[gmx-users] Incorrectly added water molecule by genbox.

[Dawid das]

Hi,

I have a following issue. Genbox seems to add a water molecule inside small
protein cavity and it does not belong there. Can I manually remove it from
*gro file? What with the numbering of residues in this situation? The
problem is that this water molecule can't be settled during minimization
and it spoils everything.

Dawid
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Re: [gmx-users] Incorrectly added water molecule by genbox.

[Mark Abraham]

On Thu, Jul 3, 2014 at 9:17 AM, Dawid das  wrote:

> Hi,
>
> I have a following issue. Genbox seems to add a water molecule inside small
> protein cavity and it does not belong there. Can I manually remove it from
> *gro file?


Yes, but you need to make a matching change to the [molecules] section of
any matching .top file.


> What with the numbering of residues in this situation?


Immaterial. The only important thing in such cases is that there is a
change; the values or the delta-value is not noticed.

Mark


> The
> problem is that this water molecule can't be settled during minimization
> and it spoils everything.
>
> Dawid
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Re: [gmx-users] regarding error during EM

[Mark Abraham]

http://www.gromacs.org/Documentation/Errors


On Thu, Jul 3, 2014 at 6:24 AM, dhaval patel 
wrote:

> *Fatal error:*
> 25 particles communicated to PME node 2 are more than 2/3 times the cut-off
> out of the domain decomposition cell of their charge group in dimension x.
> This usually means that your system is not well equilibrated.
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[gmx-users] use -maxwarn option

[Urszula Uciechowska]

Dear gromacs users,

I am trying to run coarse-grained simulations, by running grompp I got a
note to use the -maxwarn option. How to use it? I could not find any
informations in GROMACS manual/tutorials.

Best regards
Urszula Uciechowska


-
Ta wiadomość została wysłana z serwera Uniwersytetu Gdańskiego
http://www.ug.edu.pl/

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Re: [gmx-users] error in grompp command

[RINU KHATTRI]

hello everyone
my grompp related   problem atomtype CA not found has been solved now i am
using 56a3 force field for protein ligand complex with popc but srill i
didnt get em.tpr a new error



Excluding 3 bonded neighbours molecule type 'POPC'
Excluding 2 bonded neighbours molecule type 'SOL'

---
Program grompp, VERSION 4.5.5
Source code file: /build/buildd/gromacs-4.5.5/src/kernel/grompp.c, line: 523

Fatal error:
number of coordinates in coordinate file (popc128.gro, 14036)
 does not match topology (topolpopc.top, 17459)
kindly help



On Wed, Jul 2, 2014 at 3:51 PM, Justin Lemkul  wrote:

>
>
> On 7/2/14, 6:07 AM, RINU KHATTRI wrote:
>
>> hello gromacs users
>>   i used 43a1 force field(Gromacs 4.5.7) in the atomtype.atp file in the
>> place of CA CA2+ is present in ffnonbonded.itp file CA and CA2+ both are
>> present according to tutorial i have been followed  all the step
>> still em.tpr not formed
>> atomtype CA not found
>>
>>
> "CA" is the gmx.ff nomenclature for the calcium type, so that suggests
> you're mixing and matching force fields (note that gmx.ff has been removed
> from the latest Gromacs version, since it should not be used).  Without
> explicit detail of your topology (i.e. post your files so they can be
> downloaded), there's very little that can be done to suggest where things
> have gone wrong.  I strongly suspect you've mixed and matched force fields
> somewhere, which is easy to do when dealing with complex systems.  Pick a
> force field, stick to it exactly.
>
> -Justin
>
>
>
>> On Wed, Jul 2, 2014 at 3:19 PM, ERASTOVA V. <
>> valentina.erast...@durham.ac.uk
>>
>>> wrote:
>>>
>>
>>  Hi Rinu,
>>>
>>> See what forcefield files you include in your topology, then go to the
>>> force field folders and check if those indeed have that atom types.
>>> You must indeed be missing the CA type. Likely, you just forgot to
>>> include
>>> some topology file.
>>>
>>> V
>>>
>>>
>>>
>>>
>>> On 2 Jul 2014, at 10:23, gromacs.org_gmx-users-request@
>>> maillist.sys.kth.se
>>>  wrote:
>>>
>>>
>>> --
>>>
>>> Message: 2
>>> Date: Wed, 2 Jul 2014 12:26:07 +0530
>>> From: RINU KHATTRI >> nickname.mi...@gmail.com>>
>>> To: gmx-us...@gromacs.org
>>> Subject: [gmx-users] error in grompp command
>>> Message-ID:
>>> >> >> mail.gmail.com
>>>

>  Content-Type: text/plain; charset=UTF-8
>>>
>>> hello gromacs
>>> i an working on protein ligand complex with lipid membrane (popc)
>>>
>>> grompp -f minim.mdp -c popc128.gro -p topol_popc.top -o em.tpr -maxwarn
>>> -1
>>>
>>> after this fatal error atomtypes CA not found
>>> and only md.oonly mdout is formed
>>> kindly help
>>>
>>>
>>> --
>>>
>>> --
>>> Gromacs Users mailing list
>>>
>>> * Please search the archive at
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>>> posting!
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>>> send a mail to gmx-users-requ...@gromacs.org.
>>>
>>>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> 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] use -maxwarn option

[Carsten Kutzner]

Hi,

just add it to the grompp command line, e.g.:

grompp -maxwarn 1 …

See grompp -h

Best,
  Carsten


On 03 Jul 2014, at 10:51, Urszula Uciechowska 
 wrote:

> 
> Dear gromacs users,
> 
> I am trying to run coarse-grained simulations, by running grompp I got a
> note to use the -maxwarn option. How to use it? I could not find any
> informations in GROMACS manual/tutorials.
> 
> Best regards
> Urszula Uciechowska
> 
> 
> -
> Ta wiadomość została wysłana z serwera Uniwersytetu Gdańskiego
> http://www.ug.edu.pl/
> 
> -- 
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> * Please search the archive at 
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> mail to gmx-users-requ...@gromacs.org.


--
Dr. Carsten Kutzner
Max Planck Institute for Biophysical Chemistry
Theoretical and Computational Biophysics
Am Fassberg 11, 37077 Goettingen, Germany
Tel. +49-551-2012313, Fax: +49-551-2012302
http://www.mpibpc.mpg.de/grubmueller/kutzner
http://www.mpibpc.mpg.de/grubmueller/sppexa

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Re: [gmx-users] use -maxwarn option

[Christian Wagner]

Dear Urszula Uciechowska, 


The information is posted here: 
http://manual.gromacs.org/programs/gmx-grompp.html 


" The -maxwarn option can be used to override warnings printed by gmx grompp 
that otherwise halt output. In some cases, warnings are harmless, but usually 
they are not. The user is advised to carefully interpret the output messages 
before attempting to bypass them with this option." 


Best wishes, 
Chris Wagner 
- Original Message -


From: "Urszula Uciechowska"  
To: gmx-us...@gromacs.org 
Sent: Thursday, July 3, 2014 4:51:29 PM 
Subject: [gmx-users] use -maxwarn option 


Dear gromacs users, 

I am trying to run coarse-grained simulations, by running grompp I got a 
note to use the -maxwarn option. How to use it? I could not find any 
informations in GROMACS manual/tutorials. 

Best regards 
Urszula Uciechowska 


- 
Ta wiadomość została wysłana z serwera Uniwersytetu Gdańskiego 
http://www.ug.edu.pl/ 

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Re: [gmx-users] Regarding lipid topology

[Dr. Vitaly Chaban]

Unlikely anything on top of dihedrals.

Try to use VMD to see if the lipid molecules look as you like.

I do not have to handle lipid isomer simulations, fortunately.


Dr. Vitaly V. Chaban


On Wed, Jul 2, 2014 at 7:33 PM, Venkat Reddy  wrote:
> Thank you Sir. Sorry for the late reply. So, the changes like dihedral
> angle for C8-C9=C10-C11 should be 180 instead of 0 in trans state. Are
> there any other adjustments I should make to build the trans lipid isomer
> topology from cis? Thank you for your valuable time and concern.
>
>
> On Mon, Jun 16, 2014 at 4:44 PM, Dr. Vitaly Chaban 
> wrote:
>
>> Of course, no. You need to adjust your topology (force field?) to
>> distinguish between cis- and trans- states.
>>
>>
>> Dr. Vitaly V. Chaban
>>
>>
>> On Mon, Jun 16, 2014 at 11:03 AM, Venkat Reddy 
>> wrote:
>> > Dear all,
>> > I want to simulate a membrane protein system. My membrane is composed of
>> > DOPC (cis isomer) and DEPC (trans isomer). I have downloaded DOPC
>> topology
>> > from lipidbook website. Since DOPC and DEPC are isomers, can I use the
>> > topology of DOPC for DEPC also?
>> >
>> > Thank and regards
>> >
>> > Venkat Reddy Chirasani
>> > PhD student
>> > Laboratory of Computational Biophysics
>> > Department of Biotechnology
>> > IIT Madras
>> > Chennai
>> > INDIA-600036
>> > --
>> > 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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>>
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>> posting!
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>> send a mail to gmx-users-requ...@gromacs.org.
>>
>
>
>
> --
> With Best Wishes
> Venkat Reddy Chirasani
> PhD student
> Laboratory of Computational Biophysics
> Department of Biotechnology
> IIT Madras
> Chennai
> INDIA-600036
> --
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Re: [gmx-users] g_polystat sorts the eigen vector

[Chandan Choudhury]

Dear gmx users,

In my previous mail, please read eigen vectors as eigen values.
The command used was
$echo 3 | g_polystat -s md0-1.tpr -f traj.xtc -b 50 -n poly.ndx -o 3.xvg
I am using v4.6.3.

Sorry for the misleading information.

Thanks


On Thu, Jul 3, 2014 at 2:35 AM, Chandan Choudhury  wrote:

> Dear gmx users,
>
> The g_polystat tool arranges the Rg eigen vectors in the descending order.
> We cannot see how a particular eigen vector (one along the X-axis) varies
> with time. We can obviously comment the section of the g_polystat code to
> avoid the sorting. Is there a reason, why do we sort the eigen vectors? It
> would be helpful if someone help me to understand this.
>
> Thanks
> Chandan
>
> --
> Chandan Kumar Choudhury
> National Chemical Laboratory, Pune
> India
>
>


-- 

--
Chandan Kumar Choudhury
National Chemical Laboratory, Pune
India
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Re: [gmx-users] Graphene topology file

[Dr. Vitaly Chaban]

Graphene topology is like for tube, so

C  C
C ... C ... C
C  C  C   C

to the N2T file and you are done.


Dr. Vitaly V. Chaban


On Wed, Jul 2, 2014 at 5:29 PM, Justin Lemkul  wrote:
>
>
> On 7/2/14, 9:56 AM, #SUKRITI GUPTA# wrote:
>>
>> Dear all,
>>
>>
>> I want to simulate graphite in water, for which i am trying to create a
>> topology file for graphite. As its .rtp file cannot be written correctly, i
>> tried to use g_x2top command following the steps given in following
>> tutorial.
>>
>> http://chembytes.wikidot.com/grocnt
>>
>>
>> But I think this tutorial is quite old and hence suitable for older
>> version of gromacs as it still uses FF.dat file. Moreover if i am trying to
>> make a new forcefield directory with name graphite_oplsaa containing the
>> modified files like .n2t,.rtp and .itp, its giving me an error that "Could
>> not find force field 'graphite_oplsaa' in current directory, install tree or
>> GMXDATA path". When I try to add this forcefield in original path ie.
>> user/share/gromacs/top, it does not allow me to do that as i am not the
>> administrator. Can anyone please let me know how to create the topology
>> file. I require 3 graphene sheets with pbc. I have created the .pdb file
>> using nanobuilder in vmd.
>>
>
> The tutorial is indeed outdated but the logic is fairly sound.  You don't
> have to modify anything in $GMXLIB (system-wide); you can just create an
> .n2t file in the working directory and it will override the one at the force
> field level.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> 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] Regarding lipid topology

[Venkat Reddy]

Dear Sir,
I have measured the dihedral angles for both cis and trans conformations
using VMD. As expected, for cis isomer the dihedral angle was 0 and for
trans = 180. Expect this, I couldn't find any change between these isomers.


