Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 144, Issue 140

[Sarath Chandra]

Add the following line to your .bashrc or .cshrc

source /usr/local/gromacs/bin/GMXRC

and then everytime you open a new terminal gromacs will be auto sourced.

Regards,

Sarath

-- 
Sarath Chandra Dantu, PhD, ELS
Room No. 606, New BSBE Building
Department of Biosciences and Bioengineering
Indian Institute of Technology Bombay
Powai Mumbai, 400-076, India


On 25 April 2016 at 10:35, Roshan Shrestha  wrote:

> Sorry, I found my error, should have used DGMX .. However,  another
> problem arose after installation.  The program ran fine in that terminal by
> which I installed gromacs, but when I closed that terminal and opened
> another terminal, after typing gmx -h , it showed The program 'gmx' is
> currently not installed. You can install it by typing:
> sudo apt-get install gromacs
> I thought I properly installed gromacs, Did this problem came because I
> used
>
> source /usr/local/gromacs/bin/GMXRC
>
>
>
> On Mon, Apr 25, 2016 at 10:16 AM, Roshan Shrestha 
> wrote:
>
> > While rebuilding ,I gave the command cmake .. -GMX_USE_RDTSCP=OFF
> > But, it showed the error CMake Error: Could not create named generator
> > MX_USE_RDTSCP=OFF
> > Am I making any errors ?
> >
> > On Mon, Apr 25, 2016 at 12:18 AM, <
> > gromacs.org_gmx-users-requ...@maillist.sys.kth.se> wrote:
> >
> >> Send gromacs.org_gmx-users mailing list submissions to
> >> gromacs.org_gmx-users@maillist.sys.kth.se
> >>
> >> To subscribe or unsubscribe via the World Wide Web, visit
> >>
> >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> >> or, via email, send a message with subject or body 'help' to
> >> gromacs.org_gmx-users-requ...@maillist.sys.kth.se
> >>
> >> You can reach the person managing the list at
> >> gromacs.org_gmx-users-ow...@maillist.sys.kth.se
> >>
> >> When replying, please edit your Subject line so it is more specific
> >> than "Re: Contents of gromacs.org_gmx-users digest..."
> >>
> >>
> >> Today's Topics:
> >>
> >>1. Re: Error in mdrun (Roshan Shrestha)
> >>2. Re: Error in mdrun (Justin Lemkul)
> >>3. Re: Graphene sheet topology (soumadwip ghosh)
> >>4. Re: Gromacs-5.1.2 Checkpoint/restart example (Husen R)
> >>5. how to convert CHARMM36 system into virtual site system? (Albert)
> >>6. g_helix (leila salimi)
> >>
> >>
> >> --
> >>
> >> Message: 1
> >> Date: Sun, 24 Apr 2016 17:51:58 +0545
> >> From: Roshan Shrestha 
> >> To: gromacs.org_gmx-users@maillist.sys.kth.se
> >> Subject: Re: [gmx-users] Error in mdrun
> >> Message-ID:
> >> <
> >> cage0gtr3wn0xevdwm+hbud0u5mjprocm4oplx6odjkltmlx...@mail.gmail.com>
> >> Content-Type: text/plain; charset=UTF-8
> >>
> >> How to turn off that option ? I mean, the error cam up when I typed
> >>
> >> gmx mdrun -deffnm em -v
> >>
> >> So, what should command I use to turn off that option. Thanks
> >>
> >>
> >> On Sun, Apr 24, 2016 at 5:00 PM, Roshan Shrestha 
> >> wrote:
> >>
> >> > My CPU configuration is rather too old,
> >> > Architecture:  i686
> >> > CPU op-mode(s):32-bit, 64-bit
> >> > Byte Order:Little Endian
> >> > CPU(s):2
> >> > On-line CPU(s) list:   0,1
> >> > Thread(s) per core:1
> >> > Core(s) per socket:2
> >> > Socket(s): 1
> >> > Vendor ID: GenuineIntel
> >> > CPU family:6
> >> > Model: 15
> >> > Model name:Intel(R) Core(TM)2 Duo CPU E6750  @ 2.66GHz
> >> > Stepping:  11
> >> > CPU MHz:   2003.000
> >> > CPU max MHz:   2670.
> >> > CPU min MHz:   2003.
> >> > BogoMIPS:  5333.10
> >> > Virtualization:VT-x
> >> > L1d cache: 32K
> >> > L1i cache: 32K
> >> > L2 cache:  4096K
> >> > I installed Gromacs 5.0.6, but while running mdrun, I got the error:
> >> > Program gmx, VERSION 5.0.6
> >> > Source code file:
> >> >
> >>
> /build/gromacs-yTV9IQ/gromacs-5.0.6/src/gromacs/gmxlib/gmx_detect_hardware.c,
> >> > line: 212
> >> >
> >> > Fatal error:
> >> > The gmx executable was compiled to use the rdtscp CPU instruction.
> >> > However, this is not supported by the current hardware and continuing
> >> would
> >> > lead to a crash. Please rebuild GROMACS with the GMX_USE_RDTSCP=OFF
> >> CMake
> >> > option.
> >> > For more information and tips for troubleshooting, please check the
> >> GROMACS
> >> > website at http://www.gromacs.org/Documentation/Errors
> >> >
> >> > How to solve this problem ? Thanks.
> >> >
> >>
> >>
> >> --
> >>
> >> Message: 2
> >> Date: Sun, 24 Apr 2016 08:08:59 -0400
> >> From: Justin Lemkul 
> >> To: gmx-us...@gromacs.org
> >> Subject: Re: [gmx-users] Error in mdrun
> >> Message-ID: <571cb75b.7060...@vt.edu>
> >> Content-Type: text/plain; charset=windows-1252; 

Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 144, Issue 140

[Roshan Shrestha]

Sorry, I found my error, should have used DGMX .. However,  another
problem arose after installation.  The program ran fine in that terminal by
which I installed gromacs, but when I closed that terminal and opened
another terminal, after typing gmx -h , it showed The program 'gmx' is
currently not installed. You can install it by typing:
sudo apt-get install gromacs
I thought I properly installed gromacs, Did this problem came because I
used

source /usr/local/gromacs/bin/GMXRC



On Mon, Apr 25, 2016 at 10:16 AM, Roshan Shrestha 
wrote:

> While rebuilding ,I gave the command cmake .. -GMX_USE_RDTSCP=OFF
> But, it showed the error CMake Error: Could not create named generator
> MX_USE_RDTSCP=OFF
> Am I making any errors ?
>
> On Mon, Apr 25, 2016 at 12:18 AM, <
> gromacs.org_gmx-users-requ...@maillist.sys.kth.se> wrote:
>
>> Send gromacs.org_gmx-users mailing list submissions to
>> gromacs.org_gmx-users@maillist.sys.kth.se
>>
>> To subscribe or unsubscribe via the World Wide Web, visit
>>
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
>> or, via email, send a message with subject or body 'help' to
>> gromacs.org_gmx-users-requ...@maillist.sys.kth.se
>>
>> You can reach the person managing the list at
>> gromacs.org_gmx-users-ow...@maillist.sys.kth.se
>>
>> When replying, please edit your Subject line so it is more specific
>> than "Re: Contents of gromacs.org_gmx-users digest..."
>>
>>
>> Today's Topics:
>>
>>1. Re: Error in mdrun (Roshan Shrestha)
>>2. Re: Error in mdrun (Justin Lemkul)
>>3. Re: Graphene sheet topology (soumadwip ghosh)
>>4. Re: Gromacs-5.1.2 Checkpoint/restart example (Husen R)
>>5. how to convert CHARMM36 system into virtual site system? (Albert)
>>6. g_helix (leila salimi)
>>
>>
>> --
>>
>> Message: 1
>> Date: Sun, 24 Apr 2016 17:51:58 +0545
>> From: Roshan Shrestha 
>> To: gromacs.org_gmx-users@maillist.sys.kth.se
>> Subject: Re: [gmx-users] Error in mdrun
>> Message-ID:
>> <
>> cage0gtr3wn0xevdwm+hbud0u5mjprocm4oplx6odjkltmlx...@mail.gmail.com>
>> Content-Type: text/plain; charset=UTF-8
>>
>> How to turn off that option ? I mean, the error cam up when I typed
>>
>> gmx mdrun -deffnm em -v
>>
>> So, what should command I use to turn off that option. Thanks
>>
>>
>> On Sun, Apr 24, 2016 at 5:00 PM, Roshan Shrestha 
>> wrote:
>>
>> > My CPU configuration is rather too old,
>> > Architecture:  i686
