Re: [gmx-users] MMPBSA analysis on GROMACS trajectory

[masoud keramati]

Hi
They have a web site and all of things you need is there:
http://rashmikumari.github.io/g_mmpbsa/

On Mar 27, 2017 10:15 AM, "Neha Gupta"  wrote:

> Hi gromacs users,
>
> How to calculate MMPBSA analysis on Gromacs trajectory using MMPBSA tool of
> amber software package?
>
>
> Thanks,
> Neha
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Re: [gmx-users] Installing DSSP

[masoud keramati]

Hi

follow these steps:

1)sudo wget ftp://ftp.cmbi.ru.nl/pub/software/dssp/dssp-2.2.1-linux-i386 -O
/usr/local/bin/dssp

2)sudo chmod a+x /usr/local/bin/dssp

3)export DSSP=/usr/local/bin/dssp

On Fri, Feb 3, 2017 at 3:15 PM, Mark Abraham 
wrote:

> Hi,
>
> On Fri, Feb 3, 2017 at 7:52 AM soumadwip ghosh 
> wrote:
>
> > Hello all,
> >
> > I am trying to install dssp in centos 7 for determining the secondary
> > structure of a protein in combination with do_dssp. These are the steps I
> > followed:
> >
> > 1. installation directory : /opt/apps/dssp/dssp-2.2.1/
> >
> > 2. but there is no dssp executable in the dssp-2.2.1 directory
> >
> > 3. however there was a dssp.o file in the obj directory of dssp-2.2.1
> >
> > 4. we renamed the dssp.o file to dssp and moved it to dssp-2.2.1
> directory
> >
>
> That cannot possibly work. Please make sure you are following the dssp
> installation instructions.
>
> Mark
>
>
> > 5. ln -s /opt/apps/dssp/dssp2.2.1/dssp /usr/local/bin/
> >
> > 6. export dssp=/usr/local/bin/dssp
> >
> >
> >
> > but inspite of executing the above steps, when we run the do_dssp command
> > we get
> > the following error : Fatal error: DSSP executable
> > (usr/local/bin/dssp/dssp) does
> > not exist (use setenv DSSP)
> >
> > PS. we are using bash
> >
> >
> > I have read various threads on the errors related to do_dssp but could
> > not find a solution.
> >
> > Any kind of help would be appreciated.
> >
> >
> > Best,
> >
> > Soumadwip Ghosh
> >
> > Research Associate
> >
> > Indian Institute of Technology Bombay
> >
> > India
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[gmx-users] DSSP Erorr

[masoud keramati]

Hi to all

first i run 'gmx do_dssp -s md.tpr -f md.xtc' i  go this error:
Fatal error:
DSSP executable (usr/local/bin/dssp) does not exist (use setenv DSSP)

then i put dssp executable file in the path 'usr/local/bin/dssp'
and run following command : 'export DSSP=/usr/local/bin/dssp'
now when i run gmx do_dssp i get this error: 'Fatal error:
Failed to execute command: Try specifying your dssp version with the -ver
option.'
even with use of-ver option, i got the same error.
what can i do to solve this problem?

thanks for your help
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[gmx-users] DSSP Error

[masoud keramati]

Hi to all

first i run 'gmx do_dssp -s md.tpr -f md.xtc' i  go this error:
Fatal error:
DSSP executable (usr/local/bin/dssp) does not exist (use setenv DSSP)

then i put dssp executable file in the path 'usr/local/bin/dssp'
and run following command : 'export DSSP=/usr/local/bin/dssp'
now when i run gmx do_dssp i get this error: 'Fatal error:
Failed to execute command: Try specifying your dssp version with the -ver
option.'
even with use of-ver option, i got the same error.
what can i do to solve this problem?

thanks for your help
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Re: [gmx-users] Error in energy groups

[masoud keramati]

tnx Dr.Lemkul

yes the problem was in the tc-grps.
tc-grps= Protein Non-Protein
and there is no Non-Protein group in index file.
it's true that i use System for tc-grps?

On Sun, Jul 24, 2016 at 11:54 PM, Justin Lemkul <jalem...@vt.edu> wrote:

>
>
> On 7/24/16 3:17 PM, masoud keramati wrote:
>
>> Hi all
>>
>> i have a protein with six chain.
>> i create an index file that include each chain (chA chB ..)
>> in mdp file i define energy groups such that:
>> energygrps   = chA chD
>>
>> for grompp i used this command:
>> gmx grompp -f md.mdp -c npt.gro -n chains.ndx -p topol.top -o A-D.tpr
>>
>> but i got this error:
>> "Group Non-Protein referenced in the .mdp file was not found in the index
>> file.
>> Group names must match either [moleculetype] names or custom index group
>> names, in which case you must supply an index file to the '-n' option
>> of grompp "
>>
>> what's wrong with this?!
>>
>>
> You have some setting that uses Non-Protein but you haven't got that in
> your index file.  Check tc-grps as the most likely culprit.  If your index
> file *only* contains the chains that you've specified, then you're going to
> encounter problems.  In general, add groups that you need and leave the
> default groups (System, Protein, Non-Protein, etc.) in place for ease of
> use.
>
> -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] Error in energy groups