On Thu, Jul 3, 2014 at 3:07 PM, Dr. Vitaly Chaban 
wrote:

> Unlikely anything on top of dihedrals.
>
> Try to use VMD to see if the lipid molecules look as you like.
>
> I do not have to handle lipid isomer simulations, fortunately.
>
>
> Dr. Vitaly V. Chaban
>
>
> On Wed, Jul 2, 2014 at 7:33 PM, Venkat Reddy  wrote:
> > Thank you Sir. Sorry for the late reply. So, the changes like dihedral
> > angle for C8-C9=C10-C11 should be 180 instead of 0 in trans state. Are
> > there any other adjustments I should make to build the trans lipid isomer
> > topology from cis? Thank you for your valuable time and concern.
> >
> >
> > On Mon, Jun 16, 2014 at 4:44 PM, Dr. Vitaly Chaban 
> > wrote:
> >
> >> Of course, no. You need to adjust your topology (force field?) to
> >> distinguish between cis- and trans- states.
> >>
> >>
> >> Dr. Vitaly V. Chaban
> >>
> >>
> >> On Mon, Jun 16, 2014 at 11:03 AM, Venkat Reddy 
> >> wrote:
> >> > Dear all,
> >> > I want to simulate a membrane protein system. My membrane is composed
> of
> >> > DOPC (cis isomer) and DEPC (trans isomer). I have downloaded DOPC
> >> topology
> >> > from lipidbook website. Since DOPC and DEPC are isomers, can I use the
> >> > topology of DOPC for DEPC also?
> >> >
> >> > Thank and regards
> >> >
> >> > Venkat Reddy Chirasani
> >> > PhD student
> >> > Laboratory of Computational Biophysics
> >> > Department of Biotechnology
> >> > IIT Madras
> >> > Chennai
> >> > INDIA-600036
> >> > --
> >> > Gromacs Users mailing list
> >> >
> >> > * Please search the archive at
> >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> >> posting!
> >> >
> >> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >> >
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> >> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> >> send a mail to gmx-users-requ...@gromacs.org.
> >> --
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> >> send a mail to gmx-users-requ...@gromacs.org.
> >>
> >
> >
> >
> > --
> > With Best Wishes
> > Venkat Reddy Chirasani
> > PhD student
> > Laboratory of Computational Biophysics
> > Department of Biotechnology
> > IIT Madras
> > Chennai
> > INDIA-600036
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
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> posting!
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> send a mail to gmx-users-requ...@gromacs.org.
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>



-- 
With Best Wishes
Venkat Reddy Chirasani
PhD student
Laboratory of Computational Biophysics
Department of Biotechnology
IIT Madras
Chennai
INDIA-600036
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Re: [gmx-users] error in grompp command

[RINU KHATTRI]

hello gromacs users now have been removed this error after changing the
number of SOL in topol_popc.top file (counted from popc128.gro)
after that i hav used -maxwarn 1 command

result is

Generated 813 of the 2346 non-bonded parameter combinations
Excluding 3 bonded neighbours molecule type 'POPC'
Excluding 2 bonded neighbours molecule type 'SOL'
Warning: atom name 6657 in topolpopc.top and popc128.gro does not match (OW
- OW1)
Warning: atom name 6658 in topolpopc.top and popc128.gro does not match
(HW1 - HW2)
Warning: atom name 6659 in topolpopc.top and popc128.gro does not match
(HW2 - HW3)
Warning: atom name 6660 in topolpopc.top and popc128.gro does not match (OW
- OW1)
Warning: atom name 6661 in topolpopc.top and popc128.gro does not match
(HW1 - HW2)
Warning: atom name 6662 in topolpopc.top and popc128.gro does not match
(HW2 - HW3)
Warning: atom name 6663 in topolpopc.top and popc128.gro does not match (OW
- OW1)
Warning: atom name 6664 in topolpopc.top and popc128.gro does not match
(HW1 - HW2)
Warning: atom name 6665 in topolpopc.top and popc128.gro does not match
(HW2 - HW3)
Warning: atom name  in topolpopc.top and popc128.gro does not match (OW
- OW1)
Warning: atom name 6667 in topolpopc.top and popc128.gro does not match
(HW1 - HW2)
Warning: atom name 6668 in topolpopc.top and popc128.gro does not match
(HW2 - HW3)
Warning: atom name 6669 in topolpopc.top and popc128.gro does not match (OW
- OW1)
Warning: atom name 6670 in topolpopc.top and popc128.gro does not match
(HW1 - HW2)
Warning: atom name 6671 in topolpopc.top and popc128.gro does not match
(HW2 - HW3)
Warning: atom name 6672 in topolpopc.top and popc128.gro does not match (OW
- OW1)
Warning: atom name 6673 in topolpopc.top and popc128.gro does not match
(HW1 - HW2)
Warning: atom name 6674 in topolpopc.top and popc128.gro does not match
(HW2 - HW3)
Warning: atom name 6675 in topolpopc.top and popc128.gro does not match (OW
- OW1)
Warning: atom name 6676 in topolpopc.top and popc128.gro does not match
(HW1 - HW2)
(more than 20 non-matching atom names)

WARNING 1 [file topolpopc.top, line 26]:
  7380 non-matching atom names
  atom names from topolpopc.top will be used
  atom names from popc128.gro will be ignored


Analysing residue names:
There are:   128  Other residues
There are:  2460  Water residues
Analysing residues not classified as Protein/DNA/RNA/Water and splitting
into groups...
Number of degrees of freedom in T-Coupling group rest is 34725.00
Largest charge group radii for Van der Waals: 0.216, 0.216 nm
Largest charge group radii for Coulomb:   0.216, 0.216 nm
Calculating fourier grid dimensions for X Y Z
Using a fourier grid of 54x54x60, spacing 0.116 0.114 0.115
Estimate for the relative computational load of the PME mesh part: 0.36
This run will generate roughly 164 Mb of data

There was 1 warning

how tom resolve these problems
em.tpr is formed but rest of the files are not formed
help


On Thu, Jul 3, 2014 at 2:23 PM, RINU KHATTRI 
wrote:

> hello everyone
> my grompp related   problem atomtype CA not found has been solved now i am
> using 56a3 force field for protein ligand complex with popc but srill i
> didnt get em.tpr a new error
>
>
>
> Excluding 3 bonded neighbours molecule type 'POPC'
> Excluding 2 bonded neighbours molecule type 'SOL'
>
> ---
> Program grompp, VERSION 4.5.5
> Source code file: /build/buildd/gromacs-4.5.5/src/kernel/grompp.c, line:
> 523
>
> Fatal error:
> number of coordinates in coordinate file (popc128.gro, 14036)
>  does not match topology (topolpopc.top, 17459)
> kindly help
>
>
>
> On Wed, Jul 2, 2014 at 3:51 PM, Justin Lemkul  wrote:
>
>>
>>
>> On 7/2/14, 6:07 AM, RINU KHATTRI wrote:
>>
>>> hello gromacs users
>>>   i used 43a1 force field(Gromacs 4.5.7) in the atomtype.atp file in the
>>> place of CA CA2+ is present in ffnonbonded.itp file CA and CA2+ both are
>>> present according to tutorial i have been followed  all the step
>>> still em.tpr not formed
>>> atomtype CA not found
>>>
>>>
>> "CA" is the gmx.ff nomenclature for the calcium type, so that suggests
>> you're mixing and matching force fields (note that gmx.ff has been removed
>> from the latest Gromacs version, since it should not be used).  Without
>> explicit detail of your topology (i.e. post your files so they can be
>> downloaded), there's very little that can be done to suggest where things
>> have gone wrong.  I strongly suspect you've mixed and matched force fields
>> somewhere, which is easy to do when dealing with complex systems.  Pick a
>> force field, stick to it exactly.
>>
>> -Justin
>>
>>
>>
>>> On Wed, Jul 2, 2014 at 3:19 PM, ERASTOVA V. <
>>> valentina.erast...@durham.ac.uk
>>>
 wrote:

>>>
>>>  Hi Rinu,

 See what forcefield files you include in your topology, then go to the
 force field folders and check if those indeed have that atom types.
 You must indeed be missing the CA type. Likely, you just forg

Re: [gmx-users] error in grompp command

[Chandan Choudhury]

Dear Rinu,
You need to arrange the gro file is the same sequence as in the top file
(or the vice-versa).

Chandan


On Thu, Jul 3, 2014 at 3:57 PM, RINU KHATTRI 
wrote:

> hello gromacs users now have been removed this error after changing the
> number of SOL in topol_popc.top file (counted from popc128.gro)
> after that i hav used -maxwarn 1 command
>
> result is
>
> Generated 813 of the 2346 non-bonded parameter combinations
> Excluding 3 bonded neighbours molecule type 'POPC'
> Excluding 2 bonded neighbours molecule type 'SOL'
> Warning: atom name 6657 in topolpopc.top and popc128.gro does not match
> (OW
> - OW1)
> Warning: atom name 6658 in topolpopc.top and popc128.gro does not match
> (HW1 - HW2)
> Warning: atom name 6659 in topolpopc.top and popc128.gro does not match
> (HW2 - HW3)
> Warning: atom name 6660 in topolpopc.top and popc128.gro does not match
> (OW
> - OW1)
> Warning: atom name 6661 in topolpopc.top and popc128.gro does not match
> (HW1 - HW2)
> Warning: atom name 6662 in topolpopc.top and popc128.gro does not match
> (HW2 - HW3)
> Warning: atom name 6663 in topolpopc.top and popc128.gro does not match
> (OW
> - OW1)
> Warning: atom name 6664 in topolpopc.top and popc128.gro does not match
> (HW1 - HW2)
> Warning: atom name 6665 in topolpopc.top and popc128.gro does not match
> (HW2 - HW3)
> Warning: atom name  in topolpopc.top and popc128.gro does not match
> (OW
> - OW1)
> Warning: atom name 6667 in topolpopc.top and popc128.gro does not match
> (HW1 - HW2)
> Warning: atom name 6668 in topolpopc.top and popc128.gro does not match
> (HW2 - HW3)
> Warning: atom name 6669 in topolpopc.top and popc128.gro does not match
> (OW
> - OW1)
> Warning: atom name 6670 in topolpopc.top and popc128.gro does not match
> (HW1 - HW2)
> Warning: atom name 6671 in topolpopc.top and popc128.gro does not match
> (HW2 - HW3)
> Warning: atom name 6672 in topolpopc.top and popc128.gro does not match (OW
> - OW1)
> Warning: atom name 6673 in topolpopc.top and popc128.gro does not match
> (HW1 - HW2)
> Warning: atom name 6674 in topolpopc.top and popc128.gro does not match
> (HW2 - HW3)
> Warning: atom name 6675 in topolpopc.top and popc128.gro does not match (OW
> - OW1)
> Warning: atom name 6676 in topolpopc.top and popc128.gro does not match
> (HW1 - HW2)
> (more than 20 non-matching atom names)
>
> WARNING 1 [file topolpopc.top, line 26]:
>   7380 non-matching atom names
>   atom names from topolpopc.top will be used
>   atom names from popc128.gro will be ignored
>
>
> Analysing residue names:
> There are:   128  Other residues
> There are:  2460  Water residues
> Analysing residues not classified as Protein/DNA/RNA/Water and splitting
> into groups...
> Number of degrees of freedom in T-Coupling group rest is 34725.00
> Largest charge group radii for Van der Waals: 0.216, 0.216 nm
> Largest charge group radii for Coulomb:   0.216, 0.216 nm
> Calculating fourier grid dimensions for X Y Z
> Using a fourier grid of 54x54x60, spacing 0.116 0.114 0.115
> Estimate for the relative computational load of the PME mesh part: 0.36
> This run will generate roughly 164 Mb of data
>
> There was 1 warning
>
> how tom resolve these problems
> em.tpr is formed but rest of the files are not formed
> help
>
>
> On Thu, Jul 3, 2014 at 2:23 PM, RINU KHATTRI 
> wrote:
>
> > hello everyone
> > my grompp related   problem atomtype CA not found has been solved now i
> am
> > using 56a3 force field for protein ligand complex with popc but srill i
> > didnt get em.tpr a new error
> >
> >
> >
> > Excluding 3 bonded neighbours molecule type 'POPC'
> > Excluding 2 bonded neighbours molecule type 'SOL'
> >
> > ---
> > Program grompp, VERSION 4.5.5
> > Source code file: /build/buildd/gromacs-4.5.5/src/kernel/grompp.c, line:
> > 523
> >
> > Fatal error:
> > number of coordinates in coordinate file (popc128.gro, 14036)
> >  does not match topology (topolpopc.top, 17459)
> > kindly help
> >
> >
> >
> > On Wed, Jul 2, 2014 at 3:51 PM, Justin Lemkul  wrote:
> >
> >>
> >>
> >> On 7/2/14, 6:07 AM, RINU KHATTRI wrote:
> >>
> >>> hello gromacs users
> >>>   i used 43a1 force field(Gromacs 4.5.7) in the atomtype.atp file in
> the
> >>> place of CA CA2+ is present in ffnonbonded.itp file CA and CA2+ both
> are
> >>> present according to tutorial i have been followed  all the step
> >>> still em.tpr not formed
> >>> atomtype CA not found
> >>>
> >>>
> >> "CA" is the gmx.ff nomenclature for the calcium type, so that suggests
> >> you're mixing and matching force fields (note that gmx.ff has been
> removed
> >> from the latest Gromacs version, since it should not be used).  Without
> >> explicit detail of your topology (i.e. post your files so they can be
> >> downloaded), there's very little that can be done to suggest where
> things
> >> have gone wrong.  I strongly suspect you've mixed and matched force
> fields
> >> somewhere, which is easy to do when dealing with co

Re: [gmx-users] Incorrectly added water molecule by genbox.