>> > CPU op-mode(s):32-bit, 64-bit
>> > Byte Order:Little Endian
>> > CPU(s):2
>> > On-line CPU(s) list:   0,1
>> > Thread(s) per core:1
>> > Core(s) per socket:2
>> > Socket(s): 1
>> > Vendor ID: GenuineIntel
>> > CPU family:6
>> > Model: 15
>> > Model name:Intel(R) Core(TM)2 Duo CPU E6750  @ 2.66GHz
>> > Stepping:  11
>> > CPU MHz:   2003.000
>> > CPU max MHz:   2670.
>> > CPU min MHz:   2003.
>> > BogoMIPS:  5333.10
>> > Virtualization:VT-x
>> > L1d cache: 32K
>> > L1i cache: 32K
>> > L2 cache:  4096K
>> > I installed Gromacs 5.0.6, but while running mdrun, I got the error:
>> > Program gmx, VERSION 5.0.6
>> > Source code file:
>> >
>> /build/gromacs-yTV9IQ/gromacs-5.0.6/src/gromacs/gmxlib/gmx_detect_hardware.c,
>> > line: 212
>> >
>> > Fatal error:
>> > The gmx executable was compiled to use the rdtscp CPU instruction.
>> > However, this is not supported by the current hardware and continuing
>> would
>> > lead to a crash. Please rebuild GROMACS with the GMX_USE_RDTSCP=OFF
>> CMake
>> > option.
>> > For more information and tips for troubleshooting, please check the
>> GROMACS
>> > website at http://www.gromacs.org/Documentation/Errors
>> >
>> > How to solve this problem ? Thanks.
>> >
>>
>>
>> --
>>
>> Message: 2
>> Date: Sun, 24 Apr 2016 08:08:59 -0400
>> From: Justin Lemkul 
>> To: gmx-us...@gromacs.org
>> Subject: Re: [gmx-users] Error in mdrun
>> Message-ID: <571cb75b.7060...@vt.edu>
>> Content-Type: text/plain; charset=windows-1252; format=flowed
>>
>>
>>
>> On 4/24/16 8:06 AM, Roshan Shrestha wrote:
>> > How to turn off that option ? I mean, the error cam up when I typed
>> >
>> > gmx mdrun -deffnm em -v
>> >
>> > So, what should command I use to turn off that option. Thanks
>> >
>>
>> "Please rebuild GROMACS with the GMX_USE_RDTSCP=OFF CMake option."
>>
>> You have to re-compile and re-install.
>>
>> -Justin
>>
>> >
>> > On Sun, Apr 24, 2016 at 5:00 PM, Roshan Shrestha 
>> > wrote:
>> >
>> >> My CPU configuration is rather too old,
>> >> Architecture:  i686
>> >> CPU op-mode(s):32-bit, 64-bit
>> >> Byte Order:Little Endian
>> >> CPU(s):2
>> 

Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 144, Issue 140

[Roshan Shrestha]

While rebuilding ,I gave the command cmake .. -GMX_USE_RDTSCP=OFF
But, it showed the error CMake Error: Could not create named generator
MX_USE_RDTSCP=OFF
Am I making any errors ?

On Mon, Apr 25, 2016 at 12:18 AM, <
gromacs.org_gmx-users-requ...@maillist.sys.kth.se> wrote:

> Send gromacs.org_gmx-users mailing list submissions to
> gromacs.org_gmx-users@maillist.sys.kth.se
>
> To subscribe or unsubscribe via the World Wide Web, visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> or, via email, send a message with subject or body 'help' to
> gromacs.org_gmx-users-requ...@maillist.sys.kth.se
>
> You can reach the person managing the list at
> gromacs.org_gmx-users-ow...@maillist.sys.kth.se
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of gromacs.org_gmx-users digest..."
>
>
> Today's Topics:
>
>1. Re: Error in mdrun (Roshan Shrestha)
>2. Re: Error in mdrun (Justin Lemkul)
>3. Re: Graphene sheet topology (soumadwip ghosh)
>4. Re: Gromacs-5.1.2 Checkpoint/restart example (Husen R)
>5. how to convert CHARMM36 system into virtual site system? (Albert)
>6. g_helix (leila salimi)
>
>
> --
>
> Message: 1
> Date: Sun, 24 Apr 2016 17:51:58 +0545
> From: Roshan Shrestha 
> To: gromacs.org_gmx-users@maillist.sys.kth.se
> Subject: Re: [gmx-users] Error in mdrun
> Message-ID:
> <
> cage0gtr3wn0xevdwm+hbud0u5mjprocm4oplx6odjkltmlx...@mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> How to turn off that option ? I mean, the error cam up when I typed
>
> gmx mdrun -deffnm em -v
>
> So, what should command I use to turn off that option. Thanks
>
>
> On Sun, Apr 24, 2016 at 5:00 PM, Roshan Shrestha 
> wrote:
>
> > My CPU configuration is rather too old,
> > Architecture:  i686
> > CPU op-mode(s):32-bit, 64-bit
> > Byte Order:Little Endian
> > CPU(s):2
> > On-line CPU(s) list:   0,1
> > Thread(s) per core:1
> > Core(s) per socket:2
> > Socket(s): 1
> > Vendor ID: GenuineIntel
> > CPU family:6
> > Model: 15
> > Model name:Intel(R) Core(TM)2 Duo CPU E6750  @ 2.66GHz
> > Stepping:  11
> > CPU MHz:   2003.000
> > CPU max MHz:   2670.
> > CPU min MHz:   2003.
> > BogoMIPS:  5333.10
> > Virtualization:VT-x
> > L1d cache: 32K
> > L1i cache: 32K
> > L2 cache:  4096K
> > I installed Gromacs 5.0.6, but while running mdrun, I got the error:
> > Program gmx, VERSION 5.0.6
> > Source code file:
> >
> /build/gromacs-yTV9IQ/gromacs-5.0.6/src/gromacs/gmxlib/gmx_detect_hardware.c,
> > line: 212
> >
> > Fatal error:
> > The gmx executable was compiled to use the rdtscp CPU instruction.
> > However, this is not supported by the current hardware and continuing
> would
> > lead to a crash. Please rebuild GROMACS with the GMX_USE_RDTSCP=OFF CMake
> > option.
> > For more information and tips for troubleshooting, please check the
> GROMACS
> > website at http://www.gromacs.org/Documentation/Errors
> >
> > How to solve this problem ? Thanks.
> >
>
>
> --
>
> Message: 2
> Date: Sun, 24 Apr 2016 08:08:59 -0400
> From: Justin Lemkul 
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] Error in mdrun
> Message-ID: <571cb75b.7060...@vt.edu>
> Content-Type: text/plain; charset=windows-1252; format=flowed
>
>
>
> On 4/24/16 8:06 AM, Roshan Shrestha wrote:
> > How to turn off that option ? I mean, the error cam up when I typed
> >
> > gmx mdrun -deffnm em -v
> >
> > So, what should command I use to turn off that option. Thanks
> >
>
> "Please rebuild GROMACS with the GMX_USE_RDTSCP=OFF CMake option."
>
> You have to re-compile and re-install.
>
> -Justin
>
> >
> > On Sun, Apr 24, 2016 at 5:00 PM, Roshan Shrestha 
> > wrote:
> >
> >> My CPU configuration is rather too old,
> >> Architecture:  i686
> >> CPU op-mode(s):32-bit, 64-bit
> >> Byte Order:Little Endian
> >> CPU(s):2
> >> On-line CPU(s) list:   0,1
> >> Thread(s) per core:1
> >> Core(s) per socket:2
> >> Socket(s): 1
> >> Vendor ID: GenuineIntel
> >> CPU family:6
> >> Model: 15
> >> Model name:Intel(R) Core(TM)2 Duo CPU E6750  @ 2.66GHz
> >> Stepping:  11
> >> CPU MHz:   2003.000
> >> CPU max MHz:   2670.
> >> CPU min MHz:   2003.
> >> BogoMIPS:  5333.10
> >> Virtualization:VT-x
> >> L1d cache: 32K
> >> L1i cache: 32K
> >> L2 cache:  4096K
> >> I installed Gromacs 5.0.6, but while running mdrun, I got the error:
> >> Program gmx, VERSION 

[gmx-users] Standard volume of the simulation box

[Sana Saeed]

hi 
how can i find the standard volume of the simulation box, that includes ligand, 
protein and water.

