molecules] in topol-dppc.top from 128 to 126 dppc (because
 of
 this sentence in terminal:
 There are 2 lipids within cut-off range...
 1 will be removed from the upper leaflet...
 1 will be removed from the lower leaflet...)

 where is the problem from ?


 Apparently you didn't actually update the topology.
>>>
>>> 126 * 50 = 6300
>>> 6438 - 138 = 6300
>>>
>>> So your topology specifies no lipids.
>>>
>>> -Justin
>>>
>>>
>>> On Fri, Jul 15, 2016 at 2:16 PM, Justin Lemkul  wrote:
>>>



> On 7/15/16 4:56 AM, roshanak starlight wrote:
>
> excuse me i forgot that  write subject.
>
>>
>> On Fri, Jul 15, 2016 at 1:20 PM, roshanak starlight <
>> starlight@gmail.com
>>
>> wrote:
>>
>>>
>>>
>>> hello
>>
>> i use kalp-15 in dppc tutorial  that there is in this website :
>>> http://www.bevanlab.biochem.vt.edu
>>> i have 2 question about step 3 :
>>> 1.after this command : genrestr -f KALP_newbox.gro -o
>>> strong_posre.itp
>>> -fc 10 10 10 which shoud i choose ?( i choose
>>> 1:protein .
>>> is it right ?)
>>>
>>>
>>> From the tutorial:
>>
>
> "The authors of the InflateGRO script recommend using a very strong
> position-restraining force on protein heavy atoms to ensure that the
> position of the protein does not change during EM."
>
> So choose the protein heavy atoms (Protein-H).
>
> 2.where should i add a line "define = -DSTRONG_POSRES"  in minim.mdp ?
> i
>
> add it (define = -DSTRONG_POSRES ) to end of my file . is it true?
>>
>>> thank you
>>>
>>>
>>> It doesn't matter.
>>>
>>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
>
> --
>>> ==
>>>
>>> Justin A. Lemkul, Ph.D.
>>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>>
>>> Department of Pharmaceutical Sciences
>>> School of Pharmacy
>>> Health Sciences Facility II, Room 629
>>> University of Maryland, Baltimore
>>> 20 Penn St.
>>> Baltimore, MD 21201
>>>
>>> jalem...@outerbanks.umaryland.edu | (410) 706-7441
>>> http://mackerell.umaryland.edu/~jalemkul
>>>
>>> ==
>>> --
>>> Gromacs Users mailing list
>>>
>>> * Please search the 

Re: [gmx-users] g_select, only 'one' water within z>=10 and z<=10.1

[Faezeh Pousaneh]

I undrestand my command is not correct for having one water. So it is my
question how to change the command to have a single molecule?



Best regards


On Fri, Jul 15, 2016 at 3:35 PM, Justin Lemkul  wrote:

>
>
> On 7/15/16 9:28 AM, Faezeh Pousaneh wrote:
>
>> Hi,
>>
>> I want to select only a 'single' water molecule at specific part of my
>> simulation box.
>> So I try:
>>
>> g_select-selrpos whole_mol_com
>>
>> and select
>>
>> resname SOL and z >= 10 and z <= 10.1
>>
>> But depending on time frame I get more than one molecules or sometimes no
>> molecules. How can I fix it?
>>
>>
> Why do you think that the selection criteria should always return exactly
> one water?  I see no reason to think that based on what your syntax
> specifies.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
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Re: [gmx-users] question about step 3 of kalp-15 in dppc

[Justin Lemkul]

On 7/15/16 9:40 AM, roshanak starlight wrote:

should i do this ? :
 i should change dppc from  128lipid (topol_dppc.top) to 6300atom and


topol_dppc.top is only ever used for making molecules whole, and never again.


system_inflated.gro from 6348 t0 6300 ?


Do not change the .gro file at all.


but why is number of system.gro 6538 ? (6400 + 138)


In system.gro (and the corresponding topol.top) you have 128 lipids and the 
peptide.  Then InflateGRO removes two of those lipids, so you have to account 
for this in topol.top, which now has the peptide and 126 lipids.