[Dawid das]

Thank you Mark but it seems that removing one water molecule does not do
any good. I removed another one and the error arises again for another one.
What else can I do if water does not settle during minimization?
That's my minimize.mdp file.

title= minimization of mCherry
; this is a comment
integrator   = cg ; (other: steep, l-bfgs)
emtol= 1000
emstep   = 0.01
nsteps   = 2000
nstlist  = 1
ns_type  = grid
nstenergy= 50
rlist= 1.0
coulombtype  = PME
rcoulomb = 1.0
rvdw = 1.0
pbc  = xyz
freezegrps   = Protein
freezedim= Y Y Y



2014-07-03 9:55 GMT+02:00 Mark Abraham :

> On Thu, Jul 3, 2014 at 9:17 AM, Dawid das  wrote:
>
> > Hi,
> >
> > I have a following issue. Genbox seems to add a water molecule inside
> small
> > protein cavity and it does not belong there. Can I manually remove it
> from
> > *gro file?
>
>
> Yes, but you need to make a matching change to the [molecules] section of
> any matching .top file.
>
>
> > What with the numbering of residues in this situation?
>
>
> Immaterial. The only important thing in such cases is that there is a
> change; the values or the delta-value is not noticed.
>
> Mark
>
>
> > The
> > problem is that this water molecule can't be settled during minimization
> > and it spoils everything.
> >
> > Dawid
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-requ...@gromacs.org.
> >
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
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Re: [gmx-users] error in grompp command

[Justin Lemkul]

On 7/3/14, 6:27 AM, RINU KHATTRI wrote:

hello gromacs users now have been removed this error after changing the
number of SOL in topol_popc.top file (counted from popc128.gro)
after that i hav used -maxwarn 1 command

result is

Generated 813 of the 2346 non-bonded parameter combinations
Excluding 3 bonded neighbours molecule type 'POPC'
Excluding 2 bonded neighbours molecule type 'SOL'
Warning: atom name 6657 in topolpopc.top and popc128.gro does not match (OW
- OW1)
Warning: atom name 6658 in topolpopc.top and popc128.gro does not match
(HW1 - HW2)
Warning: atom name 6659 in topolpopc.top and popc128.gro does not match
(HW2 - HW3)
Warning: atom name 6660 in topolpopc.top and popc128.gro does not match (OW
- OW1)
Warning: atom name 6661 in topolpopc.top and popc128.gro does not match
(HW1 - HW2)
Warning: atom name 6662 in topolpopc.top and popc128.gro does not match
(HW2 - HW3)
Warning: atom name 6663 in topolpopc.top and popc128.gro does not match (OW
- OW1)
Warning: atom name 6664 in topolpopc.top and popc128.gro does not match
(HW1 - HW2)
Warning: atom name 6665 in topolpopc.top and popc128.gro does not match
(HW2 - HW3)
Warning: atom name  in topolpopc.top and popc128.gro does not match (OW
- OW1)
Warning: atom name 6667 in topolpopc.top and popc128.gro does not match
(HW1 - HW2)
Warning: atom name 6668 in topolpopc.top and popc128.gro does not match
(HW2 - HW3)
Warning: atom name 6669 in topolpopc.top and popc128.gro does not match (OW
- OW1)
Warning: atom name 6670 in topolpopc.top and popc128.gro does not match
(HW1 - HW2)
Warning: atom name 6671 in topolpopc.top and popc128.gro does not match
(HW2 - HW3)
Warning: atom name 6672 in topolpopc.top and popc128.gro does not match (OW
- OW1)
Warning: atom name 6673 in topolpopc.top and popc128.gro does not match
(HW1 - HW2)
Warning: atom name 6674 in topolpopc.top and popc128.gro does not match
(HW2 - HW3)
Warning: atom name 6675 in topolpopc.top and popc128.gro does not match (OW
- OW1)
Warning: atom name 6676 in topolpopc.top and popc128.gro does not match
(HW1 - HW2)
(more than 20 non-matching atom names)

WARNING 1 [file topolpopc.top, line 26]:
   7380 non-matching atom names
   atom names from topolpopc.top will be used
   atom names from popc128.gro will be ignored


Analysing residue names:
There are:   128  Other residues
There are:  2460  Water residues
Analysing residues not classified as Protein/DNA/RNA/Water and splitting
into groups...
Number of degrees of freedom in T-Coupling group rest is 34725.00
Largest charge group radii for Van der Waals: 0.216, 0.216 nm
Largest charge group radii for Coulomb:   0.216, 0.216 nm
Calculating fourier grid dimensions for X Y Z
Using a fourier grid of 54x54x60, spacing 0.116 0.114 0.115
Estimate for the relative computational load of the PME mesh part: 0.36
This run will generate roughly 164 Mb of data

There was 1 warning

how tom resolve these problems


In this case, the warnings about non-matching names are harmless and they refer 
only to different conventions in water nomenclature.  You can easily re-name the 
atoms in the coordinate file with simple sed statements, but it's not necessary 
here.  Ignoring mismatching names in other cases can be very harmful, so be advised.



em.tpr is formed but rest of the files are not formed


What other files are you looking for?  The purpose of grompp is to produce a 
.tpr file; there are other files that can be produced, but none of them are 
essential.


-Justin

--
==

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

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
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] Graphene topology file

[Justin Lemkul]

On 7/3/14, 12:48 AM, #SUKRITI GUPTA# wrote:

Dear Justin,

Thanks for the reply but I am writing the .n2t file still getting the error that 
"Could not find force field 'graphite_oplsaa' in current directory, install tree or 
GMXDATA path". What should I do? Moreover i don't think that n2t file tells program 
to use graphite_oplsaa force field.



Well, as noted before, the tutorial there relies on a very old setup, so you 
shouldn't be following it exactly.  The better approach is to:


1. Make a copy of the oplsaa.ff force field into your working directory
2. Modify its contents as needed to introduce any new atom types and bonded 
parameters
3. Write the .n2t file within that directory and make use of that one rather 
than any included in the force fields in $GMXLIB


-Justin

--
==

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

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
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] Graphene topology file

[abhijit Kayal]

Hi Sukriti,
 Copy the oplsaa.ff directory to your working directory. Then in
ffnonbonded.itp file add the following lines..
 opls_995   C  612.01100 0.000   A3.4e-01
3.61200e-01
 opls_996   C  612.01100 0.000   A3.4e-01
3.61200e-01
 opls_997   C  612.01100 0.000   A3.4e-01
3.61200e-01

Then in   atomname2type.n2t file add the following lines.
Copls_9950  12.011  2C  0.142  C 0.142
Copls_9960  12.011  3C  0.142  C 0.142  C 0.142
Copls_9970  12.011  1C  0.142

Then use g_x2top. This will work.

Thanks
 Abhijit


On Thu, Jul 3, 2014 at 3:11 PM, Dr. Vitaly Chaban 
wrote:

> Graphene topology is like for tube, so
>
> C  C
> C ... C ... C
> C  C  C   C
>
> to the N2T file and you are done.
>
>
> Dr. Vitaly V. Chaban
>
>
> On Wed, Jul 2, 2014 at 5:29 PM, Justin Lemkul  wrote:
> >
> >
> > On 7/2/14, 9:56 AM, #SUKRITI GUPTA# wrote:
> >>
> >> Dear all,
> >>
> >>
> >> I want to simulate graphite in water, for which i am trying to create a
> >> topology file for graphite. As its .rtp file cannot be written
> correctly, i
> >> tried to use g_x2top command following the steps given in following
> >> tutorial.
> >>
> >> http://chembytes.wikidot.com/grocnt
> >>
> >>
> >> But I think this tutorial is quite old and hence suitable for older
> >> version of gromacs as it still uses FF.dat file. Moreover if i am
> trying to
> >> make a new forcefield directory with name graphite_oplsaa containing the
> >> modified files like .n2t,.rtp and .itp, its giving me an error that
> "Could
> >> not find force field 'graphite_oplsaa' in current directory, install
> tree or
> >> GMXDATA path". When I try to add this forcefield in original path ie.
> >> user/share/gromacs/top, it does not allow me to do that as i am not the
> >> administrator. Can anyone please let me know how to create the topology
> >> file. I require 3 graphene sheets with pbc. I have created the .pdb file
> >> using nanobuilder in vmd.
> >>
> >
> > The tutorial is indeed outdated but the logic is fairly sound.  You don't
> > have to modify anything in $GMXLIB (system-wide); you can just create an
> > .n2t file in the working directory and it will override the one at the
> force
> > field level.
> >
> > -Justin
> >
> > --
> > ==
> >
> > Justin A. Lemkul, Ph.D.
> > Ruth L. Kirschstein NRSA Postdoctoral Fellow
> >
> > Department of Pharmaceutical Sciences
> > School of Pharmacy
> > Health Sciences Facility II, Room 601
> > 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.
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
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> send a mail to gmx-users-requ...@gromacs.org.
>



-- 
Abhijit kayal
Research Scholar
Theoretical Chemistry
IIT Kanpur
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Re: [gmx-users] Excess Heat of mixing

[Justin Lemkul]

On 7/3/14, 12:17 AM, AMNINDER SINGH wrote:

Dear People,

I am trying to calculate heat of mixing of two solvents using inter molecular 
energies.

I have calculated heat of vaporization of both solvents in pure form and 
results are in agreement with  experimental and theoretical data.

But, I can't find a right equation to calculate heat of mixing.

Any help will be highly appreciated.



Have you tried Google?

-Justin

--
==

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

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
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] Excess Heat of mixing

[Amninder]

I have tried everything...even most the results in literature are not 
consistent to each other...actually I became more confused after reading 
literature..I am hoping that some one must've calculated for water-alcohol 
mixtures and explained in detail

Sent from my iPhone

On 03-Jul-2014, at 8:42 PM, Justin Lemkul  wrote:

> 
> 
> On 7/3/14, 12:17 AM, AMNINDER SINGH wrote:
>> Dear People,
>> 
>> I am trying to calculate heat of mixing of two solvents using inter 
>> molecular energies.
>> 
>> I have calculated heat of vaporization of both solvents in pure form and 
>> results are in agreement with  experimental and theoretical data.
>> 
>> But, I can't find a right equation to calculate heat of mixing.
>> 
>> Any help will be highly appreciated.
> 
> Have you tried Google?
> 
> -Justin
> 
> -- 
> ==
> 
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
> 
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> 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] Incorrectly added water molecule by genbox.

[Mark Abraham]

The standard advice is here
http://www.gromacs.org/Documentation/How-tos/Steps_to_Perform_a_Simulation.
You should work out what the common theme is and address that, rather than
make random changes. You ought to have no need of frozen groups during EM -
you are trying to relax your starting configuration!

Mark


On Thu, Jul 3, 2014 at 12:39 PM, Dawid das  wrote:

> Thank you Mark but it seems that removing one water molecule does not do
> any good. I removed another one and the error arises again for another one.
> What else can I do if water does not settle during minimization?
> That's my minimize.mdp file.
>
> title= minimization of mCherry
> ; this is a comment
> integrator   = cg ; (other: steep, l-bfgs)
> emtol= 1000
> emstep   = 0.01
> nsteps   = 2000
> nstlist  = 1
> ns_type  = grid
> nstenergy= 50
> rlist= 1.0
> coulombtype  = PME
> rcoulomb = 1.0
> rvdw = 1.0
> pbc  = xyz
> freezegrps   = Protein
> freezedim= Y Y Y
>
>
>
> 2014-07-03 9:55 GMT+02:00 Mark Abraham :
>
> > On Thu, Jul 3, 2014 at 9:17 AM, Dawid das  wrote:
> >
> > > Hi,
> > >
> > > I have a following issue. Genbox seems to add a water molecule inside
> > small
> > > protein cavity and it does not belong there. Can I manually remove it
> > from
> > > *gro file?
> >
> >
> > Yes, but you need to make a matching change to the [molecules] section of
> > any matching .top file.
> >
> >
> > > What with the numbering of residues in this situation?
> >
> >
> > Immaterial. The only important thing in such cases is that there is a
> > change; the values or the delta-value is not noticed.
> >
> > Mark
> >
> >
> > > The
> > > problem is that this water molecule can't be settled during
> minimization
> > > and it spoils everything.
> > >
> > > Dawid
> > > --
> > > Gromacs Users mailing list
> > >
> > > * Please search the archive at
> > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > > posting!
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Re: [gmx-users] Excess Heat of mixing

[Michael Brunsteiner]

Hi Amninder,

DeltaU_mix =  -  * N_A -  * N_B

 ... average total intermolecular energy of the blend
 ... the average interaction energy of a single molecule of type A in a 
pure sample of A
 ... the average interaction energy of a single molecule of type B in a 
pure sample of B
N_A ... the number of molecules of type A in the blend
N_B ... the number of molecules of type B in the blend

usually people write H (enthalpy) instead of U (internal energy) ... as 
enthalpy is what you
get from experiments ... however the latter is simpler to calculate from MD 
results and
in most cases DeltaU  and DeltaH are very close, i.e., the difference (the 
Delta pV term) is
smaller than your overall error bars, and you can stick with U.


With the above eqns ... if you have a mixing ratio of 100% A and 0% B then your 
mixing energy
will be zero, as expected, because now  =  * N_A (the "blend" is 
now pure A),
and N_B and consequently N_B  are zero. the same goes for 0% A and 100% B 
...


an open question (and i agree that there is quite some confusion in the 
literature about this - 

not in a single paper I read (NOR in google) is this discussed explicitely) is: 
do we want to include the 

INTRA-molecular contributions to the various Us or not, and if so, all of them 
or just the intra-molecular 

non-bonded interactions?
In practice the answer probably depends on the type of mixture you consider 
(and perhaps on the force
field you use) ... often the RELATIVE energy differences you get when comparing 
different mixing ratios
(or even different compounds) are pretty similar, whether you include 
intra-molecular contributions or not
... however you might see non-neglegible differences if you have fairly 
flexible molecules whose conformation
is systematically different in the pure phase versus the blend/mixture. In the 
first case you probably want
to stick with inter-molecular contributions only since the error-contribution 
from poor sampling of the
intra-molecular contributions might be larger than the error you introduce by 
neglecting
these contributions altogether. However, if you do this you need to be careful 
regarding the evaluation of

 ,  and . If you have electrostatic long range interactions 
(i.e. you use Ewald
or PME) you might need to perform multiple reruns with part of the charges 
turned off to get the true
intermolecular energies, instead of just using energy groups and the output of 
g_energy! ... if you don't
know how to do this  there are a few discussions in this mailing list 
regarding this topic!


hope that helps... feel free to contact me if anything i wrote is unclear!

cheers
michael

I have tried everything...even most the results in literature are not 
consistent to each other...actually I became more confused after reading 
literature..I am hoping that some one must've calculated for water-alcohol 
mixtures and explained in detail Sent from my iPhone On 03-Jul-2014, at 8:42 
PM, Justin Lemkul  wrote: >>>On 7/3/14, 12:17 AM, AMNINDER 
SINGH wrote: >>Dear People, I am trying to calculate heat of mixing of two 
solvents using inter molecular energies. I have calculated heat of 
vaporization of both solvents in pure form and results are in agreement with  
experimental and theoretical data. But, I can't find a right equation to 
calculate heat of mixing. Any help will be highly appreciated. >>Have you 
tried Google? >>-Justin >>-- 
>== >>Justin A. Lemkul, Ph.D. 
>Ruth L. Kirschstein NRSA Postdoctoral Fellow >>Department of Pharmaceutical 
Sciences >School of
 Pharmacy >Health Sciences Facility II, Room 601 >University of Maryland, 
Baltimore >20 Penn St. >Baltimore, MD 21201 >>jalemkul at 
outerbanks.umaryland.edu | (410) 706-7441 
>http://mackerell.umaryland.edu/~jalemkul 
>>==


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[gmx-users] Molecular Configuration of ionic liquids

[Andy Chao]

Dear GROMACS Users:

Is there any software tool/program that allows one to construct the
molecular configuration of any ionic liquid?  As a result, the software
program would generate the PDB or GRO file that can be used in GROMACS?

