Re: [gmx-users] wt% of the solvent

[ISHRAT JAHAN]

Hi,
You have to calculate the number of alcohol and water molecules in the box
and use genbox command with -nmol option.In -nmol put number of alcohol
molecule and from the output of genbox command remove the extra number of
water molecules with the calculated one.


On Sun, Apr 2, 2017 at 12:34 AM, Sam Dav  wrote:

> Hello GROMACS users.
> I'm trying to solvate a polymer in (20 wt% alcohol +80 wt% water)
> which command should I use to get the correct percentage? I'm using linux.
> or should I calculate the number of molecules in the box.
> Thanks in advance
> --
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[gmx-users] Regarding PBC

[Dilip H N]

Hello,

I ran a energy minimization followed by nvt, npt, md simulation...and
during analysis, if i look my .gro file  structure in vmd and i write in
tkconsole as pbc box and see that *some  of the molecules are not inside
the box, they have been outside the box*, is there anything wrong..?? how
can i knw about this..?? any  influence of PBCetc.,

how can i clear all these doubts..?? is there any prescribed
book/references for it...thn it would help a lot...

-- 
With Best Regards,

DILIP.H.N
Ph.D Student



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Re: [gmx-users] Regarding topology creation

[Mark Abraham]

Hi,

pdb2gmx needs to know whether you intend a residue with a different number
to be a new molecule, or not. There's a standard TER field in PDB that can
be used to do that (and pdb2gmx has some command-line options that tune
that and related behaviour).

It's a bit more efficient to make an .itp for a single glycine, and craft
your .top with it by hand, than to make pdb2gmx recognize and construct an
identical topology for each glycine molecule.

Mark

On Sun, Apr 2, 2017 at 7:44 PM Dilip H N  wrote:

> Thank you Peter for replying..
>
> But i didnt get u ...whn i gave the gmx pdb2gmx command for one glycine
> molecule with the same above residue, it was able to create a topology file
> in Charmm FF, but with more no. of glycine molecules it is showing error..
> can u kindly explain bit ...is there any link that i should give between
> one glycine with another glycine molecule..in pdb.?? or
>
> n molecules of glycine.pdb...my 2nd glycine molecule starts with Atom
> 11 and continues...
>
> ATOM  1  N   GLY
>
> ATOM  2  H1  GLY
>
> ATOM  3  H2  GLY
>
> ATOM  4  H3  GLY
>
> ATOM  5  CA  GLY
>
> ATOM  6  HA1 GLY
>
> ATOM  7  HA2 GLY
>
> ATOM 8 C GLY
>
> ATOM  9  OT1 GLY
>
> ATOM 10  OT2 GLY
>
> ATOM 11  N   GLY
>
> ATOM 12  H1  GLY.
>
>
>
>
>
>    Sent with Mailtrack
> <
> https://mailtrack.io/install?source=signature=en=cy16f01.di...@nitk.edu.in=22
> >
>
> On Sun, Apr 2, 2017 at 9:21 PM, Peter Stern 
> wrote:
>
> > Hi,
> >
> > OT1 and OT2 are only for the C-terminal amino acids and for one glycine
> it
> > is both N-terminal and C-terminal.
> > For everything else you need to use change it to O.
> > You will have the same problem with H1, etc.  Except for N-terminal aa it
> > needs to be HN.
> >
> > Regards,
> > Peter
> >
> >
> > -Original Message-
> > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:
> > gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Dilip H
> N
> > Sent: Sunday, April 02, 2017 6:23 PM
> > To: gromacs.org_gmx-users@maillist.sys.kth.se
> > Subject: [gmx-users] Regarding topology creation
> >
> > Hello,
> > I want to create a topology for n glycine molecules
> > I have 1 glycine molecule and in charmm FF i am able to get the topology
> > of 1glycine molecule, but now i have few more glycine molesules in .pdb
> > format, but if i give the command gmx pdb2gmx -f gly.pdb -o gly.gro it
> > shows the following error..
> > Fatal error:
> > Atom OT1 in residue GLY 1 was not found in rtp entry GLY with 9 atoms
> > while sorting atoms.
> >
> > But when i gave the same command for 1 glycine molecule to create the
> > topology, the topology file was created, but now it is not creating (for
> > more glycine molecules).. why is this happening.?? since the same OT1 is
> > also present in 1 glycine molecule, why is the above error message coming
> > for more molecules..??
> >
> > here is the 1 molecule glycine.pdb (only residue)
> >
> > ATOM  1  N   GLY
> >
> > ATOM  2  H1  GLY
> >
> > ATOM  3  H2  GLY
> >
> > ATOM  4  H3  GLY
> >
> > ATOM  5  CA  GLY
> >
> > ATOM  6  HA1 GLY
> >
> > ATOM  7  HA2 GLY
> >
> > ATOM 8 C GLY
> >
> > ATOM  9  OT1 GLY
> >
> > ATOM 10  OT2 GLY
> >
> > Thank you
> >
> > --
> > With Best Regards,
> >
> > DILIP.H.N
> > Ph.D Student
> >
> >
> >
> >    Sent with Mailtrack <
> > https://mailtrack.io/install?source=signature=en;
> > referral=cy16f01.di...@nitk.edu.in=22>
> > --
> > Gromacs Users mailing list
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> > send a mail to gmx-users-requ...@gromacs.org.
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> > send a mail to gmx-users-requ...@gromacs.org.
> >
>
>
>
> --
> With Best Regards,
>
> DILIP.H.N
> Ph.D Student
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Re: [gmx-users] Regarding topology creation