-Justin


50 is atom per lipid


On Fri, Jul 15, 2016 at 5:58 PM, Justin Lemkul  wrote:




On 7/15/16 9:26 AM, roshanak starlight wrote:


hello . when i want to do energy minimizationin step 3 , with this
 command: grompp -f minim.mdp -c system_inflated.gro -p topol.top -o
em.tpr
 (or confout.gro replace em.tpr) i face with this error:

Fatal error:
number of coordinates in coordinate file (system_inflated.gro, 6438)
 does not match topology (topol.top, 138)

Earlier, right after this command : perl inflategro.pl system.gro 4 DPPC
14
system_inflated.gro 5 area.dat
, i updated [molecules] in topol-dppc.top from 128 to 126 dppc (because of
this sentence in terminal:
There are 2 lipids within cut-off range...
1 will be removed from the upper leaflet...
1 will be removed from the lower leaflet...)

where is the problem from ?



Apparently you didn't actually update the topology.

126 * 50 = 6300
6438 - 138 = 6300

So your topology specifies no lipids.

-Justin


On Fri, Jul 15, 2016 at 2:16 PM, Justin Lemkul  wrote:





On 7/15/16 4:56 AM, roshanak starlight wrote:

excuse me i forgot that  write subject.


On Fri, Jul 15, 2016 at 1:20 PM, roshanak starlight <
starlight@gmail.com

wrote:




hello


i use kalp-15 in dppc tutorial  that there is in this website :
http://www.bevanlab.biochem.vt.edu
i have 2 question about step 3 :
1.after this command : genrestr -f KALP_newbox.gro -o strong_posre.itp
-fc 10 10 10 which shoud i choose ?( i choose
1:protein .
is it right ?)



From the tutorial:


"The authors of the InflateGRO script recommend using a very strong
position-restraining force on protein heavy atoms to ensure that the
position of the protein does not change during EM."

So choose the protein heavy atoms (Protein-H).

2.where should i add a line "define = -DSTRONG_POSRES"  in minim.mdp ? i


add it (define = -DSTRONG_POSRES ) to end of my file . is it true?

thank you


It doesn't matter.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

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

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
--
Gromacs Users mailing list

* Please search the archive at
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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

==
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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

==
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Re: [gmx-users] Supercomputing facility

[sun]

Thank you very much.

Sent from my iPhone

> On 15-Jul-2016, at 7:20 am, André Farias de Moura  wrote:
> 
> Hi Suniba,
> 
> assuming that # 5 is GROMACS, then # 2-4 are the required dependencies to
> have GROMACS running, # 8 is parallel and # 9 is Y.
> 
> all the other questions refer to the allocation size and the best answer is
> usually bigger is better. In practice, the largest possible size of the
> allocation depends either on how much money you can afford (if it is paid
> for) or on the limits imposed by your system admin (if it is not paid for).
> 
> I hope it helps
> 
> Andre
> 
> 
>> On Thu, Jul 14, 2016 at 3:19 PM, sun  wrote:
>> 
>> Hello Users and experts
>> 
>> We are going to create an account for a supercomputing facility. They have
>> asked to fill a form to initiate the process. I am confused about certain
>> terms as I belong to biology background. Please help me with these specific
>> terms and what should I fill in to get good performance and enhnaced speed
>> of Gromacs for mdruns. We will be 3 student using this facility.
>> 
>> Estimated computing usage requirement:-
>> 1) CPU cores:
>> 2)Special requirements
>> 3)Compilers
>> 4)Libraries
>> 5)Applications/Tools
>> 6)Scratch area (in GB)
>> 7)Home area (in GB)
>> 8)Nature of code (parallel/series)
>> 9)Application code readiness(Y/N)
>> 
>> Please help me fill this form so that I can apply as early as possible.
>> With Regards
>> Suniba
>> 
>> Sent from my iPhone
>> --
>> 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.
> 
> 
> 
> -- 
> _
> 
> Prof. Dr. André Farias de Moura
> Department of Chemistry
> Federal University of São Carlos
> São Carlos - Brazil
> phone: +55-16-3351-8090
> -- 
> Gromacs Users mailing list
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> * Please search the archive at 
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Re: [gmx-users] question about step 3 of kalp-15 in dppc

[roshanak starlight]

should i do this ? :
 i should change dppc from  128lipid (topol_dppc.top) to 6300atom and
system_inflated.gro from 6348 t0 6300 ?
but why is number of system.gro 6538 ? (6400 + 138)
50 is atom per lipid


On Fri, Jul 15, 2016 at 5:58 PM, Justin Lemkul  wrote:

>
>
> On 7/15/16 9:26 AM, roshanak starlight wrote:
>
>> hello . when i want to do energy minimizationin step 3 , with this
>>  command: grompp -f minim.mdp -c system_inflated.gro -p topol.top -o
>> em.tpr
>>  (or confout.gro replace em.tpr) i face with this error:
>>
>> Fatal error:
>> number of coordinates in coordinate file (system_inflated.gro, 6438)
>>  does not match topology (topol.top, 138)
>>
>> Earlier, right after this command : perl inflategro.pl system.gro 4 DPPC
>> 14
>> system_inflated.gro 5 area.dat
>> , i updated [molecules] in topol-dppc.top from 128 to 126 dppc (because of
>> this sentence in terminal:
>> There are 2 lipids within cut-off range...
>> 1 will be removed from the upper leaflet...
>> 1 will be removed from the lower leaflet...)
>>
>> where is the problem from ?
>>
>>
> Apparently you didn't actually update the topology.
>
> 126 * 50 = 6300
> 6438 - 138 = 6300
>
> So your topology specifies no lipids.
>
> -Justin
>
>
> On Fri, Jul 15, 2016 at 2:16 PM, Justin Lemkul  wrote:
>>
>>
>>>
>>> On 7/15/16 4:56 AM, roshanak starlight wrote:
>>>
>>> excuse me i forgot that  write subject.

 On Fri, Jul 15, 2016 at 1:20 PM, roshanak starlight <
 starlight@gmail.com

 wrote:
>
>
 hello

> i use kalp-15 in dppc tutorial  that there is in this website :
> http://www.bevanlab.biochem.vt.edu
> i have 2 question about step 3 :
> 1.after this command : genrestr -f KALP_newbox.gro -o strong_posre.itp
> -fc 10 10 10 which shoud i choose ?( i choose
> 1:protein .
> is it right ?)
>
>
 From the tutorial:
>>>
>>> "The authors of the InflateGRO script recommend using a very strong
>>> position-restraining force on protein heavy atoms to ensure that the
>>> position of the protein does not change during EM."
>>>
>>> So choose the protein heavy atoms (Protein-H).
>>>
>>> 2.where should i add a line "define = -DSTRONG_POSRES"  in minim.mdp ? i
>>>
 add it (define = -DSTRONG_POSRES ) to end of my file . is it true?
> thank you
>
>
> It doesn't matter.
>>>
>>> -Justin
>>>
>>> --
>>> ==
>>>
>>> Justin A. Lemkul, Ph.D.
>>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>>
>>> Department of Pharmaceutical Sciences
>>> School of Pharmacy
>>> Health Sciences Facility II, Room 629
>>> University of Maryland, Baltimore
>>> 20 Penn St.
>>> Baltimore, MD 21201
>>>
>>> jalem...@outerbanks.umaryland.edu | (410) 706-7441
>>> http://mackerell.umaryland.edu/~jalemkul
>>>
>>> ==
>>> --
>>> Gromacs Users mailing list
>>>
>>> * Please search the archive at
>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>>> posting!
>>>
>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>
>>> * For (un)subscribe requests visit
>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>>> send a mail to gmx-users-requ...@gromacs.org.
>>>
>>>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
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Re: [gmx-users] question about step 3 of kalp-15 in dppc

[Justin Lemkul]

On 7/15/16 9:26 AM, roshanak starlight wrote:

hello . when i want to do energy minimizationin step 3 , with this
 command: grompp -f minim.mdp -c system_inflated.gro -p topol.top -o em.tpr
 (or confout.gro replace em.tpr) i face with this error:

Fatal error:
number of coordinates in coordinate file (system_inflated.gro, 6438)
 does not match topology (topol.top, 138)

Earlier, right after this command : perl inflategro.pl system.gro 4 DPPC 14
system_inflated.gro 5 area.dat
, i updated [molecules] in topol-dppc.top from 128 to 126 dppc (because of
this sentence in terminal:
There are 2 lipids within cut-off range...
1 will be removed from the upper leaflet...
1 will be removed from the lower leaflet...)

where is the problem from ?



Apparently you didn't actually update the topology.

126 * 50 = 6300
6438 - 138 = 6300

So your topology specifies no lipids.

-Justin


On Fri, Jul 15, 2016 at 2:16 PM, Justin Lemkul  wrote:




On 7/15/16 4:56 AM, roshanak starlight wrote:


excuse me i forgot that  write subject.