Thanks!

Andy
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[gmx-users] hardware setup for gmx

[Michael Brunsteiner]

Hi,

can anybody recommend a hardware setup to perform MD runs (with PME) that has a 
good 
price-performance ratio? ... in particular I'd be interested in learning which 
combinations 
of CPU and GPU can be expected to provide a good FLOPS-per-dollar ratio with 
the more
recent gmx versions (4.6 or 5.0)?

thanks in advance for any recommendations!

Michael



ps: if your opinion is highly subjective and/or perhaps prone to make 
particular hardware vendors
really sad, you might want to send your answer only to my email rather than to 
all gmx-users)



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[gmx-users] gmx-5.0 features

[Michael Brunsteiner]

Hi,

I am sorry in case I overlooked the answers in the release-notes,
but I didn't find there answers to:
1) does gmx-5.0 support free energy calculations + GPU ?

2) does gmx-5.0 support double precision + GPU ?


cheers
michael

===


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[gmx-users] problem with calculating angles and dynamic selections

[gigo]

Hi!
I find it impossible to calculate (some) angles between atoms using 
dynamic selection in 'gmx gangle' command. The problem is, that the 
dynamic selection mechanism persistently sorts numbers of atoms 
specified in the input. So, if I have atoms A, B and C with ascending 
indexes, I am not able to calculate angle B-A-C - I only get value for 
A-B-C, no matter how I order them in the command line. Is there any way 
to do it without writing an index file (which I have to parse anyway, 
because the same mechanism sorts atoms in 'gmx select'...)? If not, I 
will submit a feature request on redmine - something like -nosort 
option...

Regards,

Grzegorz Wieczorek
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[gmx-users] Problems with NFS

[Natalia Alveal F.]

Dear Gromacs users,

I need your help, because when i run a dynamic in the cluster of my lab,
the program makes the connection with NFS lost and my dynamics stop,
together with the others of my coworkers.
The version is GROMACS 4.5.4.

This is the error:

Could not chdir to home directory /home/fmontenegro: No such file or
directory
-bash: /home/fmontenegro/.ncbirc: No such file or directory

I hope can help me.
Best regards!

-- 
Natalia Alveal Fuentealba
Ingeniera en Bioinformática
Laboratory of Membranes Proteins Structure and Signalling
Departamento de Fisiología
Pontificia Universidad Católica de Chile
Alameda 340, Santiago, Chile
Fono: 56-2-3542877
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Re: [gmx-users] Problems with NFS

[Victor Rosas Garcia]

Hello Natalia,

The error says that it is trying to change to a directory named
/home/fmontenegro, but that such a directory does not exist. This is not a
GROMACS error, but a problem related to how the cluster is setup.  Your
cluster administrator should be able to help with this problem.

Best regards

Victor


2014-07-03 9:52 GMT-05:00 Natalia Alveal F. :

> Dear Gromacs users,
>
> I need your help, because when i run a dynamic in the cluster of my lab,
> the program makes the connection with NFS lost and my dynamics stop,
> together with the others of my coworkers.
> The version is GROMACS 4.5.4.
>
> This is the error:
>
> Could not chdir to home directory /home/fmontenegro: No such file or
> directory
> -bash: /home/fmontenegro/.ncbirc: No such file or directory
>
> I hope can help me.
> Best regards!
>
> --
> Natalia Alveal Fuentealba
> Ingeniera en Bioinformática
> Laboratory of Membranes Proteins Structure and Signalling
> Departamento de Fisiología
> Pontificia Universidad Católica de Chile
> Alameda 340, Santiago, Chile
> Fono: 56-2-3542877
> --
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> posting!
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Re: [gmx-users] Problems with NFS

[Natalia Alveal F.]

This error is just for confirming that NFS falls, that is not functioning.
But when run Gromacs, the connection with NFs is lost just few time of
compute. This not happen when run NAMD 2.9 alone.

And this is the command for the cluster:
nohup /opt/openmpi/bin/mpirun -hostfile myhostfile2
/opt/bio/gromacs/bin/mdrun -v -s md.tpr -deffnm md &

I hope can help me!!
Best regards from Chile.


2014-07-03 11:20 GMT-04:00 Victor Rosas Garcia :

> Hello Natalia,
>
> The error says that it is trying to change to a directory named
> /home/fmontenegro, but that such a directory does not exist. This is not a
> GROMACS error, but a problem related to how the cluster is setup.  Your
> cluster administrator should be able to help with this problem.
>
> Best regards
>
> Victor
>
>
> 2014-07-03 9:52 GMT-05:00 Natalia Alveal F. :
>
> > Dear Gromacs users,
> >
> > I need your help, because when i run a dynamic in the cluster of my lab,
> > the program makes the connection with NFS lost and my dynamics stop,
> > together with the others of my coworkers.
> > The version is GROMACS 4.5.4.
> >
> > This is the error:
> >
> > Could not chdir to home directory /home/fmontenegro: No such file or
> > directory
> > -bash: /home/fmontenegro/.ncbirc: No such file or directory
> >
> > I hope can help me.
> > Best regards!
> >
> > --
> > Natalia Alveal Fuentealba
> > Ingeniera en Bioinformática
> > Laboratory of Membranes Proteins Structure and Signalling
> > Departamento de Fisiología
> > Pontificia Universidad Católica de Chile
> > Alameda 340, Santiago, Chile
> > Fono: 56-2-3542877
> > --
> > Gromacs Users mailing list
> >
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> > posting!
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>



-- 
Natalia Alveal Fuentealba
Ingeniera en Bioinformática
Laboratory of Membranes Proteins Structure and Signalling
Departamento de Fisiología
Pontificia Universidad Católica de Chile
Alameda 340, Santiago, Chile
Fono: 56-2-3542877
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[gmx-users] Cross correlation/Normalised covariance calculation problems

[Bailey A.]

Dear all,

I've got a discrepancy between cross correlations that I previously calculated 
using Ran Freidman's amended version of g_covar and GROMACS version 3.3.3, and 
those I've done myself from using gromacs 4.6.4 and MATLAB that I'm bit baffled 
by. (I no longer have access to GROMACS 3.3.3 and don't really want to 
reinstall it.).

The discrepancy is that with Ran's code using the same trajectory (this was a 
sanity check for further calculations) I got about 1500 correlations above an 
absolute cross correlation coefficient of 0.7, whereas I get about 750 
correlations using my code.

I only have the log file for Ran's GROMACS 3.3.3 g_covar output and this has 
the same value for the trace of covariance matrix as for the GROMACS 4.6.4 
output, and the eigenvalues appear to be the same for both calculations. And I 
have the xpm plot of the cross correlation matrix from Ran's output, which 
visually looks the same as what I'm plotting in MATLAB for the whole cross 
correlation map from -1 to 1, but not for when I've filtered to correlations 
|r| >0.7. (I originally amended Ran's file to change the threshold from 0.5 to 
0.7).

What I've done (from reading Tsjerk's messages in the archive) is output an 
ascii file from g_covar then reconstructed the covariance matrix and converted 
it to normalised covariance as per:

C_ij =  / sqrt (  *  )

And this was where I got lost following Ran's code. What I did next was to 
extract the 3 parts of the 3N matrix I got from the equation above, and sum 
them together and divide by 3 to get a N x N matrix and then  I've looped 
through to extract where |r|>0.7. Ran's code appears to output one third of the 
entire matrix, I may have this wrong, but I'm not au fait with C and was 
struggling with the code. Does what I've done make sense? I can post my code or 
email direct if that helps.

To compare the first 10 outputs, this is my MATLAB output:

Atom Atom Correlation
4  1  0.91
5  2  0.85
6  3  0.78
7  1  0.80
7  4  0.93
8  2  0.75
8  5  0.89
9  6  0.81
10   1  0.79
10   4  0.86

And this is the first 10 outputs from previous calculation using Ran's code:

Atom Atom Correlation
1  2  0.84
2  3  0.88
3  4  0.87
4  5  0.85
4  6  0.75
5  6  0.85
5  7  0.72
6  7  0.86
6  8  0.73
7  8  0.87

And as I mentioned, MATLAB gives me about 750 correlations, whilst Ran's gives 
me about 1500. So I'm a bit baffled, if anyone has an ideas as to where I'm 
going wrong? When I map them onto my protein, both solutions look plausible, 
but I'm not sure which is correct!

Many thanks,

Alistair


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Re: [gmx-users] Problems with NFS

[Victor Rosas Garcia]

So, if NFS is not functioning, there is little we can do on this list to
help.  My only guess about it is that maybe NFS is working but the home
directories have not been exported to the working nodes. Perhaps a failure
of NIS or LDAP configuration?

I do not have experience with NAMD, so I cannot comment on why the error
does not arise in that case.

Again, my recommendation is to talk to your system administrator about the
lack of the directory on a node where it is supposed to be.

Best regards

Victor


2014-07-03 11:22 GMT-05:00 Natalia Alveal F. :

> This error is just for confirming that NFS falls, that is not functioning.
> But when run Gromacs, the connection with NFs is lost just few time of
> compute. This not happen when run NAMD 2.9 alone.
>
> And this is the command for the cluster:
> nohup /opt/openmpi/bin/mpirun -hostfile myhostfile2
> /opt/bio/gromacs/bin/mdrun -v -s md.tpr -deffnm md &
>
> I hope can help me!!
> Best regards from Chile.
>
>
> 2014-07-03 11:20 GMT-04:00 Victor Rosas Garcia :
>
> > Hello Natalia,
> >
> > The error says that it is trying to change to a directory named
> > /home/fmontenegro, but that such a directory does not exist. This is not
> a
> > GROMACS error, but a problem related to how the cluster is setup.  Your
> > cluster administrator should be able to help with this problem.
> >
> > Best regards
> >
> > Victor
> >
> >
> > 2014-07-03 9:52 GMT-05:00 Natalia Alveal F. :
> >
> > > Dear Gromacs users,
> > >
> > > I need your help, because when i run a dynamic in the cluster of my
> lab,
> > > the program makes the connection with NFS lost and my dynamics stop,
> > > together with the others of my coworkers.
> > > The version is GROMACS 4.5.4.
> > >
> > > This is the error:
> > >
> > > Could not chdir to home directory /home/fmontenegro: No such file or
> > > directory
> > > -bash: /home/fmontenegro/.ncbirc: No such file or directory
> > >
> > > I hope can help me.
> > > Best regards!
> > >
> > > --
> > > Natalia Alveal Fuentealba
> > > Ingeniera en Bioinformática
> > > Laboratory of Membranes Proteins Structure and Signalling
> > > Departamento de Fisiología
> > > Pontificia Universidad Católica de Chile
> > > Alameda 340, Santiago, Chile
> > > Fono: 56-2-3542877
> > > --
> > > 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.
> >
>
>
>
> --
> Natalia Alveal Fuentealba
> Ingeniera en Bioinformática
> Laboratory of Membranes Proteins Structure and Signalling
> Departamento de Fisiología
> Pontificia Universidad Católica de Chile
> Alameda 340, Santiago, Chile
> Fono: 56-2-3542877
> --
> 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] problem with calculating angles and dynamic selections

[Venkat Reddy]

Hi,
Have you tried gmx gangle -g1 vector -g2 vector -group1 resname RES and
name A B -group2 resname RES and name A C

I have valid results using the above command. In fact, I didn't find any
problem with -g1 angle also.


On Thu, Jul 3, 2014 at 7:42 PM, gigo  wrote:

> Hi!
> I find it impossible to calculate (some) angles between atoms using
> dynamic selection in 'gmx gangle' command. The problem is, that the dynamic
> selection mechanism persistently sorts numbers of atoms specified in the
> input. So, if I have atoms A, B and C with ascending indexes, I am not able
> to calculate angle B-A-C - I only get value for A-B-C, no matter how I
> order them in the command line. Is there any way to do it without writing
> an index file (which I have to parse anyway, because the same mechanism
> sorts atoms in 'gmx select'...)? If not, I will submit a feature request on
> redmine - something like -nosort option...
> Regards,
>
> Grzegorz Wieczorek
> --
> 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.
>



-- 
With Best Wishes
Venkat Reddy Chirasani
PhD student
Laboratory of Computational Biophysics
Department of Biotechnology
IIT Madras
Chennai
INDIA-600036
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Re: [gmx-users] Problems with NFS

[Natalia Alveal F.]

we known that gromacs not find the directories. When mount the directories
in NFS, that we dont known is why gromacs makes that NFS falls down.

Any help!
Best regards.