[masoud keramati]

Hi all

i have a protein with six chain.
i create an index file that include each chain (chA chB ..)
in mdp file i define energy groups such that:
energygrps   = chA chD

for grompp i used this command:
gmx grompp -f md.mdp -c npt.gro -n chains.ndx -p topol.top -o A-D.tpr

but i got this error:
"Group Non-Protein referenced in the .mdp file was not found in the index
file.
Group names must match either [moleculetype] names or custom index group
names, in which case you must supply an index file to the '-n' option
of grompp "

what's wrong with this?!

thank for your help : )
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Re: [gmx-users] Calculating Distance

[masoud keramati]

choose a atom, then calculate the transition vector of it with use of the
initial and final coordinate.


On Mon, May 16, 2016 at 11:50 AM, Sanket Ghawali 
wrote:

> Dear, gmx-users,
>
> Hello everyone,
> I'm simulating a peptide in an SDS micelle. The simulation was
> performed for 100ns
> When I visualize the trajectory in VMD, the peptide moves to the SDS
> interface where initially it was placed in the center,  the results
> are as expected. I would like to calculate the distance the peptide
> has traveled or moved from the center to the interface
>
>
> Any suggestions on how to go about doing this?
>
> Thanks,
>
> Sanket
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[gmx-users] calculate electrostatic force

[masoud keramati]

Hi to all,

i have two peptides that bind together,
how i can calculate the electrostatic forces between these peptide atoms?

tnx :)
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Re: [gmx-users] what means of contact in mindist?

[masoud keramati]

tnx dear tsjerk

can i use this option for analysis of  hydrophobic interaction?
is distance 0.6 nm good choice for this purpose?

On Mon, Feb 1, 2016 at 4:14 PM, Tsjerk Wassenaar <tsje...@gmail.com> wrote:

> Hey :)
>
> It tells how many pairs of atoms lie within a distance r (typically 0.6
> nm).
>
> Cheers,
>
> Tsjerk
>
> On Mon, Feb 1, 2016 at 1:08 PM, masoud keramati <keramati.ma3...@gmail.com
> >
> wrote:
>
> > Hi all
> >
> > what means of "number of contact" in  gmx mindist command?
> >
> > what we can understand from it's result?
> >
> >
> >
> > Best
> > --
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> >
>
>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
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Re: [gmx-users] what means of contact in mindist?

[masoud keramati]

Hi

i mean interactions between hydrophobic residues in a protein-ligand
complex.

On Mon, Feb 1, 2016 at 5:06 PM, Mark Abraham <mark.j.abra...@gmail.com>
wrote:

> Hi,
>
> First, what do you mean by a "hydrophobic interaction?"
>
> Mark
>
> On Mon, Feb 1, 2016 at 2:25 PM masoud keramati <keramati.ma3...@gmail.com>
> wrote:
>
> > tnx dear tsjerk
> >
> > can i use this option for analysis of  hydrophobic interaction?
> > is distance 0.6 nm good choice for this purpose?
> >
> > On Mon, Feb 1, 2016 at 4:14 PM, Tsjerk Wassenaar <tsje...@gmail.com>
> > wrote:
> >
> > > Hey :)
> > >
> > > It tells how many pairs of atoms lie within a distance r (typically 0.6
> > > nm).
> > >
> > > Cheers,
> > >
> > > Tsjerk
> > >
> > > On Mon, Feb 1, 2016 at 1:08 PM, masoud keramati <
> > keramati.ma3...@gmail.com
> > > >
> > > wrote:
> > >
> > > > Hi all
> > > >
> > > > what means of "number of contact" in  gmx mindist command?
> > > >
> > > > what we can understand from it's result?
> > > >
> > > >
> > > >
> > > > Best
> > > > --
> > > > Gromacs Users mailing list
> > > >
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> > > > posting!
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> > > >
> > >
> > >
> > >
> > > --
> > > Tsjerk A. Wassenaar, Ph.D.
> > > --
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[gmx-users] what means of contact in mindist?

[masoud keramati]

Hi all

what means of "number of contact" in  gmx mindist command?

what we can understand from it's result?



Best
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Re: [gmx-users] Cannot write trajectory frame

[masoud keramati]

i just install the 64bit linux and problem solved :-)