On Fri, Jul 15, 2016 at 1:20 PM, roshanak starlight <
starlight@gmail.com


wrote:



hello

i use kalp-15 in dppc tutorial  that there is in this website :
http://www.bevanlab.biochem.vt.edu
i have 2 question about step 3 :
1.after this command : genrestr -f KALP_newbox.gro -o strong_posre.itp
-fc 10 10 10 which shoud i choose ?( i choose 1:protein .
is it right ?)




From the tutorial:

"The authors of the InflateGRO script recommend using a very strong
position-restraining force on protein heavy atoms to ensure that the
position of the protein does not change during EM."

So choose the protein heavy atoms (Protein-H).

2.where should i add a line "define = -DSTRONG_POSRES"  in minim.mdp ? i

add it (define = -DSTRONG_POSRES ) to end of my file . is it true?
thank you



It doesn't matter.

-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

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

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

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

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http://mackerell.umaryland.edu/~jalemkul

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Re: [gmx-users] g_select, only 'one' water within z>=10 and z<=10.1

[Justin Lemkul]

On 7/15/16 9:28 AM, Faezeh Pousaneh wrote:

Hi,

I want to select only a 'single' water molecule at specific part of my
simulation box.
So I try:

g_select-selrpos whole_mol_com

and select

resname SOL and z >= 10 and z <= 10.1

But depending on time frame I get more than one molecules or sometimes no
molecules. How can I fix it?



Why do you think that the selection criteria should always return exactly one 
water?  I see no reason to think that based on what your syntax specifies.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

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

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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[gmx-users] g_select, only 'one' water within z>=10 and z<=10.1

[Faezeh Pousaneh]

Hi,

I want to select only a 'single' water molecule at specific part of my
simulation box.
So I try:

g_select-selrpos whole_mol_com

and select

resname SOL and z >= 10 and z <= 10.1

But depending on time frame I get more than one molecules or sometimes no
molecules. How can I fix it?

Thank you!
Best regards
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Re: [gmx-users] question about step 3 of kalp-15 in dppc

[roshanak starlight]

hello . when i want to do energy minimizationin step 3 , with this
 command: grompp -f minim.mdp -c system_inflated.gro -p topol.top -o em.tpr
 (or confout.gro replace em.tpr) i face with this error:

Fatal error:
number of coordinates in coordinate file (system_inflated.gro, 6438)
 does not match topology (topol.top, 138)

Earlier, right after this command : perl inflategro.pl system.gro 4 DPPC 14
system_inflated.gro 5 area.dat
, i updated [molecules] in topol-dppc.top from 128 to 126 dppc (because of
this sentence in terminal:
There are 2 lipids within cut-off range...
1 will be removed from the upper leaflet...
1 will be removed from the lower leaflet...)

where is the problem from ?

On Fri, Jul 15, 2016 at 2:16 PM, Justin Lemkul  wrote:

>
>
> On 7/15/16 4:56 AM, roshanak starlight wrote:
>
>> excuse me i forgot that  write subject.
>>
>> On Fri, Jul 15, 2016 at 1:20 PM, roshanak starlight <
>> starlight@gmail.com
>>
>>> wrote:
>>>
>>
>> hello
>>> i use kalp-15 in dppc tutorial  that there is in this website :
>>> http://www.bevanlab.biochem.vt.edu
>>> i have 2 question about step 3 :
>>> 1.after this command : genrestr -f KALP_newbox.gro -o strong_posre.itp
>>> -fc 10 10 10 which shoud i choose ?( i choose 1:protein .
>>> is it right ?)
>>>
>>
> From the tutorial:
>
> "The authors of the InflateGRO script recommend using a very strong
> position-restraining force on protein heavy atoms to ensure that the
> position of the protein does not change during EM."
>
> So choose the protein heavy atoms (Protein-H).
>
> 2.where should i add a line "define = -DSTRONG_POSRES"  in minim.mdp ? i
>>> add it (define = -DSTRONG_POSRES ) to end of my file . is it true?
>>> thank you
>>>
>>>
> It doesn't matter.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==
> --
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Re: [gmx-users] Question: how fix protein without loops

[Mark Abraham]

Hi,

I'm not sure what you're trying to do, or why loops are a concern. Are you
trying to generate position restraints for multiple molecules when
assembled together?