2014-07-03 12:36 GMT-04:00 Victor Rosas Garcia :

> So, if NFS is not functioning, there is little we can do on this list to
> help.  My only guess about it is that maybe NFS is working but the home
> directories have not been exported to the working nodes. Perhaps a failure
> of NIS or LDAP configuration?
>
> I do not have experience with NAMD, so I cannot comment on why the error
> does not arise in that case.
>
> Again, my recommendation is to talk to your system administrator about the
> lack of the directory on a node where it is supposed to be.
>
> Best regards
>
> Victor
>
>
> 2014-07-03 11:22 GMT-05:00 Natalia Alveal F. :
>
> > This error is just for confirming that NFS falls, that is not
> functioning.
> > But when run Gromacs, the connection with NFs is lost just few time of
> > compute. This not happen when run NAMD 2.9 alone.
> >
> > And this is the command for the cluster:
> > nohup /opt/openmpi/bin/mpirun -hostfile myhostfile2
> > /opt/bio/gromacs/bin/mdrun -v -s md.tpr -deffnm md &
> >
> > I hope can help me!!
> > Best regards from Chile.
> >
> >
> > 2014-07-03 11:20 GMT-04:00 Victor Rosas Garcia :
> >
> > > Hello Natalia,
> > >
> > > The error says that it is trying to change to a directory named
> > > /home/fmontenegro, but that such a directory does not exist. This is
> not
> > a
> > > GROMACS error, but a problem related to how the cluster is setup.  Your
> > > cluster administrator should be able to help with this problem.
> > >
> > > Best regards
> > >
> > > Victor
> > >
> > >
> > > 2014-07-03 9:52 GMT-05:00 Natalia Alveal F. :
> > >
> > > > Dear Gromacs users,
> > > >
> > > > I need your help, because when i run a dynamic in the cluster of my
> > lab,
> > > > the program makes the connection with NFS lost and my dynamics stop,
> > > > together with the others of my coworkers.
> > > > The version is GROMACS 4.5.4.
> > > >
> > > > This is the error:
> > > >
> > > > Could not chdir to home directory /home/fmontenegro: No such file or
> > > > directory
> > > > -bash: /home/fmontenegro/.ncbirc: No such file or directory
> > > >
> > > > I hope can help me.
> > > > Best regards!
> > > >
> > > > --
> > > > Natalia Alveal Fuentealba
> > > > Ingeniera en Bioinformática
> > > > Laboratory of Membranes Proteins Structure and Signalling
> > > > Departamento de Fisiología
> > > > Pontificia Universidad Católica de Chile
> > > > Alameda 340, Santiago, Chile
> > > > Fono: 56-2-3542877
> > > > --
> > > > 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.
> > >
> >
> >
> >
> > --
> > Natalia Alveal Fuentealba
> > Ingeniera en Bioinformática
> > Laboratory of Membranes Proteins Structure and Signalling
> > Departamento de Fisiología
> > Pontificia Universidad Católica de Chile
> > Alameda 340, Santiago, Chile
> > Fono: 56-2-3542877
> > --
> > 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.
>



-- 
Natalia Alveal Fuentealba
Ingeniera en Bioinformática
Laboratory of Membranes Proteins Structure and Signalling
Departamento de Fisiología
Pontificia Universidad Católica de Chile
Alameda 340, Santiago, Chile
Fono: 56-2-3542877
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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 (u

Re: [gmx-users] Problems with NFS

[Victor Rosas Garcia]

Then you need to do some troubleshooting. Using GROMACS is a complex
process, so you have to be very systematic in narrowing down the source of
the problem.

First, see if you can run GROMACS locally, in a single machine  (preferably
one of the nodes in the cluster) using only one thread and then several
threads. If GROMACS does not work, then it may be an installation problem.
If GROMACS works, then try some small calculation using a couple of nodes.
A failure at this point could mean a problem with the openmpi
installation.  Are there any other programs in the cluster that use openmpi?


Hope this helps

Victor


2014-07-03 11:46 GMT-05:00 Natalia Alveal F. :

> we known that gromacs not find the directories. When mount the directories
> in NFS, that we dont known is why gromacs makes that NFS falls down.
>
> Any help!
> Best regards.
>
>
> 2014-07-03 12:36 GMT-04:00 Victor Rosas Garcia :
>
> > So, if NFS is not functioning, there is little we can do on this list to
> > help.  My only guess about it is that maybe NFS is working but the home
> > directories have not been exported to the working nodes. Perhaps a
> failure
> > of NIS or LDAP configuration?
> >
> > I do not have experience with NAMD, so I cannot comment on why the error
> > does not arise in that case.
> >
> > Again, my recommendation is to talk to your system administrator about
> the
> > lack of the directory on a node where it is supposed to be.
> >
> > Best regards
> >
> > Victor
> >
> >
> > 2014-07-03 11:22 GMT-05:00 Natalia Alveal F. :
> >
> > > This error is just for confirming that NFS falls, that is not
> > functioning.
> > > But when run Gromacs, the connection with NFs is lost just few time of
> > > compute. This not happen when run NAMD 2.9 alone.
> > >
> > > And this is the command for the cluster:
> > > nohup /opt/openmpi/bin/mpirun -hostfile myhostfile2
> > > /opt/bio/gromacs/bin/mdrun -v -s md.tpr -deffnm md &
> > >
> > > I hope can help me!!
> > > Best regards from Chile.
> > >
> > >
> > > 2014-07-03 11:20 GMT-04:00 Victor Rosas Garcia  >:
> > >
> > > > Hello Natalia,
> > > >
> > > > The error says that it is trying to change to a directory named
> > > > /home/fmontenegro, but that such a directory does not exist. This is
> > not
> > > a
> > > > GROMACS error, but a problem related to how the cluster is setup.
>  Your
> > > > cluster administrator should be able to help with this problem.
> > > >
> > > > Best regards
> > > >
> > > > Victor
> > > >
> > > >
> > > > 2014-07-03 9:52 GMT-05:00 Natalia Alveal F. :
> > > >
> > > > > Dear Gromacs users,
> > > > >
> > > > > I need your help, because when i run a dynamic in the cluster of my
> > > lab,
> > > > > the program makes the connection with NFS lost and my dynamics
> stop,
> > > > > together with the others of my coworkers.
> > > > > The version is GROMACS 4.5.4.
> > > > >
> > > > > This is the error:
> > > > >
> > > > > Could not chdir to home directory /home/fmontenegro: No such file
> or
> > > > > directory
> > > > > -bash: /home/fmontenegro/.ncbirc: No such file or directory
> > > > >
> > > > > I hope can help me.
> > > > > Best regards!
> > > > >
> > > > > --
> > > > > Natalia Alveal Fuentealba
> > > > > Ingeniera en Bioinformática
> > > > > Laboratory of Membranes Proteins Structure and Signalling
> > > > > Departamento de Fisiología
> > > > > Pontificia Universidad Católica de Chile
> > > > > Alameda 340, Santiago, Chile
> > > > > Fono: 56-2-3542877
> > > > > --
> > > > > 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.
> > > >
> > >
> > >
> > >
> > > --
> > > Natalia Alveal Fuentealba
> > > Ingeniera en Bioinformática
> > > Laboratory of Membranes Proteins Structure and Signalling
> > > Departamento de Fisiología
> > > Pontificia Universidad Católica de Chile
> > > Alameda 340, Santiago, Chile
> > > Fono: 56-2-3542877
> > > --
> > > 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:

[gmx-users] Restarts with 5.0

[Ali Khan]

Hi Everyone,

I have a simulation running with gromacs 4.6.5. Is it possible to stop the
simulation and restart from a check point with version 5.0? I attempted to
do it and got the following output:

*GROMACS:gmx mdrun, VERSION 5.0*

*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 mdrun, VERSION 5.0*
*Executable:   /home/akk5r/gromacs/bin/gmx*
*Library dir:  /home/akk5r/gromacs/share/gromacs/top*
*Command line:*
*  mdrun -v -maxh 168 -nt 12 -deffnm md_0_100 -cpi md_0_100.cpt*

*Reading file md_0_100.tpr, VERSION 4.6.5 (single precision)*
*Note: file tpx version 83, software tpx version 100*
*Changing nstlist from 5 to 25, rlist from 1.2 to 1.223*

*The number of OpenMP threads was set by environment variable
OMP_NUM_THREADS to 12*

*Reading checkpoint file md_0_100.cpt generated: Thu Jul  3 00:38:43 2014*



*---*
*Program mdrun, VERSION 5.0*
*Source code file:
/home/akk5r/Downloads/gromacs-5.0/src/gromacs/gmxlib/checkpoint.c, line:
2029*

*Fatal error:*
*Output file appending requested, but input and checkpoint states are not
identical.*
*Stopping the run to prevent you from ruining all your data...*
*You can try with the -noappend option, and get more info in the log file.*

*For more information and tips for troubleshooting, please check the
GROMACS*
*website at http://www.gromacs.org/Documentation/Errors
*
*---*

Best Wishes,
Ali Khan
-- 
Gromacs Users mailing list

* Please search the archive at 
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mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] problem with calculating angles and dynamic selections

[Venkat Reddy]

Hi,
I have tried gmx gangle -g1 angle option. Its sorting the atoms specified
in the input. I think it might be a bug. gmx gangle  -g1 vector -g2 vector
is doing fine.


On Thu, Jul 3, 2014 at 7:42 PM, gigo  wrote:

> Hi!
> I find it impossible to calculate (some) angles between atoms using
> dynamic selection in 'gmx gangle' command. The problem is, that the dynamic
> selection mechanism persistently sorts numbers of atoms specified in the
> input. So, if I have atoms A, B and C with ascending indexes, I am not able
> to calculate angle B-A-C - I only get value for A-B-C, no matter how I
> order them in the command line. Is there any way to do it without writing
> an index file (which I have to parse anyway, because the same mechanism
> sorts atoms in 'gmx select'...)? If not, I will submit a feature request on
> redmine - something like -nosort option...
> Regards,
>
> Grzegorz Wieczorek
> --
> 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.
>



-- 
With Best Wishes
Venkat Reddy Chirasani
PhD student
Laboratory of Computational Biophysics
Department of Biotechnology
IIT Madras
Chennai
INDIA-600036
-- 
Gromacs Users mailing list

* Please search the archive at 
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Re: [gmx-users] Molecular Configuration of ionic liquids (Andy Chao)

[Andrey Frolov]

You can use "Packmol" http://www.ime.unicamp.br/~martinez/packmol/

Andrey Frolov


>Dear GROMACS Users:
>
>Is there any software tool/program that allows one to construct the
>molecular configuration of any ionic liquid?  As a result, the software
>program would generate the PDB or GRO file that can be used in GROMACS?
>
>Thanks!
>
>Andy
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Re: [gmx-users] Restarts with 5.0

[Mark Abraham]

On Jul 3, 2014 7:07 PM, "Ali Khan"  wrote:
>
> Hi Everyone,
>
> I have a simulation running with gromacs 4.6.5. Is it possible to stop the
> simulation and restart from a check point with version 5.0?

Yes, but as the message says, you're not allowed to append to the files.
And your paper's reviewer would laugh at you for switching method
mid-experiment unless you do a lot work to show the difference was
immaterial. So, generally, you should not consider such a switch.

Mark

> I attempted to
> do it and got the following output:
>
> *GROMACS:gmx mdrun, VERSION 5.0*
>
> *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 mdrun, VERSION 5.0*
> *Executable:   /home/akk5r/gromacs/bin/gmx*
> *Library dir:  /home/akk5r/gromacs/share/gromacs/top*
> *Command line:*
> *  mdrun -v -maxh 168 -nt 12 -deffnm md_0_100 -cpi md_0_100.cpt*
>
> *Reading file md_0_100.tpr, VERSION 4.6.5 (single precision)*
> *Note: file tpx version 83, software tpx version 100*
> *Changing nstlist from 5 to 25, rlist from 1.2 to 1.223*
>
> *The number of OpenMP threads was set by environment variable
> OMP_NUM_THREADS to 12*
>
> *Reading checkpoint file md_0_100.cpt generated: Thu Jul  3 00:38:43 2014*
>
>
>
> *---*
> *Program mdrun, VERSION 5.0*
> *Source code file:
> /home/akk5r/Downloads/gromacs-5.0/src/gromacs/gmxlib/checkpoint.c, line:
> 2029*
>
> *Fatal error:*
> *Output file appending requested, but input and checkpoint states are not
> identical.*
> *Stopping the run to prevent you from ruining all your data...*
> *You can try with the -noappend option, and get more info in the log
file.*
>
> *For more information and tips for troubleshooting, please check the
> GROMACS*
> *website at http://www.gromacs.org/Documentation/Errors
> *
> *---*
>
> Best Wishes,
> Ali Khan
> --
> Gromacs Users mailing list
>
> * Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
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send a mail to gmx-users-requ...@gromacs.org.
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Re: [gmx-users] Restarts with 5.0

[Ali Khan]

Fair enough. Thank you.


On Thu, Jul 3, 2014 at 3:26 PM, Mark Abraham 
wrote:

> On Jul 3, 2014 7:07 PM, "Ali Khan"  wrote:
> >
> > Hi Everyone,
> >
> > I have a simulation running with gromacs 4.6.5. Is it possible to stop
> the
> > simulation and restart from a check point with version 5.0?
>
> Yes, but as the message says, you're not allowed to append to the files.
> And your paper's reviewer would laugh at you for switching method
> mid-experiment unless you do a lot work to show the difference was
> immaterial. So, generally, you should not consider such a switch.
>
> Mark
>
> > I attempted to
> > do it and got the following output:
> >
> > *GROMACS:gmx mdrun, VERSION 5.0*
> >
> > *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 mdrun, VERSION 5.0*
> > *Executable:   /home/akk5r/gromacs/bin/gmx*
> > *Library dir:  /home/akk5r/gromacs/share/gromacs/top*
> > *Command line:*
> > *  mdrun -v -maxh 168 -nt 12 -deffnm md_0_100 -cpi md_0_100.cpt*
> >
> > *Reading file md_0_100.tpr, VERSION 4.6.5 (single precision)*
> > *Note: file tpx version 83, software tpx version 100*
> > *Changing nstlist from 5 to 25, rlist from 1.2 to 1.223*
> >
> > *The number of OpenMP threads was set by environment variable
> > OMP_NUM_THREADS to 12*
> >
> > *Reading checkpoint file md_0_100.cpt generated: Thu Jul  3 00:38:43
> 2014*
> >
> >
> >
> > *---*
> > *Program mdrun, VERSION 5.0*
> > *Source code file:
> > /home/akk5r/Downloads/gromacs-5.0/src/gromacs/gmxlib/checkpoint.c, line:
> > 2029*
> >
> > *Fatal error:*
> > *Output file appending requested, but input and checkpoint states are not
> > identical.*
> > *Stopping the run to prevent you from ruining all your data...*
> > *You can try with the -noappend option, and get more info in the log
> file.*
> >
> > *For more information and tips for troubleshooting, please check the
> > GROMACS*
> > *website at http://www.gromacs.org/Documentation/Errors
> > *
> > *---*
> >
> > Best Wishes,
> > Ali Khan
> > --
> > 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.
>
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Re: [gmx-users] Problems with NFS

[Mark Abraham]

Hi,

GROMACS doesn't "make NFS go down," but it might expose the problem that
exists anyway - which happens frequently on clusters that aren't set up
appropriately. The GROMACS checkpoint process requires that the file system
be present, so that the checkpoint process can compute and record hash sums
of files that have been written to disk, so that GROMACS can guarantee the
integrity of your output with minimal loss, even if there's a power outage.
Your cluster admins are the people to whom to speak. Perhaps NAMD has
no/different checkpointing.