[Dilip H N]

Thank you Peter for replying..

But i didnt get u ...whn i gave the gmx pdb2gmx command for one glycine
molecule with the same above residue, it was able to create a topology file
in Charmm FF, but with more no. of glycine molecules it is showing error..
can u kindly explain bit ...is there any link that i should give between
one glycine with another glycine molecule..in pdb.?? or

n molecules of glycine.pdb...my 2nd glycine molecule starts with Atom
11 and continues...

ATOM  1  N   GLY

ATOM  2  H1  GLY

ATOM  3  H2  GLY

ATOM  4  H3  GLY

ATOM  5  CA  GLY

ATOM  6  HA1 GLY

ATOM  7  HA2 GLY

ATOM 8 C GLY

ATOM  9  OT1 GLY

ATOM 10  OT2 GLY

ATOM 11  N   GLY

ATOM 12  H1  GLY.





   Sent with Mailtrack


On Sun, Apr 2, 2017 at 9:21 PM, Peter Stern 
wrote:

> Hi,
>
> OT1 and OT2 are only for the C-terminal amino acids and for one glycine it
> is both N-terminal and C-terminal.
> For everything else you need to use change it to O.
> You will have the same problem with H1, etc.  Except for N-terminal aa it
> needs to be HN.
>
> Regards,
> Peter
>
>
> -Original Message-
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:
> gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Dilip H N
> Sent: Sunday, April 02, 2017 6:23 PM
> To: gromacs.org_gmx-users@maillist.sys.kth.se
> Subject: [gmx-users] Regarding topology creation
>
> Hello,
> I want to create a topology for n glycine molecules
> I have 1 glycine molecule and in charmm FF i am able to get the topology
> of 1glycine molecule, but now i have few more glycine molesules in .pdb
> format, but if i give the command gmx pdb2gmx -f gly.pdb -o gly.gro it
> shows the following error..
> Fatal error:
> Atom OT1 in residue GLY 1 was not found in rtp entry GLY with 9 atoms
> while sorting atoms.
>
> But when i gave the same command for 1 glycine molecule to create the
> topology, the topology file was created, but now it is not creating (for
> more glycine molecules).. why is this happening.?? since the same OT1 is
> also present in 1 glycine molecule, why is the above error message coming
> for more molecules..??
>
> here is the 1 molecule glycine.pdb (only residue)
>
> ATOM  1  N   GLY
>
> ATOM  2  H1  GLY
>
> ATOM  3  H2  GLY
>
> ATOM  4  H3  GLY
>
> ATOM  5  CA  GLY
>
> ATOM  6  HA1 GLY
>
> ATOM  7  HA2 GLY
>
> ATOM 8 C GLY
>
> ATOM  9  OT1 GLY
>
> ATOM 10  OT2 GLY
>
> Thank you
>
> --
> With Best Regards,
>
> DILIP.H.N
> Ph.D Student
>
>
>
>    Sent with Mailtrack <
> https://mailtrack.io/install?source=signature=en;
> referral=cy16f01.di...@nitk.edu.in=22>
> --
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> send a mail to gmx-users-requ...@gromacs.org.
>



-- 
With Best Regards,

DILIP.H.N
Ph.D Student
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Re: [gmx-users] does gmx2016.3 support Nvidia 1080Ti?