Mark

On Fri, Jul 15, 2016 at 2:18 PM Ann Vakhrusheva 
wrote:

> Hello!
> I would like to restrain my protein but without loops before minimization.
> Can anyone advise me something?
> I was trying to make ndx file. As I understand, in this format all
> residues starts from 1 and don't split into chains by numbers (I mean, for
> example, a chain B doesn't start from 1, but continues a chain A). My
> protein has 2 chains (+2 chains of DNA), so when I want to exclude loops in
> chain B, I get restraints starts not from beginning of chain B, but
> subsequent restraints starting in chain A.
> So I have the error, that my chain B doesn't correspond to the molecule
> and I have to move it to the right molecule (in my file
> 'topol_Protein_chain_B.itp' the chain B starts from 1 as separate chain).
> Maybe I can change numbering in list of residues during make_ndx? Or maybe
> here's another way?
> Thank you for any help.
> --
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[gmx-users] Question: how fix protein without loops

[Ann Vakhrusheva]

Hello! 
I would like to restrain my protein but without loops before minimization. Can 
anyone advise me something?
I was trying to make ndx file. As I understand, in this format all residues 
starts from 1 and don't split into chains by numbers (I mean, for example, a 
chain B doesn't start from 1, but continues a chain A). My protein has 2 chains 
(+2 chains of DNA), so when I want to exclude loops in chain B, I get 
restraints starts not from beginning of chain B, but subsequent restraints 
starting in chain A. 
So I have the error, that my chain B doesn't correspond to the molecule and I 
have to move it to the right molecule (in my file 'topol_Protein_chain_B.itp' 
the chain B starts from 1 as separate chain). 
Maybe I can change numbering in list of residues during make_ndx? Or maybe 
here's another way?
Thank you for any help.
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Re: [gmx-users] periodic boundary conditions

[Mark Abraham]

Hi,

On Wed, Jul 13, 2016 at 5:50 PM Mohsen Ramezanpour <
ramezanpour.moh...@gmail.com> wrote:

> Hi Mark,
>
> Thanks for your reply.
>
> The 6 around 1 setup is also periodic.
>
> I understand this. However, we can argue the same for 6-1 system as well.
> Right?
>

Sure, but that's not the point. The point revolves around whether the
properties of your simulation system suitably resemble those found in the
real world. If that's a single cylinder of lipid suspended in some other
milieu, then neither of the periodic systems is particularly representative.


> If one edge of this hexagonal deforms, the other side also deforms and in
> fact we are applying a symmetry to our system.
>

Yeah, but only you know whether you are trying to study a
pseudo-crystalline form, or something else? The former is easier, because
you can accept periodicity as part of a model, but the conclusions may not
be applicable outside of that modelling regime...

Mark

The question is: which system is big enough (or suitable) to include this
> effect?
>
> What I am interested in is the structural properties of these systems and
> lipid-lipid interactions.
>
> Cheers
>
> On Wed, Jul 13, 2016 at 2:23 AM, Mark Abraham 
> wrote:
>
> > Hi,
> >
> > These are different systems. Your 6-around-1 setup (whether itself
> > hexagonally periodic or not) has degrees of freedom that the single
> > hexagonal cell cannot access. In the latter case, if a wall on one edge
> of
> > the cell deforms, then the corresponding wall on the far side of the cell
> > has the matching deformation. However the 6-around-1 can e.g. deform each
> > wall of the central hexagonal cell independently. Whether any of these
> make
> > a "correct" model depends what you're trying to model.
> >
> > Mark
> >
> > On Wed, Jul 13, 2016 at 2:41 AM Mohsen Ramezanpour <
> > ramezanpour.moh...@gmail.com> wrote:
> >
> > > Dear gromacs-users,
> > >
> > > Doing simulations on lipid HII phase, I came to a question which I
> could
> > > not get happy with my answer. I appreciate your opinion in advance:
> > >
> > > Imagine you have a cylinder made of lipids with waters only inside the
> > > cylinder, which is long enough and can be run for enough time so that
> > there
> > > is no problem from sampling aspect. A hexagonal pbc has been also
> applied
> > > to this cylinder properly.
> > >
> > > In the other system, you have 7 cyinders with 1 central and 6 on the
> > > corners of hexagon. The only main difference with the case above will
> be
> > a
> > > larger unit cell and less symmetry of the system.
> > >
> > > Do you expect the results of these two simulations be different, if you
> > are
> > > interested in structural properties?
> > >
> > > In other words: does pbc exactly treats the central cylinder as if
> there
> > > was 6 extra cylinders around the it? Can it reproduce the correct
> > > environment the central cylinder feels around?
> > >
> > > Cheer,
> > > Mohsen
> > >
> > >
> > >
> > > --
> > > *Rewards work better than punishment ...*
> > > --
> > > 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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> > >
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> >
>
>
>
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Re: [gmx-users] truncating LJ potentials