Mark
On Jul 3, 2014 6:47 PM, "Natalia Alveal F."  wrote:

> we known that gromacs not find the directories. When mount the directories
> in NFS, that we dont known is why gromacs makes that NFS falls down.
>
> Any help!
> Best regards.
>
>
> 2014-07-03 12:36 GMT-04:00 Victor Rosas Garcia :
>
> > So, if NFS is not functioning, there is little we can do on this list to
> > help.  My only guess about it is that maybe NFS is working but the home
> > directories have not been exported to the working nodes. Perhaps a
> failure
> > of NIS or LDAP configuration?
> >
> > I do not have experience with NAMD, so I cannot comment on why the error
> > does not arise in that case.
> >
> > Again, my recommendation is to talk to your system administrator about
> the
> > lack of the directory on a node where it is supposed to be.
> >
> > Best regards
> >
> > Victor
> >
> >
> > 2014-07-03 11:22 GMT-05:00 Natalia Alveal F. :
> >
> > > This error is just for confirming that NFS falls, that is not
> > functioning.
> > > But when run Gromacs, the connection with NFs is lost just few time of
> > > compute. This not happen when run NAMD 2.9 alone.
> > >
> > > And this is the command for the cluster:
> > > nohup /opt/openmpi/bin/mpirun -hostfile myhostfile2
> > > /opt/bio/gromacs/bin/mdrun -v -s md.tpr -deffnm md &
> > >
> > > I hope can help me!!
> > > Best regards from Chile.
> > >
> > >
> > > 2014-07-03 11:20 GMT-04:00 Victor Rosas Garcia  >:
> > >
> > > > Hello Natalia,
> > > >
> > > > The error says that it is trying to change to a directory named
> > > > /home/fmontenegro, but that such a directory does not exist. This is
> > not
> > > a
> > > > GROMACS error, but a problem related to how the cluster is setup.
>  Your
> > > > cluster administrator should be able to help with this problem.
> > > >
> > > > Best regards
> > > >
> > > > Victor
> > > >
> > > >
> > > > 2014-07-03 9:52 GMT-05:00 Natalia Alveal F. :
> > > >
> > > > > Dear Gromacs users,
> > > > >
> > > > > I need your help, because when i run a dynamic in the cluster of my
> > > lab,
> > > > > the program makes the connection with NFS lost and my dynamics
> stop,
> > > > > together with the others of my coworkers.
> > > > > The version is GROMACS 4.5.4.
> > > > >
> > > > > This is the error:
> > > > >
> > > > > Could not chdir to home directory /home/fmontenegro: No such file
> or
> > > > > directory
> > > > > -bash: /home/fmontenegro/.ncbirc: No such file or directory
> > > > >
> > > > > I hope can help me.
> > > > > Best regards!
> > > > >
> > > > > --
> > > > > Natalia Alveal Fuentealba
> > > > > Ingeniera en Bioinformática
> > > > > Laboratory of Membranes Proteins Structure and Signalling
> > > > > Departamento de Fisiología
> > > > > Pontificia Universidad Católica de Chile
> > > > > Alameda 340, Santiago, Chile
> > > > > Fono: 56-2-3542877
> > > > > --
> > > > > 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.
> > > >
> > >
> > >
> > >
> > > --
> > > Natalia Alveal Fuentealba
> > > Ingeniera en Bioinformática
> > > Laboratory of Membranes Proteins Structure and Signalling
> > > Departamento de Fisiología
> > > Pontificia Universidad Católica de Chile
> > > Alameda 340, Santiago, Chile
> > > Fono: 56-2-3542877
> > > --
> > > 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 

[gmx-users] Difference between charmm22 and charmm27 force fields.

[Dawid das]

Dear gromacs experts,

I have a question not related directly to gromacs program.
Is there difference in parameters for protein (aminoacids) atom types
between charmm22 and charmm27? In other words, may I use parameters for
charmm22 for a new non standard aminoacid residue if I use charmm27 for all
other aminoacids?
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Re: [gmx-users] Difference between charmm22 and charmm27 force fields.

[Justin Lemkul]

On 7/3/14, 4:30 PM, Dawid das wrote:

Dear gromacs experts,

I have a question not related directly to gromacs program.
Is there difference in parameters for protein (aminoacids) atom types
between charmm22 and charmm27? In other words, may I use parameters for
charmm22 for a new non standard aminoacid residue if I use charmm27 for all
other aminoacids?



There is a pervasive nomenclature mistake that people often make.  There is no 
such thing as a CHARMM27 protein force field.  CHARMM27 is a nucleic acid force 
field.  The confusion comes with the fact that when CHARMM27 was released, so 
too was the CHARMM22/CMAP force field for proteins, which introduces the CMAP 
terms on the CHARMM22 force field for better secondary structure sampling.  The 
CHARMM22/CMAP and CHARMM27 force fields are compatible, but technically 
different force fields.  What Gromacs distributes in "charmm27.ff" in terms of 
proteins is actually CHARMM22/CMAP.


So after all that, the real answer is: it's probably fine, because the protein 
force field is actually CHARMM22/CMAP.  If your residue predates the 
introduction of CMAP (i.e. some old parameter set from over 10 years ago), you 
should verify that inclusion of such terms does not cause problems (it 
shouldn't, but you never know).


-Justin

--
==

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

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
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] Problems with NFS

[Natalia Alveal F.]

Thanks Mark and Victor. I will see the checkpoint files.
Best regards!!


2014-07-03 15:38 GMT-04:00 Mark Abraham :

> Hi,
>
> GROMACS doesn't "make NFS go down," but it might expose the problem that
> exists anyway - which happens frequently on clusters that aren't set up
> appropriately. The GROMACS checkpoint process requires that the file system
> be present, so that the checkpoint process can compute and record hash sums
> of files that have been written to disk, so that GROMACS can guarantee the
> integrity of your output with minimal loss, even if there's a power outage.
> Your cluster admins are the people to whom to speak. Perhaps NAMD has
> no/different checkpointing.
>
> Mark
> On Jul 3, 2014 6:47 PM, "Natalia Alveal F."  wrote:
>
> > we known that gromacs not find the directories. When mount the
> directories
> > in NFS, that we dont known is why gromacs makes that NFS falls down.
> >
> > Any help!
> > Best regards.
> >
> >
> > 2014-07-03 12:36 GMT-04:00 Victor Rosas Garcia :
> >
> > > So, if NFS is not functioning, there is little we can do on this list
> to
> > > help.  My only guess about it is that maybe NFS is working but the home
> > > directories have not been exported to the working nodes. Perhaps a
> > failure
> > > of NIS or LDAP configuration?
> > >
> > > I do not have experience with NAMD, so I cannot comment on why the
> error
> > > does not arise in that case.
> > >
> > > Again, my recommendation is to talk to your system administrator about
> > the
> > > lack of the directory on a node where it is supposed to be.
> > >
> > > Best regards
> > >
> > > Victor
> > >
> > >
> > > 2014-07-03 11:22 GMT-05:00 Natalia Alveal F. :
> > >
> > > > This error is just for confirming that NFS falls, that is not
> > > functioning.
> > > > But when run Gromacs, the connection with NFs is lost just few time
> of
> > > > compute. This not happen when run NAMD 2.9 alone.
> > > >
> > > > And this is the command for the cluster:
> > > > nohup /opt/openmpi/bin/mpirun -hostfile myhostfile2
> > > > /opt/bio/gromacs/bin/mdrun -v -s md.tpr -deffnm md &
> > > >
> > > > I hope can help me!!
> > > > Best regards from Chile.
> > > >
> > > >
> > > > 2014-07-03 11:20 GMT-04:00 Victor Rosas Garcia <
> rosas.vic...@gmail.com
> > >:
> > > >
> > > > > Hello Natalia,
> > > > >
> > > > > The error says that it is trying to change to a directory named
> > > > > /home/fmontenegro, but that such a directory does not exist. This
> is
> > > not
> > > > a
> > > > > GROMACS error, but a problem related to how the cluster is setup.
> >  Your
> > > > > cluster administrator should be able to help with this problem.
> > > > >
> > > > > Best regards
> > > > >
> > > > > Victor
> > > > >
> > > > >
> > > > > 2014-07-03 9:52 GMT-05:00 Natalia Alveal F. :
> > > > >
> > > > > > Dear Gromacs users,
> > > > > >
> > > > > > I need your help, because when i run a dynamic in the cluster of
> my
> > > > lab,
> > > > > > the program makes the connection with NFS lost and my dynamics
> > stop,
> > > > > > together with the others of my coworkers.
> > > > > > The version is GROMACS 4.5.4.
> > > > > >
> > > > > > This is the error:
> > > > > >
> > > > > > Could not chdir to home directory /home/fmontenegro: No such file
> > or
> > > > > > directory
> > > > > > -bash: /home/fmontenegro/.ncbirc: No such file or directory
> > > > > >
> > > > > > I hope can help me.
> > > > > > Best regards!
> > > > > >
> > > > > > --
> > > > > > Natalia Alveal Fuentealba
> > > > > > Ingeniera en Bioinformática
> > > > > > Laboratory of Membranes Proteins Structure and Signalling
> > > > > > Departamento de Fisiología
> > > > > > Pontificia Universidad Católica de Chile
> > > > > > Alameda 340, Santiago, Chile
> > > > > > Fono: 56-2-3542877
> > > > > > --
> > > > > > 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.
> > > > >
> > > >
> > > >
> > > >
> > > > --
> > > > Natalia Alveal Fuentealba
> > > > Ingeniera en Bioinformática
> > > > Laboratory of Membranes Proteins Structure and Signalling
> > > > Departamento de Fisiología
> > > > Pontificia Universidad Católica 

[gmx-users] -extend problem

[gromacs query]

Hi All

I generated my npt.tpr with:


tinit=0

dt=0.002

nsteps=125000

I am trying to extend simulation for 250 ps like this:

tpbconv_mpi -s npt.tpr -o npt_new.tpr -extend 250


But when I used this npt_new.tpr simulation it ran for 500 ps. Have I
missed something?


Also one more thing why the Gromacs user archive search engine does not
work like before?


Thanks for any help

JIom
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Re: [gmx-users] -extend problem

[Justin Lemkul]

On 7/3/14, 6:05 PM, gromacs query wrote:

Hi All

I generated my npt.tpr with:


tinit=0

dt=0.002

nsteps=125000

I am trying to extend simulation for 250 ps like this:

tpbconv_mpi -s npt.tpr -o npt_new.tpr -extend 250


But when I used this npt_new.tpr simulation it ran for 500 ps. Have I
missed something?



If you simply pass npt_new.tpr to mdrun, that's what you should expect.  If you 
use mdrun -cpi to pick up from the last checkpoint at 250 ps, then you'll get an 
extended run instead of one that starts from t = 0.




Also one more thing why the Gromacs user archive search engine does not
work like before?



The Nabble archive?  It was disabled months ago.

-Justin

--
==

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

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
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] -extend problem

[gromacs query]

Hi Justin

Sorry, I should have mentioned that I used -cpi : here is my mdrun command
after tpbconv


tpbconv_mpi -s npt.tpr -o npt_new.tpr -extend 250


mdrun_mpi -s npt_new.tpr -o traj.trr -e ener.edr -c conf_prev.gro -g md.log
-cpo state_new.cpt -cpi state_prev.cpt


On Thu, Jul 3, 2014 at 11:07 PM, Justin Lemkul  wrote:

>
>
> On 7/3/14, 6:05 PM, gromacs query wrote:
>
>> Hi All
>>
>> I generated my npt.tpr with:
>>
>>
>> tinit=0
>>
>> dt=0.002
>>
>> nsteps=125000
>>
>> I am trying to extend simulation for 250 ps like this:
>>
>> tpbconv_mpi -s npt.tpr -o npt_new.tpr -extend 250
>>
>>
>> But when I used this npt_new.tpr simulation it ran for 500 ps. Have I
>> missed something?
>>
>>
> If you simply pass npt_new.tpr to mdrun, that's what you should expect.
>  If you use mdrun -cpi to pick up from the last checkpoint at 250 ps, then
> you'll get an extended run instead of one that starts from t = 0.
>
>
>
>> Also one more thing why the Gromacs user archive search engine does not
>> work like before?
>>
>>
> The Nabble archive?  It was disabled months ago.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> 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] -extend problem

[Justin Lemkul]

On 7/3/14, 6:34 PM, gromacs query wrote:

Hi Justin

Sorry, I should have mentioned that I used -cpi : here is my mdrun command
after tpbconv


tpbconv_mpi -s npt.tpr -o npt_new.tpr -extend 250


mdrun_mpi -s npt_new.tpr -o traj.trr -e ener.edr -c conf_prev.gro -g md.log
-cpo state_new.cpt -cpi state_prev.cpt



The .log file will have details of what is going on.  If the run proceeded from 
0-500 ps, the input .cpt file was not read.


-Justin



On Thu, Jul 3, 2014 at 11:07 PM, Justin Lemkul  wrote:




On 7/3/14, 6:05 PM, gromacs query wrote:


Hi All

I generated my npt.tpr with:


tinit=0

dt=0.002

nsteps=125000

I am trying to extend simulation for 250 ps like this:

tpbconv_mpi -s npt.tpr -o npt_new.tpr -extend 250


But when I used this npt_new.tpr simulation it ran for 500 ps. Have I
missed something?