 Sana Saeed Khan,
Research Assistant
Chemoinformatics Lab
Graduate Student, MS bioinfo
Department of Bioinformatics
Soongsil University, Seoul, South Korea.
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[gmx-users] g_helix

[leila salimi]

Dear all,

I have a question regarding to calculate g_helix, I am not sure about the
index numbers for using g_helix!
Should I use the all atom numbers of protein that I have? If not please
explain to me which indexes of protein I have to choose.

The same for do_dssp, I have to use the all atom numbers of protein or the
residue numbers of protein!

Thanks in advance,
Leila
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[gmx-users] how to convert CHARMM36 system into virtual site system?

[Albert]

Hello:

I've built a membrane system from CHARMM-GUI with CHARMM36 FF. I am just 
wondering how can we convert the lipids molecule to virtual site lipids?


Thank you very much

Albert
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Re: [gmx-users] Gromacs-5.1.2 Checkpoint/restart example

[Husen R]

Hi,

Thanks a lot !
I'll try it,..

Regards,


Husen

On Sun, Apr 24, 2016 at 6:54 PM, Justin Lemkul  wrote:

>
>
> On 4/24/16 12:04 AM, Husen R wrote:
>
>> Dear all,
>>
>> is there any complete documentation discussing checkpoint/restart in
>> Gromacs-5.1.2 ?
>> I found this link that discuss checkpoint (
>> http://www.gromacs.org/Documentation/How-tos/Extending_Simulations) and
>> this link that discuss restart (
>> http://www.gromacs.org/Documentation/How-tos/Doing_Restarts) but these
>> are
>> not specifically for gromacs 5.1.2.
>>
>>
> There are no differences for 5.1.2, so that information is all relevant.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
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>
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Re: [gmx-users] Graphene sheet topology

[soumadwip ghosh]

Thanks Justin as always for your prompt reply.

I have now created the graphene topology the way u suggested that is I
issued the following command

1. g_x2top -f file.gro -o graphene.top -pbc: I did not prefer to use the
-noparam option since it does not print the k0, k1 and similar values.

2. I have now started the simulation with all my mdp files (ions.mdp,
minim.mdp, nvt.mdp, npt.mdp and md.mdp) containing the "periodic
molecules=yes" line and as of now the simulation is running fine. But the
last one crashed around 25 ns showing the Lincs warnings and stuffs so
keeping my fingers crossed.

3. I am keeping the dihedral function type 1 as per your suggestion.

Please let me know if what I am doing right now as mentioned above makes
sense or not. I will update on the outcomes of my simulation even if
everything goes right.


Thanks once again for the reply Justin..:)

Soumadwip Ghosh
Senior Research Fellow
Indian Institute of Technology Bombay
India
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Re: [gmx-users] Error in mdrun

[Justin Lemkul]

On 4/24/16 8:06 AM, Roshan Shrestha wrote:

How to turn off that option ? I mean, the error cam up when I typed

gmx mdrun -deffnm em -v

So, what should command I use to turn off that option. Thanks



"Please rebuild GROMACS with the GMX_USE_RDTSCP=OFF CMake option."

You have to re-compile and re-install.

-Justin



On Sun, Apr 24, 2016 at 5:00 PM, Roshan Shrestha 
wrote:


My CPU configuration is rather too old,
Architecture:  i686
CPU op-mode(s):32-bit, 64-bit
Byte Order:Little Endian
CPU(s):2
On-line CPU(s) list:   0,1
Thread(s) per core:1
Core(s) per socket:2
Socket(s): 1
Vendor ID: GenuineIntel
CPU family:6
Model: 15
Model name:Intel(R) Core(TM)2 Duo CPU E6750  @ 2.66GHz
Stepping:  11
CPU MHz:   2003.000
CPU max MHz:   2670.
CPU min MHz:   2003.
BogoMIPS:  5333.10
Virtualization:VT-x
L1d cache: 32K
L1i cache: 32K
L2 cache:  4096K
I installed Gromacs 5.0.6, but while running mdrun, I got the error:
Program gmx, VERSION 5.0.6
Source code file:
/build/gromacs-yTV9IQ/gromacs-5.0.6/src/gromacs/gmxlib/gmx_detect_hardware.c,
line: 212

Fatal error:
The gmx executable was compiled to use the rdtscp CPU instruction.
However, this is not supported by the current hardware and continuing would
lead to a crash. Please rebuild GROMACS with the GMX_USE_RDTSCP=OFF CMake
option.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors

How to solve this problem ? Thanks.