[Mark Abraham]

Hi,

On Thu, Jul 14, 2016 at 11:37 PM Irem Altan  wrote:

> Hi,
>
> I decided to test this for a system of sodium and chloride ions (based on
> http://www.gromacs.org/@api/deki/files/94/=gromacs_nb.pdf ):
>
> Guyana Rwanda Oman Macau Angola Cameroon Senegal
> 8
> 1NA  Na1   0.131   0.116   0.051
> 2NA  Na2   0.137   0.111   0.047
> 3NA  Na3   0.124   0.110   0.053
> 4NA  Na4   0.131   0.115   0.051
> 5CL  Cl5   0.009   0.109   0.051
> 6CL  Cl6   0.000   0.111   0.049
> 7CL  Cl7   0.010   0.112   0.061
> 8CL  Cl8   0.009   0.109   0.052
>0.5   0.5   0.5
>
> I’m trying to do a test energy minimization but grompp gives me the
> following errors:
>
> ERROR 1 [file minim.mdp]:
>   With Verlet lists only cut-off and PME LJ interactions are supported
>
>
> ERROR 2 [file minim.mdp]:
>   With Verlet lists only cut-off, reaction-field, PME and Ewald
>   electrostatics are supported
>
>
> NOTE 1 [file minim.mdp]:
>   With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
>   that with the Verlet scheme, nstlist has no effect on the accuracy of
>   your simulation.
>
> Setting the LD random seed to 2498183954
>
> ---
> Program gmx grompp, VERSION 5.1.2
> Source code file:
> /Users/irem/Downloads/gromacs-5.1.2/src/gromacs/gmxpreprocess/topio.c,
> line: 755
>
> Fatal error:
> Syntax error - File topol.top, line 21
> Last line read:
> '[ atomtypes ]'
> Invalid order for directive atomtypes
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> ---
>
> Does this mean I can’t use Verlet neighbor lists with custom non-bonded
> interaction potentials?


Correct (as I said in my first sentence in this thread).


> And does that in turn mean that I can’t use GPUs in my simulations?
>

Correct. We have been working on this, but it isn't ready yet.


> Also, could you help me figure out how to fix the error in the topology
> file? The contents of the relevant files are as listed below.
>

The error is on point - you haven't honored the required order for
directives (see examples and text in chapter 5), e.g. because [ defaults ]
must be first.

Mark

Best,
> Irem
>
> ———
>
> minim.mdp:
> —
>
> ; minim.mdp - used as input into grompp to generate em.tpr
> integrator  = steep ; Algorithm (steep = steepest descent
> minimization)
> emtol   = 1000.0; Stop minimization when the maximum force
> < 1000.0 kJ/mol/nm
> emstep  = 0.01  ; Energy step size
> nsteps  = 5 ; Maximum number of (minimization) steps
> to perform
>
> ; Parameters describing how to find the neighbors of each atom and how to
> calculate the interactions
> nstlist = 1 ; Frequency to update the neighbor
> list and long range forces
> cutoff-scheme   = Verlet
> ns_type = grid  ; Method to determine neighbor
> list (simple, grid)
> rcoulomb= 1.0   ; Short-range electrostatic cut-off
> rvdw= 1.0   ; Short-range Van der Waals cut-off
> pbc = xyz   ; Periodic Boundary Conditions
> (yes/no)
>
> ; custom potentials
> vdw-type = user
> coulombtype = user
> energygrps = sodium chloride
> energygrp_table = sodium sodium chloride chloride
>
> topol.top:
> -
>
> [ atomtypes ]
> Na  Na   22.991   A  1.0e-03  1.0e-06
> Cl  Cl   35.45   -1   A  2.0e-03  9.0e-06
>
> [ nonbond_params ]
> Na  Cl   1   2.22213706E-03  3.43076954E-06
>
> [ moleculetype ]
> ; Namenrexcl
> Ion_chain_A 3
>
> [ atoms ]
> ;   nr   type  resnr residue  atom   cgnr charge   mass
> typeBchargeB  massB
> ; residue   1 NA  rtp NA   q +1.0
>  1 Na  1 NA Na  1  1  22.99   ;
> qtot 1
> ; residue   2 NA  rtp NA   q +1.0
>  2 Na  2 NA Na  2  1  22.99   ;
> qtot 2
> ; residue   3 NA  rtp NA   q +1.0
>  3 Na  3 NA Na  3  1  22.99   ;
> qtot 3
> ; residue   4 NA  rtp NA   q +1.0
>  4 Na  4 NA Na  4  1  22.99   ;
> qtot 4
> ; residue   5 CL  rtp CL   q -1.0
>  5 Cl  5 CL Cl  5 -1  35.45   ;
> qtot 3
>
> ; Include Position restraint file
> #ifdef POSRES
> #include "posre.itp"
> #endif
>
> [ system ]
> ; Name
> Protein
>
> [ molecules ]
> ; Compound#mols
> Ion_chain_A 1
>
> index.ndx:
> -
>
> [ sodium ]
> 1 2 3 4
> [ chloride ]
> 5 6 7 8
>
>
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>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> 