If you simply pass npt_new.tpr to mdrun, that's what you should expect.
  If you use mdrun -cpi to pick up from the last checkpoint at 250 ps, then
you'll get an extended run instead of one that starts from t = 0.




Also one more thing why the Gromacs user archive search engine does not
work like before?



The Nabble archive?  It was disabled months ago.

-Justin

--
==

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

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
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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* 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 601
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] -extend problem

[gromacs query]

Hi

forgive my ignorance but I could not find whether my cpt was read
successfully or not as I dont see anything in log file as which files were
taken as input. Or any keyword I should search for?


On Thu, Jul 3, 2014 at 11:36 PM, Justin Lemkul  wrote:

>
>
> On 7/3/14, 6:34 PM, gromacs query wrote:
>
>> Hi Justin
>>
>> Sorry, I should have mentioned that I used -cpi : here is my mdrun command
>> after tpbconv
>>
>>
>> tpbconv_mpi -s npt.tpr -o npt_new.tpr -extend 250
>>
>>
>> mdrun_mpi -s npt_new.tpr -o traj.trr -e ener.edr -c conf_prev.gro -g
>> md.log
>> -cpo state_new.cpt -cpi state_prev.cpt
>>
>>
> The .log file will have details of what is going on.  If the run proceeded
> from 0-500 ps, the input .cpt file was not read.
>
> -Justin
>
>
>
>> On Thu, Jul 3, 2014 at 11:07 PM, Justin Lemkul  wrote:
>>
>>
>>>
>>> On 7/3/14, 6:05 PM, gromacs query wrote:
>>>
>>>  Hi All

 I generated my npt.tpr with:


 tinit=0

 dt=0.002

 nsteps=125000

 I am trying to extend simulation for 250 ps like this:

 tpbconv_mpi -s npt.tpr -o npt_new.tpr -extend 250


 But when I used this npt_new.tpr simulation it ran for 500 ps. Have I
 missed something?


  If you simply pass npt_new.tpr to mdrun, that's what you should expect.
>>>   If you use mdrun -cpi to pick up from the last checkpoint at 250 ps,
>>> then
>>> you'll get an extended run instead of one that starts from t = 0.
>>>
>>>
>>>
>>>  Also one more thing why the Gromacs user archive search engine does not
 work like before?


  The Nabble archive?  It was disabled months ago.
>>>
>>> -Justin
>>>
>>> --
>>> ==
>>>
>>> Justin A. Lemkul, Ph.D.
>>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>>
>>> Department of Pharmaceutical Sciences
>>> School of Pharmacy
>>> Health Sciences Facility II, Room 601
>>> 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 601
> 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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mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] -extend problem

[Justin Lemkul]

On 7/3/14, 6:51 PM, gromacs query wrote:

Hi

forgive my ignorance but I could not find whether my cpt was read
successfully or not as I dont see anything in log file as which files were
taken as input. Or any keyword I should search for?



If the .cpt file was read, it will say "Reading checkpoint file" just after the 
input settings list and before the DD information.


-Justin



On Thu, Jul 3, 2014 at 11:36 PM, Justin Lemkul  wrote:




On 7/3/14, 6:34 PM, gromacs query wrote:


Hi Justin

Sorry, I should have mentioned that I used -cpi : here is my mdrun command
after tpbconv


tpbconv_mpi -s npt.tpr -o npt_new.tpr -extend 250


mdrun_mpi -s npt_new.tpr -o traj.trr -e ener.edr -c conf_prev.gro -g
md.log
-cpo state_new.cpt -cpi state_prev.cpt



The .log file will have details of what is going on.  If the run proceeded
from 0-500 ps, the input .cpt file was not read.

-Justin




On Thu, Jul 3, 2014 at 11:07 PM, Justin Lemkul  wrote:




On 7/3/14, 6:05 PM, gromacs query wrote:

  Hi All


I generated my npt.tpr with:


tinit=0

dt=0.002

nsteps=125000

I am trying to extend simulation for 250 ps like this:

tpbconv_mpi -s npt.tpr -o npt_new.tpr -extend 250


But when I used this npt_new.tpr simulation it ran for 500 ps. Have I
missed something?


  If you simply pass npt_new.tpr to mdrun, that's what you should expect.

   If you use mdrun -cpi to pick up from the last checkpoint at 250 ps,
then
you'll get an extended run instead of one that starts from t = 0.



  Also one more thing why the Gromacs user archive search engine does not

work like before?


  The Nabble archive?  It was disabled months ago.


-Justin

--
==

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

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
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 601
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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* 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 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

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

==
--
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* Please search the archive at 
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mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] -extend problem

[gromacs query]

Hi Justin

Indeed this key word 'Reading checkpoint file" is missing. I noted that I
used same command in CPU (for other system) it was working fine. But now am
running on GPU with same command and cpt file is not read. Dont know whats
happening. Please suggest

regards


On Thu, Jul 3, 2014 at 11:58 PM, Justin Lemkul  wrote:

>
>
> On 7/3/14, 6:51 PM, gromacs query wrote:
>
>> Hi
>>
>> forgive my ignorance but I could not find whether my cpt was read
>> successfully or not as I dont see anything in log file as which files were
>> taken as input. Or any keyword I should search for?
>>
>>
> If the .cpt file was read, it will say "Reading checkpoint file" just
> after the input settings list and before the DD information.
>
>
> -Justin
>
>
>> On Thu, Jul 3, 2014 at 11:36 PM, Justin Lemkul  wrote:
>>
>>
>>>
>>> On 7/3/14, 6:34 PM, gromacs query wrote:
>>>
>>>  Hi Justin

 Sorry, I should have mentioned that I used -cpi : here is my mdrun
 command
 after tpbconv


 tpbconv_mpi -s npt.tpr -o npt_new.tpr -extend 250


 mdrun_mpi -s npt_new.tpr -o traj.trr -e ener.edr -c conf_prev.gro -g
 md.log
 -cpo state_new.cpt -cpi state_prev.cpt


  The .log file will have details of what is going on.  If the run
>>> proceeded
>>> from 0-500 ps, the input .cpt file was not read.
>>>
>>> -Justin
>>>
>>>
>>>
>>>  On Thu, Jul 3, 2014 at 11:07 PM, Justin Lemkul  wrote:



> On 7/3/14, 6:05 PM, gromacs query wrote:
>
>   Hi All
>
>>
>> I generated my npt.tpr with:
>>
>>
>> tinit=0
>>
>> dt=0.002
>>
>> nsteps=125000
>>
>> I am trying to extend simulation for 250 ps like this:
>>
>> tpbconv_mpi -s npt.tpr -o npt_new.tpr -extend 250
>>
>>
>> But when I used this npt_new.tpr simulation it ran for 500 ps. Have I
>> missed something?
>>
>>
>>   If you simply pass npt_new.tpr to mdrun, that's what you should
>> expect.
>>
>If you use mdrun -cpi to pick up from the last checkpoint at 250 ps,
> then
> you'll get an extended run instead of one that starts from t = 0.
>
>
>
>   Also one more thing why the Gromacs user archive search engine does
> not
>
>> work like before?
>>
>>
>>   The Nabble archive?  It was disabled months ago.
>>
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> 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 601
>>> 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 601
> 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.

Re: [gmx-users] -extend problem

[gromacs query]

Hi

Sorry I think I found the error. I was using wrong name of -cpi file. But
its strange that mdrun does not  complain even if it could not find the
file and it still ran the job.




On Fri, Jul 4, 2014 at 12:31 AM, gromacs query 
wrote:

> Hi Justin
>
> Indeed this key word 'Reading checkpoint file" is missing. I noted that I
> used same command in CPU (for other system) it was working fine. But now am
> running on GPU with same command and cpt file is not read. Dont know whats
> happening. Please suggest
>
> regards
>
>
> On Thu, Jul 3, 2014 at 11:58 PM, Justin Lemkul  wrote:
>
>>
>>
>> On 7/3/14, 6:51 PM, gromacs query wrote:
>>
>>> Hi
>>>
>>> forgive my ignorance but I could not find whether my cpt was read
>>> successfully or not as I dont see anything in log file as which files
>>> were
>>> taken as input. Or any keyword I should search for?
>>>
>>>
>> If the .cpt file was read, it will say "Reading checkpoint file" just
>> after the input settings list and before the DD information.
>>
>>
>> -Justin
>>
>>
>>> On Thu, Jul 3, 2014 at 11:36 PM, Justin Lemkul  wrote:
>>>
>>>

 On 7/3/14, 6:34 PM, gromacs query wrote:

  Hi Justin
>
> Sorry, I should have mentioned that I used -cpi : here is my mdrun
> command
> after tpbconv
>
>
> tpbconv_mpi -s npt.tpr -o npt_new.tpr -extend 250
>
>
> mdrun_mpi -s npt_new.tpr -o traj.trr -e ener.edr -c conf_prev.gro -g
> md.log
> -cpo state_new.cpt -cpi state_prev.cpt
>
>
>  The .log file will have details of what is going on.  If the run
 proceeded
 from 0-500 ps, the input .cpt file was not read.

 -Justin



  On Thu, Jul 3, 2014 at 11:07 PM, Justin Lemkul 
> wrote:
>
>
>
>> On 7/3/14, 6:05 PM, gromacs query wrote:
>>
>>   Hi All
>>
>>>
>>> I generated my npt.tpr with:
>>>
>>>
>>> tinit=0
>>>
>>> dt=0.002
>>>
>>> nsteps=125000
>>>
>>> I am trying to extend simulation for 250 ps like this:
>>>
>>> tpbconv_mpi -s npt.tpr -o npt_new.tpr -extend 250
>>>
>>>
>>> But when I used this npt_new.tpr simulation it ran for 500 ps. Have I
>>> missed something?
>>>
>>>
>>>   If you simply pass npt_new.tpr to mdrun, that's what you should
>>> expect.
>>>
>>If you use mdrun -cpi to pick up from the last checkpoint at 250
>> ps,
>> then
>> you'll get an extended run instead of one that starts from t = 0.
>>
>>
>>
>>   Also one more thing why the Gromacs user archive search engine does
>> not
>>
>>> work like before?
>>>
>>>
>>>   The Nabble archive?  It was disabled months ago.
>>>
>>
>> -Justin
>>
>> --
>> ==
>>
>> Justin A. Lemkul, Ph.D.
>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>
>> Department of Pharmaceutical Sciences
>> School of Pharmacy
>> Health Sciences Facility II, Room 601
>> 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 601
 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 601
>> University of Maryland, Baltimore
>> 20 Penn St.
>> Balt

[gmx-users] 答复: -extend problem

[#ZHANG HAIPING#]

Dear gromacs users:
Can anyone tell me why  the total potential energy initially rises rapidly 
after which it relaxes again during a MD simulaiton? Thanks.



Best regards,

发件人: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 代表 gromacs query 

发送时间: 2014年7月4日 7:56
收件人: Discussion list for GROMACS users
主题: Re: [gmx-users] -extend problem

Hi

Sorry I think I found the error. I was using wrong name of -cpi file. But
its strange that mdrun does not  complain even if it could not find the
file and it still ran the job.




On Fri, Jul 4, 2014 at 12:31 AM, gromacs query 
wrote:

> Hi Justin
>
> Indeed this key word 'Reading checkpoint file" is missing. I noted that I
> used same command in CPU (for other system) it was working fine. But now am
> running on GPU with same command and cpt file is not read. Dont know whats
> happening. Please suggest
>
> regards
>
>
> On Thu, Jul 3, 2014 at 11:58 PM, Justin Lemkul  wrote:
>
>>
>>
>> On 7/3/14, 6:51 PM, gromacs query wrote:
>>
>>> Hi
>>>
>>> forgive my ignorance but I could not find whether my cpt was read
>>> successfully or not as I dont see anything in log file as which files
>>> were
>>> taken as input. Or any keyword I should search for?
>>>
>>>
>> If the .cpt file was read, it will say "Reading checkpoint file" just
>> after the input settings list and before the DD information.
>>
>>
>> -Justin
>>
>>
>>> On Thu, Jul 3, 2014 at 11:36 PM, Justin Lemkul  wrote:
>>>
>>>

 On 7/3/14, 6:34 PM, gromacs query wrote:

  Hi Justin
>
> Sorry, I should have mentioned that I used -cpi : here is my mdrun
> command
> after tpbconv
>
>
> tpbconv_mpi -s npt.tpr -o npt_new.tpr -extend 250
>
>
> mdrun_mpi -s npt_new.tpr -o traj.trr -e ener.edr -c conf_prev.gro -g
> md.log
> -cpo state_new.cpt -cpi state_prev.cpt
>
>
>  The .log file will have details of what is going on.  If the run
 proceeded
 from 0-500 ps, the input .cpt file was not read.

 -Justin



  On Thu, Jul 3, 2014 at 11:07 PM, Justin Lemkul 
> wrote:
>
>
>
>> On 7/3/14, 6:05 PM, gromacs query wrote:
>>
>>   Hi All
>>
>>>
>>> I generated my npt.tpr with:
>>>
>>>
>>> tinit=0
>>>
>>> dt=0.002
>>>
>>> nsteps=125000
>>>
>>> I am trying to extend simulation for 250 ps like this:
>>>
>>> tpbconv_mpi -s npt.tpr -o npt_new.tpr -extend 250
>>>
>>>
>>> But when I used this npt_new.tpr simulation it ran for 500 ps. Have I
>>> missed something?
>>>
>>>
>>>   If you simply pass npt_new.tpr to mdrun, that's what you should
>>> expect.
>>>
>>If you use mdrun -cpi to pick up from the last checkpoint at 250
>> ps,
>> then
>> you'll get an extended run instead of one that starts from t = 0.
>>
>>
>>
>>   Also one more thing why the Gromacs user archive search engine does
>> not
>>
>>> work like before?
>>>
>>>
>>>   The Nabble archive?  It was disabled months ago.
>>>
>>
>> -Justin
>>
>> --
>> ==
>>
>> Justin A. Lemkul, Ph.D.
>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>
>> Department of Pharmaceutical Sciences
>> School of Pharmacy
>> Health Sciences Facility II, Room 601
>> 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 601
 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] Inter-hydrogen bond half life

[sidra rafi]

i ran 50ns antibody-antigen MD simulation. now i want to calculate
inter-hydrogen bond half life (only those hydrogen bond half life that
makes between antibody and antigen). how i can calculate and interpret it?