--
==

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

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

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

==
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Re: [gmx-users] Error in mdrun

[Roshan Shrestha]

How to turn off that option ? I mean, the error cam up when I typed

gmx mdrun -deffnm em -v

So, what should command I use to turn off that option. Thanks


On Sun, Apr 24, 2016 at 5:00 PM, Roshan Shrestha 
wrote:

> My CPU configuration is rather too old,
> Architecture:  i686
> CPU op-mode(s):32-bit, 64-bit
> Byte Order:Little Endian
> CPU(s):2
> On-line CPU(s) list:   0,1
> Thread(s) per core:1
> Core(s) per socket:2
> Socket(s): 1
> Vendor ID: GenuineIntel
> CPU family:6
> Model: 15
> Model name:Intel(R) Core(TM)2 Duo CPU E6750  @ 2.66GHz
> Stepping:  11
> CPU MHz:   2003.000
> CPU max MHz:   2670.
> CPU min MHz:   2003.
> BogoMIPS:  5333.10
> Virtualization:VT-x
> L1d cache: 32K
> L1i cache: 32K
> L2 cache:  4096K
> I installed Gromacs 5.0.6, but while running mdrun, I got the error:
> Program gmx, VERSION 5.0.6
> Source code file:
> /build/gromacs-yTV9IQ/gromacs-5.0.6/src/gromacs/gmxlib/gmx_detect_hardware.c,
> line: 212
>
> Fatal error:
> The gmx executable was compiled to use the rdtscp CPU instruction.
> However, this is not supported by the current hardware and continuing would
> lead to a crash. Please rebuild GROMACS with the GMX_USE_RDTSCP=OFF CMake
> option.
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
>
> How to solve this problem ? Thanks.
>
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Re: [gmx-users] Graphene sheet topology

[Justin Lemkul]

On 4/23/16 1:37 AM, soumadwip ghosh wrote:

Hello all,
  I am currently working on the interaction between a flat
graphene sheet and nucleic acids at various physiological conditions. I am
using CHARMM 27 force field and GROMACS 4.5.6 for MD simulations. Here is
my work order

1. I created a graphene.top file according to the tutorial by Andrea Minoia.
2. I went upto NPT equilibration without any problem but my MDrun crashes
printing the following error (I modified the .n2t and other CHARMM 27
forcefield files according to the tutorial)

Fatal error:
25 particles communicated to PME node 4 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.

 From the mails in the mailing list I am assuming that my graphene topology
has something terribly bad since I have worked with the particular nucleic
acid in CHARMM27 and it does not have any issue. I am uploading the pdb and
itp files of my graphene sheet followed by the md.mdp and md.log file. Any
kind of help to troubleshoot this error would be greatly appreciated.

pdb file of graphene:
https://drive.google.com/open?id=0B7SBnQ5YXQSLQWVod3psQTFwSzg

graphene.itp: https://drive.google.com/open?id=0B7SBnQ5YXQSLTXlqci1aX3NzU3c

the visualization of graphene.pdb:
https://drive.google.com/open?id=0B7SBnQ5YXQSLMExiSG5GR3VIMjA

My md.mdp file:
https://drive.google.com/open?id=0B7SBnQ5YXQSLMmd1di1jbHpubFE

the md.log file I obtained:
https://drive.google.com/open?id=0B7SBnQ5YXQSLdXZDZVNDOFJqVDg

PS: I forgot to issue the -pbc while executing the g_x2top command and also
did not change the dihedral function type from 1 to 3 as suggested in the
tutorial. Can this be a reason for the above error to occur?