Re: [gmx-users] question about step 3 of kalp-15 in dppc

[Justin Lemkul]

On 7/15/16 4:56 AM, roshanak starlight wrote:

excuse me i forgot that  write subject.

On Fri, Jul 15, 2016 at 1:20 PM, roshanak starlight 

Re: [gmx-users] GPU Not Being Utilized during mdrun

[Justin Lemkul]

On 7/14/16 10:35 PM, Vito Spadavecchio wrote:

Szilard

You are correct; I misspoke. It appears that the GPU is doing *something*,
but I it would seem it is severely under performing (near the point where
its basically doing nothing).

the entire log, not just parts, in particular we want to see the

header, perf table



xyz@Turing:~/Desktop/xyz_MD/APO_xyz$ gmx mdrun -deffnm md_0_2 -nb gpu
   :-) GROMACS - gmx mdrun, VERSION 5.1.2 (-:

GROMACS is written by:
 Emile Apol  Rossen Apostolov  Herman J.C. BerendsenPar
Bjelkmar
 Aldert van Buuren   Rudi van Drunen Anton Feenstra   Sebastian Fritsch
  Gerrit Groenhof   Christoph Junghans   Anca HamuraruVincent Hindriksen
 Dimitrios KarkoulisPeter KassonJiri Kraus  Carsten Kutzner

Per Larsson  Justin A. Lemkul   Magnus Lundborg   Pieter Meulenhoff
   Erik Marklund  Teemu Murtola   Szilard Pall   Sander Pronk
   Roland Schulz Alexey Shvetsov Michael Shirts Alfons Sijbers
   Peter TielemanTeemu Virolainen  Christian WennbergMaarten 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) 2001-2015, 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 mdrun, VERSION 5.1.2
Executable:   /usr/local/gromacs/bin/gmx
Data prefix:  /usr/local/gromacs
Command line:
  gmx mdrun -deffnm md_0_2 -nb gpu


Back Off! I just backed up md_0_2.log to ./#md_0_2.log.1#

Running on 1 node with total 4 cores, 8 logical cores, 1 compatible GPU
Hardware detected:
  CPU info:
Vendor: GenuineIntel
Brand:  Intel(R) Core(TM) i7-6700K CPU @ 4.00GHz
SIMD instructions most likely to fit this hardware: AVX2_256
SIMD instructions selected at GROMACS compile time: AVX2_256
  GPU info:
Number of GPUs detected: 1
#0: NVIDIA GeForce GTX 1080, compute cap.: 6.1, ECC:  no, stat:
compatible

Reading file md_0_2.tpr, VERSION 5.1.2 (single precision)
Changing nstlist from 10 to 40, rlist from 1 to 1.099

Using 1 MPI thread
Using 8 OpenMP threads

1 compatible GPU is present, with ID 0
1 GPU auto-selected for this run.
Mapping of GPU ID to the 1 PP rank in this node: 0


Back Off! I just backed up md_0_2.trr to ./#md_0_2.trr.1#

Back Off! I just backed up md_0_2.xtc to ./#md_0_2.xtc.1#

Back Off! I just backed up md_0_2.edr to ./#md_0_2.edr.1#
starting mdrun 'Protein in water'
50 steps,   1000.0 ps.


