Re: [gmx-users] -t option?

[Hadi Rahmaninejad]

Thanks Mehdi,

Best,
Hadi

On Wed, Sep 18, 2019 at 12:38 PM Mahdi Bagherpoor 
wrote:

> Hi Hadi,
>
> It is well explained in Gromacs tutorial, in the below:
> http://www.mdtutorials.com/gmx/lysozyme/07_equil2.html
>
> "Note that we are now including the -t flag to include the checkpoint file
> from the *NVT* equilibration"
>
> Cheers,
> Mahdi
> On Wed, Sep 18, 2019 at 5:43 PM Hadi Rahmaninejad 
> wrote:
>
> > Hello dear users,
> >
> > I am going to run a simulation according to a tutorial, but there is an
> > option of "-t nvt.cpt" that I don't know what is it, and I couldn't find
> > any explanation for that. I appreciate if any of you can give me a short
> > description of what is that doing,
> >
> > Best wishes,
> > Hadi
> > --
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> >
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Re: [gmx-users] Tetrahedral Order Parameter

[Dallas Warren]

I can't provide advice directly, but more generally ... try things out,
experiment. All it takes is a bit of time and it will help you get a better
understanding of how things work. Plus you will get further faster doing it
yourself, rather than waiting a day or two for someone else to respond with
some help, which may or may not be exactly what you are after. If you still
can't figure it out, post exactly what you have done, what the output was,
how it deviated from what expected etc.

Plus you should be able to find a few instances of others using the command
via a web search.

Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.war...@monash.edu
-
When the only tool you own is a hammer, every problem begins to resemble a
nail.


On Thu, 19 Sep 2019 at 06:36, m g  wrote:

> Dear Justi,I want to calculate the Tetrahedral Order Parameter (Q) for
> water in my simulation system. I used "gmx hydorder" command but it is not
> clear for me. what kinds of flag must be use exactly? how can I set correct
> number for "-sgang1 and -sgang2" flags? This command is very confusing. how
> can I get Q?Thanks,Sana
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[gmx-users] Tetrahedral Order Parameter

[m g]

Dear Justi,I want to calculate the Tetrahedral Order Parameter (Q) for water in 
my simulation system. I used "gmx hydorder" command but it is not clear for me. 
what kinds of flag must be use exactly? how can I set correct number for 
"-sgang1 and -sgang2" flags? This command is very confusing. how can I get 
Q?Thanks,Sana
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Re: [gmx-users] -t option?

[Mahdi Bagherpoor]

Hi Hadi,

It is well explained in Gromacs tutorial, in the below:
http://www.mdtutorials.com/gmx/lysozyme/07_equil2.html

"Note that we are now including the -t flag to include the checkpoint file
from the *NVT* equilibration"

Cheers,
Mahdi
On Wed, Sep 18, 2019 at 5:43 PM Hadi Rahmaninejad 
wrote:

> Hello dear users,
>
> I am going to run a simulation according to a tutorial, but there is an
> option of "-t nvt.cpt" that I don't know what is it, and I couldn't find
> any explanation for that. I appreciate if any of you can give me a short
> description of what is that doing,
>
> Best wishes,
> Hadi
> --
> 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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> send a mail to gmx-users-requ...@gromacs.org.
>
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[gmx-users] -t option?

[Hadi Rahmaninejad]

Hello dear users,

I am going to run a simulation according to a tutorial, but there is an
option of "-t nvt.cpt" that I don't know what is it, and I couldn't find
any explanation for that. I appreciate if any of you can give me a short
description of what is that doing,

Best wishes,
Hadi
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Re: [gmx-users] Amber 14SB force-field problem with residue HID

[Kevin]

Thank you Justin for your reply. I totally understand the risk of using a
user-contributed force-field. And that is why I am trying to fix it (and
test it). Then I rather put my question more as a force-field building
question, asking how pdb2gmx generates the list of impropers from the
topology. Hope you could share your experience on this so I could fix it by
myself.

Thanks,
Kevin

On Thu, 12 Sep 2019 at 19:08, Kevin  wrote:

> Dear Users,
>
> I have encountered a problem with the Amber force-field downloaded from
> http://www.gromacs.org/Downloads/User_contributions/Force_fields.
> Whenever I feed this forcefield to pdb2gmx and get a residue HID for
> protein topology, it will cause error message: "No default Proper Dih.
> types". This error can simply be solved by swapping the second and third
> indices on the line number given with the error message.
>
> I tried to dig into the reason behind this error. First, the error line
> contains atomtypes in a sequence of "CT  CC  CV  NA" which CANNOT be found
> in ffbonded.itp. Instead, "CT  CV  CC  NA" can be found in ffbonded.itp and
> I guess that is why my solution worked. However, when I look at the
> topology of HID, I was confused:
>
> [ impropers ]
> -CCA N H
> CA+N C O
> CG   CE1   ND1   HD1
> CG   NE2   CD2   HD2
>ND1   NE2   CE1   HE1
>ND1   CD2CGCB
>
> Converting from atom name to atomtypes, there is no either "CT  CC  CV
> NA" or "CT  CV  CC  NA" in impropers. However, "ND1   CD2CGCB" is
> very likely to be the folk just written in a reversed sequence. More
> interestingly, I gave a try on the Amber ff99*-ILDN forcefield, the HID
> topology appears to be nearly the same but no error message was produced.
> The error was always found in the second [dihedrals] block, so I assume it
> is referred to impropers. That gave me two questions:
> 1. How does impropers be constructed by pdb2gmx?
> 2. Why different forcefields seem to give different sequence of atomtypes
> for imporpers.
>
> In fact, Q2 makes absolutely no sense, so I think I must be missing
> something.
>
> Any comment is greatly appreciated.
>
> Regards,
> Kevin
> The Ohio State University
>
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[gmx-users] gmx trjorder help