Thanks for any help

With best regards,

SIDRA RAFI,

Jr.Research Fellow,P-103
Email: sidraraf...@gmail.com, sidra.r...@iccs.edu
Dr. Panjwani Center for Molecular Medicine and Drug Research,
International Center for Chemical and Biological Sciences,
University of Karachi
www.iccs.edu/pcmd/index.php
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Re: [gmx-users] Graphene topology file

[#SUKRITI GUPTA#]

Dear Justin and Abhijit,

Thanks a lot for your help. Now I am able to make the topology file but while 
doing grompp for energy minimisation its not taking the dihedral values on its 
own.

Regards
Sukriti


Sukriti Gupta (Ms) | PhD Student | Energy Research Institute @ NTU (ERI@N) | 
Nanyang Technological University
Interdisciplinary Graduate School | Office: N1.3-B4-14, 62 Nanyang Drive, 
Singapore(637459)
Tel: (65) 81164191 GMT+8h | Email:sukriti...@e.ntu.edu.sg | Web:erian.ntu.edu.sg


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

Sent: Thursday, July 3, 2014 6:43 PM
To: gmx-us...@gromacs.org; vvcha...@gmail.com
Subject: Re: [gmx-users] Graphene topology file

Hi Sukriti,
 Copy the oplsaa.ff directory to your working directory. Then in
ffnonbonded.itp file add the following lines..
 opls_995   C  612.01100 0.000   A3.4e-01
3.61200e-01
 opls_996   C  612.01100 0.000   A3.4e-01
3.61200e-01
 opls_997   C  612.01100 0.000   A3.4e-01
3.61200e-01

Then in   atomname2type.n2t file add the following lines.
Copls_9950  12.011  2C  0.142  C 0.142
Copls_9960  12.011  3C  0.142  C 0.142  C 0.142
Copls_9970  12.011  1C  0.142

Then use g_x2top. This will work.

Thanks
 Abhijit


On Thu, Jul 3, 2014 at 3:11 PM, Dr. Vitaly Chaban 
wrote:

> Graphene topology is like for tube, so
>
> C  C
> C ... C ... C
> C  C  C   C
>
> to the N2T file and you are done.
>
>
> Dr. Vitaly V. Chaban
>
>
> On Wed, Jul 2, 2014 at 5:29 PM, Justin Lemkul  wrote:
> >
> >
> > On 7/2/14, 9:56 AM, #SUKRITI GUPTA# wrote:
> >>
> >> Dear all,
> >>
> >>
> >> I want to simulate graphite in water, for which i am trying to create a
> >> topology file for graphite. As its .rtp file cannot be written
> correctly, i
> >> tried to use g_x2top command following the steps given in following
> >> tutorial.
> >>
> >> http://chembytes.wikidot.com/grocnt
> >>
> >>
> >> But I think this tutorial is quite old and hence suitable for older
> >> version of gromacs as it still uses FF.dat file. Moreover if i am
> trying to
> >> make a new forcefield directory with name graphite_oplsaa containing the
> >> modified files like .n2t,.rtp and .itp, its giving me an error that
> "Could
> >> not find force field 'graphite_oplsaa' in current directory, install
> tree or
> >> GMXDATA path". When I try to add this forcefield in original path ie.
> >> user/share/gromacs/top, it does not allow me to do that as i am not the
> >> administrator. Can anyone please let me know how to create the topology
> >> file. I require 3 graphene sheets with pbc. I have created the .pdb file
> >> using nanobuilder in vmd.
> >>
> >
> > The tutorial is indeed outdated but the logic is fairly sound.  You don't
> > have to modify anything in $GMXLIB (system-wide); you can just create an
> > .n2t file in the working directory and it will override the one at the
> force
> > field level.
> >
> > -Justin
> >
> > --
> > ==
> >
> > Justin A. Lemkul, Ph.D.
> > Ruth L. Kirschstein NRSA Postdoctoral Fellow
> >
> > Department of Pharmaceutical Sciences
> > School of Pharmacy
> > Health Sciences Facility II, Room 601
> > 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.
> --
> 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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>



--
Abhijit kayal
Research Scholar
Theoretical Chemistry
IIT Kanpur
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[gmx-users] why the energy items in gromacs is different from charmm?

[wliu]

Hi,

I have a following issue:
I use the force field CHARMM22-CMAP (that is charmm27-CMAP) in 
gromacs to calculate the chignolin.pdb, I want to know the energy items 
of just this one conformation. I choose to run a very simple md, just 
one step. my input file writes as follows:


md.mdp
emtol= 10
emstep   = 0.001
niter= 1
fcstep   = 0
nstcgsteep   = 1000
nbfgscorr= 10
rtpi = 0.05
nstxout  = 0
nstvout  = 0
nstfout  = 0
nstlog   = 100
nstcalcenergy= -1
nstenergy= 10
nstxtcout= 100
xtc-precision= 1000
energygrps   = System


And I also use CHARMM with the same force field CHARMM22-CMAP, but the 
enerCHARMM.pl command to calculate chignolin's energy items. But I found 
that their results are quite different. I'd like to list below:


  charmm22 gromacs/md22
chignolin(kcal/mol)
angles 20.9848   /
bonds  22.7760195.141
cmap   -0.0595 -0.0684
dihedrals  46.0533   /
elec   19.5690   /
impropers   0.0002  0.014
total  453415.3682 201520.813
ureyb   2.7128 38.779
vdwaals453303.3316   /
proper dihedral  / 46.478
LJ-14/ 82.409
Coulomb-14   /650.335
LJ (SR)  / 201106.699
Coulomb (SR) /   -598.990


torsion45.994  46.4236
=  -0.0595 =   -0.0684
 + 46.0533  +  46.478
 +  0.0002  +   0.014   ( I 
have Unified their unit to kcal/mol)


I want to know why their results shown such a difference? I also use 
step=0 and minimization method to try, but nearly the same result. 
Theoretically，Two different MD programs calculating one same structure 
should give out the results which differ no more than 0.01kcal/mol, but, 
this makes me confused. So could you please help me find where the 
problem is or the reasons?

Thank you!

Looking forward to your kind reply！


Sincerely yours,
Wei Liu，

w...@itcs.ecnu.edu.cn
East China Normal University
ShangHai，china，200062


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Re: [gmx-users] problem with calculating angles and dynamic selections

[Teemu Murtola]

No, this is not a bug, but a result of a conscious design. Internally, the
selections are always evaluated as sets of atoms, which are (currently)
handled as a sorted list of indices. So any basic selection operation
always results in sorted atoms. If you want something else, you can use
"permute", "merge" or "plus" (which is only necessary for those few tools
that put significance to the order of atoms).

In addition to simplifying the implementation, this is much clearer. Or
what order would you expect the atoms to be if you provide a selection
"name C A B", and your system has 10 A atoms, 5 B atoms and 3 C atoms? How
about if the system has molecules with multiple residues (so that splitting
by molecule or by residue results in different ordering)? Or if you combine
two arbitrary unsorted expressions with "and" or "or"?
On Jul 3, 2014 8:04 PM, "Venkat Reddy"  wrote:

> Hi,
> I have tried gmx gangle -g1 angle option. Its sorting the atoms specified
> in the input. I think it might be a bug. gmx gangle  -g1 vector -g2 vector
> is doing fine.
>
>
> On Thu, Jul 3, 2014 at 7:42 PM, gigo  wrote:
>
> > Hi!
> > I find it impossible to calculate (some) angles between atoms using
> > dynamic selection in 'gmx gangle' command. The problem is, that the
> dynamic
> > selection mechanism persistently sorts numbers of atoms specified in the
> > input. So, if I have atoms A, B and C with ascending indexes, I am not
> able
> > to calculate angle B-A-C - I only get value for A-B-C, no matter how I
> > order them in the command line. Is there any way to do it without writing
> > an index file (which I have to parse anyway, because the same mechanism
> > sorts atoms in 'gmx select'...)? If not, I will submit a feature request
> on
> > redmine - something like -nosort option...
> > Regards,
> >
> > Grzegorz Wieczorek
> > --
> > 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.
> >
>
>
>
> --
> With Best Wishes
> Venkat Reddy Chirasani
> PhD student
> Laboratory of Computational Biophysics
> Department of Biotechnology
> IIT Madras
> Chennai
> INDIA-600036
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> Gromacs Users mailing list
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[gmx-users] regarding group selection in output

[RINU KHATTRI]

hello every one now i am in

trjconv -s em.tpr -f dppc128.gro -o dppc128_whole.gro -pbc mol -ur compact

this command but in out put they are asking

Will write gro: Coordinate file in Gromos-87 format
Reading file em.tpr, VERSION 4.5.5 (single precision)
Reading file em.tpr, VERSION 4.5.5 (single precision)
Select group for output
Group 0 ( System) has 14036 elements
Group 1 (  Other) has  6656 elements
Group 2 (   POPC) has  6656 elements
Group 3 (  Water) has  7380 elements
Group 4 (SOL) has  7380 elements
Group 5 (  non-Water) has  6656 elements

 i am unable to understand which group to select

is this command is ok or i have to use set of command to center or
jump the ligand

kindly help
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Re: [gmx-users] Graphene topology file

[abhijit Kayal]

Hi Sukriti,
   Can you tell me the g_x2top command you have given and the grompp output.

Thanks
Abhijit


On Fri, Jul 4, 2014 at 10:01 AM, #SUKRITI GUPTA# 
wrote:

> Dear Justin and Abhijit,
>
> Thanks a lot for your help. Now I am able to make the topology file but
> while doing grompp for energy minimisation its not taking the dihedral
> values on its own.
>
> Regards
> Sukriti
> 
>
> Sukriti Gupta (Ms) | PhD Student | Energy Research Institute @ NTU (ERI@N)
> | Nanyang Technological University
> Interdisciplinary Graduate School | Office: N1.3-B4-14, 62 Nanyang Drive,
> Singapore(637459)
> Tel: (65) 81164191 GMT+8h | Email:sukriti...@e.ntu.edu.sg | Web:
> erian.ntu.edu.sg
>
> 
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <
> gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of abhijit
> Kayal 
> Sent: Thursday, July 3, 2014 6:43 PM
> To: gmx-us...@gromacs.org; vvcha...@gmail.com
> Subject: Re: [gmx-users] Graphene topology file
>
> Hi Sukriti,
>  Copy the oplsaa.ff directory to your working directory. Then in
> ffnonbonded.itp file add the following lines..
>  opls_995   C  612.01100 0.000   A3.4e-01
> 3.61200e-01
>  opls_996   C  612.01100 0.000   A3.4e-01
> 3.61200e-01
>  opls_997   C  612.01100 0.000   A3.4e-01
> 3.61200e-01
>
> Then in   atomname2type.n2t file add the following lines.
> Copls_9950  12.011  2C  0.142  C 0.142
> Copls_9960  12.011  3C  0.142  C 0.142  C 0.142
> Copls_9970  12.011  1C  0.142
>
> Then use g_x2top. This will work.
>
> Thanks
>  Abhijit
>
>
> On Thu, Jul 3, 2014 at 3:11 PM, Dr. Vitaly Chaban 
> wrote:
>
> > Graphene topology is like for tube, so
> >
> > C  C
> > C ... C ... C
> > C  C  C   C
> >
> > to the N2T file and you are done.
> >
> >
> > Dr. Vitaly V. Chaban
> >
> >
> > On Wed, Jul 2, 2014 at 5:29 PM, Justin Lemkul  wrote:
> > >
> > >
> > > On 7/2/14, 9:56 AM, #SUKRITI GUPTA# wrote:
> > >>
> > >> Dear all,
> > >>
> > >>
> > >> I want to simulate graphite in water, for which i am trying to create
> a
> > >> topology file for graphite. As its .rtp file cannot be written
> > correctly, i
> > >> tried to use g_x2top command following the steps given in following
> > >> tutorial.
> > >>
> > >> http://chembytes.wikidot.com/grocnt
> > >>
> > >>
> > >> But I think this tutorial is quite old and hence suitable for older
> > >> version of gromacs as it still uses FF.dat file. Moreover if i am
> > trying to
> > >> make a new forcefield directory with name graphite_oplsaa containing
> the
> > >> modified files like .n2t,.rtp and .itp, its giving me an error that
> > "Could
> > >> not find force field 'graphite_oplsaa' in current directory, install
> > tree or
> > >> GMXDATA path". When I try to add this forcefield in original path ie.
> > >> user/share/gromacs/top, it does not allow me to do that as i am not
> the
> > >> administrator. Can anyone please let me know how to create the
> topology
> > >> file. I require 3 graphene sheets with pbc. I have created the .pdb
> file
> > >> using nanobuilder in vmd.
> > >>
> > >
> > > The tutorial is indeed outdated but the logic is fairly sound.  You
> don't
> > > have to modify anything in $GMXLIB (system-wide); you can just create
> an
> > > .n2t file in the working directory and it will override the one at the
> > force
> > > field level.
> > >
> > > -Justin
> > >
> > > --
> > > ==
> > >
> > > Justin A. Lemkul, Ph.D.
> > > Ruth L. Kirschstein NRSA Postdoctoral Fellow
> > >
> > > Department of Pharmaceutical Sciences
> > > School of Pharmacy
> > > Health Sciences Facility II, Room 601
> > > 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.
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
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> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-requ...@gromacs.org.
> >
>
>
>
> --
> Abhijit kayal
> Research Scholar
> Theoretical Chemistry
> IIT Kanpur
> --
> Gromacs Users maili