- the output of nvidia-smi dmon executing *during* mdrun's execution


heres a snapshot:

# gpu   pwr  tempsm   mem   enc   dec  mclk  pclk

# Idx W C % % % %   MHz   MHz
 0   1175156 3 0 0  4513  1847
0   1155254 3 0 0  4513  1847
0   1175247 3 0 0  4513  1847
0   1015252 3 0 0  4513  1848
0   1195354 3 0 0  4513  1847
0   1155354 3 0 0  4513  1848
0   1065454 3 0 0  4513  1848
0   1185454 3 0 0  4513  1849
0945452 3 0 0  4513  1848
0   1105552 3 0 0  4513  1849
0   1165553 3 0 0  4513  1854
0   1265551 3 0 0  4513  1854
0   1195651 3 0 0  4513  1855
0   1165652 3 0 0  4513  1855
0   1165653 3 0 0  4513  1855
0   1205753 3 0 0  4513  1855
0   1135754 3 0 0  4513  1855



and here's the tail of the performance in .log

Reading file md_0_2.tpr, VERSION 5.1.2 (single precision)

Changing nstlist from 10 to 40, rlist from 1 to 1.099
Using 1 MPI thread
Using 8 OpenMP threads
1 compatible GPU is present, with ID 0
1 GPU auto-selected for this run.
Mapping of GPU ID to the 1 PP rank in this node: 0

Back Off! I just backed up md_0_2.trr to ./#md_0_2.trr.1#
Back Off! I just backed up md_0_2.xtc to ./#md_0_2.xtc.1#
Back Off! I just backed up md_0_2.edr to ./#md_0_2.edr.1#
starting mdrun 'Protein in water'
50 steps,   1000.0 ps.
Writing final coordinates.
Back Off! I just backed up md_0_2.gro to ./#md_0_2.gro.1#
   Core t (s)   Wall t (s)(%)
   Time:25285.344 3409.337  741.6
 56:49
 (ns/day)(hour/ns)
Performance:   25.3420.947
gcq#11: "She's Not Bad, She's Just Genetically Mean" (Captain Beefheart)



As we can see, 

[gmx-users] Pulling: Fix the position of a molecule

[Daniele Veclani]

Dear Gromacs Users

I'm simulating a system of two molecule (A,B unbound). Right now, I am trying
to generate the configurations and then make Umbrella Sampling Simulations.

I have this problem: While I generate the configurations I observed that the
molecule A comes out of the box and makes the calculation fail.

I've used the position restraint generating posre.itp file for molecule A, but
analyzing the trajectories I see that the molecule A moves and comes out of
the box.

How can I fix the problem? I attached my files for the topology, and
poste.itp .mdp

I use Gromacs 5.0.4.

Best regards.
D.V.
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Re: [gmx-users] question about step 3 of kalp-15 in dppc

[roshanak starlight]

excuse me i forgot that  write subject.

On Fri, Jul 15, 2016 at 1:20 PM, roshanak starlight  wrote:

> hello
> i use kalp-15 in dppc tutorial  that there is in this website :
> http://www.bevanlab.biochem.vt.edu
> i have 2 question about step 3 :
> 1.after this command : genrestr -f KALP_newbox.gro -o strong_posre.itp
> -fc 10 10 10 which shoud i choose ?( i choose 1:protein .
> is it right ?)
> 2.where should i add a line "define = -DSTRONG_POSRES"  in minim.mdp ? i
> add it (define = -DSTRONG_POSRES ) to end of my file . is it true?
> thank you
>
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[gmx-users] (no subject)

[roshanak starlight]

hello
i use kalp-15 in dppc tutorial  that there is in this website :
http://www.bevanlab.biochem.vt.edu
i have 2 question about step 3 :
1.after this command : genrestr -f KALP_newbox.gro -o strong_posre.itp -fc
10 10 10 which shoud i choose ?( i choose 1:protein . is it
right ?)
2.where should i add a line "define = -DSTRONG_POSRES"  in minim.mdp ? i
add it (define = -DSTRONG_POSRES ) to end of my file . is it true?
thank you
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Re: [gmx-users] Problems with TI on GPUs

[Yannic Alber]

Hi all,

sorry for the long delay, but we were quite busy lately.

Concerning our problem:
1. We tested the GPUs intensively and even with a 100% usage on both cards
and both CPUs the temperature isn't a problem.
2. We also tried to run the simulation with both cards explicitly, but all
tests failed.
3. We get the same errors regardless of the gromacs version (we tried 5.1.0
and 5.1.2)

The following link leads to a log file with the typical error:
https://depot.tu-dortmund.de/ahd67

Best regards,

Yannic

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