Your sheet appears to be periodic, so yes, you need to treat it as such (also by 
adding "periodic_molecules = yes" in the .mdp file).  Otherwise, your atoms are 
at very close distance at the box edges and things explode.


CHARMM uses periodic dihedrals, so the function type is 1 (though we usually use 
9 because CHARMM often applies multiple terms to each dihedral).  But if you 
only have one multiplicity per dihedral, type 1 is fine (and setting it to 9 
would be equivalent in this case).


-Justin

--
==

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

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

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

==
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Re: [gmx-users] Gromacs-5.1.2 Checkpoint/restart example

[Justin Lemkul]

On 4/24/16 12:04 AM, Husen R wrote:

Dear all,

is there any complete documentation discussing checkpoint/restart in
Gromacs-5.1.2 ?
I found this link that discuss checkpoint (
http://www.gromacs.org/Documentation/How-tos/Extending_Simulations) and
this link that discuss restart (
http://www.gromacs.org/Documentation/How-tos/Doing_Restarts) but these are
not specifically for gromacs 5.1.2.



There are no differences for 5.1.2, so that information is all relevant.

-Justin

--
==

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

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

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

==
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[gmx-users] md example for protein complex dissociation

[Brett]

Dear All,

Will you please show me examples that with by biological significance, a 
protein complex dissociated into its sub-unit during the md process?

Brett

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Re: [gmx-users] Error in mdrun

[Mark Abraham]

Hi,

You could try rebuilding with that option turned off :-)

Mark

On Sun, Apr 24, 2016 at 1:15 PM Roshan Shrestha  wrote:

> My CPU configuration is rather too old,
> Architecture:  i686
> CPU op-mode(s):32-bit, 64-bit
> Byte Order:Little Endian
> CPU(s):2
> On-line CPU(s) list:   0,1
> Thread(s) per core:1
> Core(s) per socket:2
> Socket(s): 1
> Vendor ID: GenuineIntel
> CPU family:6
> Model: 15
> Model name:Intel(R) Core(TM)2 Duo CPU E6750  @ 2.66GHz
> Stepping:  11
> CPU MHz:   2003.000
> CPU max MHz:   2670.
> CPU min MHz:   2003.
> BogoMIPS:  5333.10
> Virtualization:VT-x
> L1d cache: 32K
> L1i cache: 32K
> L2 cache:  4096K
> I installed Gromacs 5.0.6, but while running mdrun, I got the error:
> Program gmx, VERSION 5.0.6
> Source code file:
>
> /build/gromacs-yTV9IQ/gromacs-5.0.6/src/gromacs/gmxlib/gmx_detect_hardware.c,
> line: 212
>
> Fatal error:
> The gmx executable was compiled to use the rdtscp CPU instruction. However,
> this is not supported by the current hardware and continuing would lead to
> a crash. Please rebuild GROMACS with the GMX_USE_RDTSCP=OFF CMake option.
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
>
> How to solve this problem ? Thanks.
> --
> 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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[gmx-users] Error in mdrun

[Roshan Shrestha]

My CPU configuration is rather too old,
Architecture:  i686
CPU op-mode(s):32-bit, 64-bit
Byte Order:Little Endian
CPU(s):2
On-line CPU(s) list:   0,1
Thread(s) per core:1
Core(s) per socket:2
Socket(s): 1
Vendor ID: GenuineIntel
CPU family:6
Model: 15
Model name:Intel(R) Core(TM)2 Duo CPU E6750  @ 2.66GHz
Stepping:  11
CPU MHz:   2003.000
CPU max MHz:   2670.
CPU min MHz:   2003.
BogoMIPS:  5333.10
Virtualization:VT-x
L1d cache: 32K
L1i cache: 32K
L2 cache:  4096K
I installed Gromacs 5.0.6, but while running mdrun, I got the error:
Program gmx, VERSION 5.0.6
Source code file:
/build/gromacs-yTV9IQ/gromacs-5.0.6/src/gromacs/gmxlib/gmx_detect_hardware.c,
line: 212

Fatal error:
The gmx executable was compiled to use the rdtscp CPU instruction. However,
this is not supported by the current hardware and continuing would lead to
a crash. Please rebuild GROMACS with the GMX_USE_RDTSCP=OFF CMake option.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors

How to solve this problem ? Thanks.
-- 
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