[Mark Abraham]

Hi,

Yes, it's supported - both NVIDIA and GROMACS aim at backward
compatibility, such that new hardware will run old code. And the 10xx
series is not old with respect to the 2016 GROMACS series, either. Your
problem likely lies with coordinating driver and/or CUDA versions
appropriately, e.g. your nvidia-smi is using a driver from a different CUDA
version than is linked with GROMACS.

Mark

On Sun, Apr 2, 2017 at 6:02 PM 维维  wrote:

> Hi, gromacs users
>
>   I have installed a CUDA version  of Gromacs 2016.3 with the newst Nvidia
> 1080Ti graphic card. The  installation goes well and I see GPU support CUDA
> in version info of  Gromacs. However, I see a NOTE saying "Error occurred
> during GPU  detection: no CUDA-capable device is detected. Can not use GPU
> acceleration, will fall back to CPU kernels."
>
>
>I am quite sure that card is set on my machine, which can be firmed by
> /dev/nvidia0. Also I can see the card stat with command "nvidia-smi".
>
>
>So I am really comfused of the problem. Why gromacs can not recognize
> 1080Ti graphic card. Thank you for your generous help in advance!
> --
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[gmx-users] does gmx2016.3 support Nvidia 1080Ti?

[????]

Hi, gromacs users

  I have installed a CUDA version  of Gromacs 2016.3 with the newst Nvidia 
1080Ti graphic card. The  installation goes well and I see GPU support CUDA in 
version info of  Gromacs. However, I see a NOTE saying "Error occurred during 
GPU  detection: no CUDA-capable device is detected. Can not use GPU  
acceleration, will fall back to CPU kernels."


   I am quite sure that card is set on my machine, which can be firmed by  
/dev/nvidia0. Also I can see the card stat with command "nvidia-smi". 


   So I am really comfused of the problem. Why gromacs can not recognize  
1080Ti graphic card. Thank you for your generous help in advance!
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Re: [gmx-users] Regarding topology creation

[Peter Stern]

Hi,

OT1 and OT2 are only for the C-terminal amino acids and for one glycine it is 
both N-terminal and C-terminal.
For everything else you need to use change it to O.
You will have the same problem with H1, etc.  Except for N-terminal aa it needs 
to be HN.

Regards,
Peter


-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Dilip H 
N
Sent: Sunday, April 02, 2017 6:23 PM
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: [gmx-users] Regarding topology creation

Hello,
I want to create a topology for n glycine molecules
I have 1 glycine molecule and in charmm FF i am able to get the topology of 
1glycine molecule, but now i have few more glycine molesules in .pdb format, 
but if i give the command gmx pdb2gmx -f gly.pdb -o gly.gro it shows the 
following error..
Fatal error:
Atom OT1 in residue GLY 1 was not found in rtp entry GLY with 9 atoms while 
sorting atoms.

But when i gave the same command for 1 glycine molecule to create the topology, 
the topology file was created, but now it is not creating (for more glycine 
molecules).. why is this happening.?? since the same OT1 is also present in 1 
glycine molecule, why is the above error message coming for more molecules..??

here is the 1 molecule glycine.pdb (only residue)

ATOM  1  N   GLY

ATOM  2  H1  GLY

ATOM  3  H2  GLY

ATOM  4  H3  GLY

ATOM  5  CA  GLY

ATOM  6  HA1 GLY

ATOM  7  HA2 GLY

ATOM 8 C GLY

ATOM  9  OT1 GLY

ATOM 10  OT2 GLY

Thank you

--
With Best Regards,

DILIP.H.N
Ph.D Student



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[gmx-users] Regarding topology creation

[Dilip H N]

Hello,
I want to create a topology for n glycine molecules
I have 1 glycine molecule and in charmm FF i am able to get the topology of
1glycine molecule, but now i have few more glycine molesules in .pdb
format, but if i give the command
gmx pdb2gmx -f gly.pdb -o gly.gro
it shows the following error..
Fatal error:
Atom OT1 in residue GLY 1 was not found in rtp entry GLY with 9 atoms
while sorting atoms.