[Pandya, Akash]

Hi,


I used gmx trjorder to order my ligand molecules based on the distance from the 
COM of my protein using the command below:

gmx trjorder -f Traj.gro -s Traj.tpr -n ProteinLIG.ndx -o ordered.gro -nshell 
nshell1.xvg -b 2 -e 2 -na 10 -r 0.5



I viewed the nshell1.xvg file to see how many ligand molecules were found 
within the shell at a particular time. I know in the gromacs manual it says 
"When an index group of the first n waters is made, the ordered trajectory can 
be used with any GROMACS program to analyze the n closest waters". I presume 
that I can use this for my ligand molecules too.

The problem I have with this is the "ordered" trajectory file contains all the 
ligand molecules even the ones not within the cut-off. Can anybody help with 
this?


Akash

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Re: [gmx-users] RAM usage of gmx msd

[Mark Abraham]

Hi,

It's likely that using the same index file is the problem. The numbers it
contains are interpreted relative to the tpr file, so if you make a subset
of the tpr file, then it's on you to understand whether the necessary
indices have changed or not.

Mark

On Tue, 17 Sep 2019 at 14:58, Martin Kern 
wrote:

> Hi John,
>
> thanks for your answer. The mdrun_key_atoms.xtc FILE is only around 500
> MB in size. But the issue here wasn't RAM usage but a segmentation
> fault. gmx msd requires a tpr file and I guess that my tpr and xtc files
> didn't fit together. Skipping frames might work without the need of a
> modified tpr file. I'll try that tomorrow.
>
> Am 17.09.2019 um 12:09 schrieb John Whittaker:
> > Hi Martin,
> >
> >
> >> Hello everyone.
> >>
> >> I simulated a cell membrane and would like to calculate lateral
> >> diffusion of lipids. I tried this using the gmx msd command.
> >> Unfortunately this uses enormous amounts of RAM. The process runs
> >> without error until it is killed by the operating system. No output file
> >> is created at that time.
> >>
> >> The membrane contains around 400 lipids and I simulated for 1100ns which
> >> is 22 frames. The total size of the xtc file is around 150 GB. I use
> >> GROMACS 2016.4 with GPU support. The command I used was:
> >> gmx msd -s mdrun.tpr -f mdrun.xtc -n key_atoms.ndx -lateral z -o
> >> lateraal_diffusion.xvg
> >>
> >> I found an old email that also mentions the high RAM usage of gmx msd
> >> but it didn't get a reply.
> >>
> https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2018-January/118014.html
> >>
> >> I also tried reducing the RAM usage by creating a trajectory that only
> >> includes the key atoms. This attempt resulted in a segmentation fault.
> >> Here is what I tried:
> >> gmx trjconv -f mdrun.xtc -n key_atoms.ndx -o mdrun_key_atoms.xtc
> >> gmx convert-tpr -f mdrun.tpr -n key_atoms.ndx -o mdrun_key_atoms.tpr
> >> gmx msd -s mdrun_key_atoms.tpr -f mdrun_key_atoms.xtc -n key_atoms.ndx
> >> -lateral z -o lateraal_diffusion.xvg
> > How big is the "mdrun_key_atoms.xtc" trajectory? It's possible that this
> > file is still too large for the amount of RAM available on your machine.
> >
> > Are you able to break this trajectory down into smaller chunks that are
> > more manageable? You could also use the -skip or -dt options of gmx
> > trjconv in order to write only every "n" frames.
> >
> > Hope this helps,
> >
> > John
> >
> >
> >> I'm grateful for any suggestion.
> >>
> >> Best regards
> >> Martin Kern
> >>
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> >
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[gmx-users] SIMD options - detection program issue

[Stefano Guglielmo]

 Hi all,
an update, hopefully the last one, I have been annoying you for too long.
I decided to replace centOS with Mint 19.2. I compiled Gromacs 2019.2,
setting -DGMX_SIMD=AUTO resulted again in the same error of compilation of
detect program (Did not detect build CPU vendor - detection program did not
compile - Detection for best SIMD instructions failed, using SIMD - None --
SIMD instructions disabled). So I set manually -DGMX_SIMD to avx2_128 or
avx2_256. The compilation worked fine and I tried to run the two
simulations in parallel on the two gpus
(gmx mdrun -deffnm run -nb gpu -pme gpu -ntomp 28 -ntmpi 1 -npme 0
-gputasks 00 -pin on -pinoffset 0 -pinstride 1
plus
gmx mdrun -deffnm run2 -nb gpu -pme gpu -ntomp 28 -ntmpi 1 -npme 0
-gputasks 11 -pin on -pinoffset 28 -pinstride 1)
and in both cases the system proved stable without any crash. Maybe the old
kernel of centos (3.10) was not that smart in managing the cpu (I also
found some posts on the web regarding issues of threadripper 2990wx and
centos).
Still I can not find an explanation of the compilation error of detect
program.
Anyway, thanks to all of you for sharing suggestions and opinions,
Stefano


-- 
Stefano GUGLIELMO PhD
Assistant Professor of Medicinal Chemistry
Department of Drug Science and Technology
Via P. Giuria 9
10125 Turin, ITALY
ph. +39 (0)11 6707178



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