But when i gave the same command for 1 glycine molecule to create the
topology, the topology file was created, but now it is not creating (for
more glycine molecules).. why is this happening.?? since the same OT1 is
also present in 1 glycine molecule, why is the above error message coming
for more molecules..??

here is the 1 molecule glycine.pdb (only residue)

ATOM  1  N   GLY

ATOM  2  H1  GLY

ATOM  3  H2  GLY

ATOM  4  H3  GLY

ATOM  5  CA  GLY

ATOM  6  HA1 GLY

ATOM  7  HA2 GLY

ATOM 8 C GLY

ATOM  9  OT1 GLY

ATOM 10  OT2 GLY

Thank you

-- 
With Best Regards,

DILIP.H.N
Ph.D Student



   Sent with Mailtrack

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Re: [gmx-users] Calculation of configurational entropy

[David van der Spoel]

On 02/04/17 14:20, Saumyak Mukherjee wrote:

Dear Users,

I want to calculate the configurational entropy of certain water molecules
in a protein water system. Can you kindly inform me how to do it?
Basically it is not meaningful since first most water molecules are 
rigid in simulation, meaning there is only translational and rotational 
entropy, and second they will diffuse and be replace by others.



From different forums I have seen that it can be down by using g_covar and

g_anaeig programs. But I don't clearly understand the use. From this I am
getting just a single entropy value. How an I get the entropy as a function
of time?

There is no such thing.

In theory you can compute entropy over parts of a trajectory and print 
it as a function of time for each block, but those blocks need to be 
long to be meaningful.


Thanks in advance,
Saumyak




--
David van der Spoel, Ph.D., Professor of Biology
Head of Department, Cell & Molecular Biology, Uppsala University.
Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
http://www.icm.uu.se
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[gmx-users] Calculation of configurational entropy

[Saumyak Mukherjee]

Dear Users,

I want to calculate the configurational entropy of certain water molecules
in a protein water system. Can you kindly inform me how to do it?

>From different forums I have seen that it can be down by using g_covar and
g_anaeig programs. But I don't clearly understand the use. From this I am
getting just a single entropy value. How an I get the entropy as a function
of time?

Thanks in advance,
Saumyak

-- 

*Saumyak Mukherjee*

Junior Research Fellow
Prof. Biman Bagchi's Group
Solid State and Structural Chemistry Unit
Indian Institute of Science
Bangalore - 560012

Mob : 8017292426
Alternative e-mail : saumyakmukher...@gmail.com
smukher...@sscu.iisc.ernet.in

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[gmx-users] gmx mdrun

[Neha Gupta]

Hi gromacs users,


I am using Gromacs 5.1.1 in windows cygwin.

When I run long calculations my CPU switches off automatically (just before
writing the coordinate file .gro) . How to prevent this and ensure
longevity of CPU?

Running on 1 node with total 8 logical cores
Hardware detected:
  CPU info:
Vendor: AuthenticAMD
Brand:  AMD FX-8370E Eight-Core Processor
Family: 21  model:  2  stepping:  0



I also observed these in log file


SIMD instructions most likely to fit this hardware: AVX_128_FMA
 SIMD instructions selected at GROMACS compile time: SSE4.1


Binary not matching hardware - you might be losing performance.
SIMD instructions most likely to fit this hardware: AVX_128_FMA
SIMD instructions selected at GROMACS compile time: SSE4.1


The current CPU can measure timings more accurately than the code in gmx
was configured to use. This might affect your simulation speed as accurate
timings are needed for load-balancing.
Please consider rebuilding gmx with the GMX_USE_RDTSCP=ON CMake option.



Thanks,
Neha
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