On 1/4/16, masoud keramati <keramati.ma3...@gmail.com> wrote:
> tnx dear Mark for your respond ;-)
> +
> Dear teemu
> yes my OS is 32-bit and version of gromacs is 5.x
> with installing 64bit OS, can i solve this problem?
>
> On Sun, Jan 3, 2016 at 6:53 PM, Teemu Murtola <teemu.murt...@gmail.com>
> wrote:
>
>> This is true, but unfortunately recent versions of Gromacs may not
>> properly
>> use the support present in 32-bit operating systems because of
>> http://redmine.gromacs.org/issues/1834.
>>
>> You haven't specified your Gromacs version or anything else about your
>> environment, so there is not much more we can guess.
>>
>> Best regards,
>> Teemu
>>
>> On Sun, Jan 3, 2016, 15:25 Mark Abraham <mark.j.abra...@gmail.com> wrote:
>>
>> > Hi,
>> >
>> > Most modern file systems do not have such a limitation, and all modern
>> > operating systems support at least one of them, so all you need to do
>> > is
>> > have disks formatted accordingly.
>> >
>> > Mark
>> >
>> > On Sun, Jan 3, 2016 at 1:22 PM masoud keramati <
>> keramati.ma3...@gmail.com>
>> > wrote:
>> >
>> > > yes that's true .. and i'm searching for a way to remove this
>> limitation
>> > > but ,what you mean by "get a real one" ?
>> > >
>> > > On Sun, Jan 3, 2016 at 2:02 PM, Mark Abraham
>> > > <mark.j.abra...@gmail.com
>> >
>> > > wrote:
>> > >
>> > > > Hi,
>> > > >
>> > > > As you've read in the archive, this depends solely on your file
>> system.
>> > > Get
>> > > > a real one! :-)
>> > > >
>> > > > Mark
>> > > >
>> > > > On Sun, 3 Jan 2016 11:17 masoud keramati
>> > > > <keramati.ma3...@gmail.com>
>> > > > wrote:
>> > > >
>> > > > > Hello and happy new year!
>> > > > >
>> > > > > i have seen this issue in archive,
>> > > > > the problem is with .trr size that can not reach more than 2GB
>> > > > > and
>> i
>> > > > think
>> > > > > that is my problem too.
>> > > > > my question is ,can i write .trr file with another file name and
>> then
>> > > > > finally append them?
>> > > > > is it a true way?
>> > > > >
>> > > > >
>> > > > > tnx for your responding ;-)
>> > > > > --
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Re: [gmx-users] Problem using gromacs

[masoud keramati]

in OPLS ff when i use tip3p  water  i got this error but if tip3p selected
then there no problem and it's interesting!

On Mon, Jan 4, 2016 at 2:18 PM, Justin Lemkul  wrote:

>
>
> On 1/4/16 4:27 AM, soumi  wrote:
>
>> Respected Sir,
>>I am new user of gromacs. When I use the following command
>> gmx grompp -f ions.mdp -c 1aki_solv.gro -p topol.top -o ions.tpr
>>
>> I get the following error :Number of coordinates in coordinate file does
>> not match topology file.
>> Please tell me how can I correct the number of coordinates in gromacs?
>>
>>
>
> http://www.gromacs.org/Documentation/Errors#Number_of_coordinates_in_coordinate_file_does_not_match_topology
>
> Since you've (presumably) already solvated the system, you probably forgot
> to let genbox adjust your topology for you via the -p option.  Based on
> your file naming, I assume you're following my lysozyme tutorial, which
> lays everything out exactly, so be sure you're using the exact commands and
> you know what each option is doing.
>
> -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
>
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> http://mackerell.umaryland.edu/~jalemkul
>
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Re: [gmx-users] Cannot write trajectory frame

[masoud keramati]

tnx dear Mark for your respond ;-)
+
Dear teemu
yes my OS is 32-bit and version of gromacs is 5.x
with installing 64bit OS, can i solve this problem?

On Sun, Jan 3, 2016 at 6:53 PM, Teemu Murtola <teemu.murt...@gmail.com>
wrote:

> This is true, but unfortunately recent versions of Gromacs may not properly
> use the support present in 32-bit operating systems because of
> http://redmine.gromacs.org/issues/1834.
>
> You haven't specified your Gromacs version or anything else about your
> environment, so there is not much more we can guess.
>
> Best regards,
> Teemu
>
> On Sun, Jan 3, 2016, 15:25 Mark Abraham <mark.j.abra...@gmail.com> wrote:
>
> > Hi,
> >
> > Most modern file systems do not have such a limitation, and all modern
> > operating systems support at least one of them, so all you need to do is
> > have disks formatted accordingly.
> >
> > Mark
> >
> > On Sun, Jan 3, 2016 at 1:22 PM masoud keramati <
> keramati.ma3...@gmail.com>
> > wrote:
> >
> > > yes that's true .. and i'm searching for a way to remove this
> limitation
> > > but ,what you mean by "get a real one" ?
> > >
> > > On Sun, Jan 3, 2016 at 2:02 PM, Mark Abraham <mark.j.abra...@gmail.com
> >
> > > wrote:
> > >
> > > > Hi,
> > > >
> > > > As you've read in the archive, this depends solely on your file
> system.
> > > Get
> > > > a real one! :-)
> > > >
> > > > Mark
> > > >
> > > > On Sun, 3 Jan 2016 11:17 masoud keramati <keramati.ma3...@gmail.com>
> > > > wrote:
> > > >
> > > > > Hello and happy new year!
> > > > >
> > > > > i have seen this issue in archive,
> > > > > the problem is with .trr size that can not reach more than 2GB and
> i
> > > > think
> > > > > that is my problem too.
> > > > > my question is ,can i write .trr file with another file name and
> then
> > > > > finally append them?
> > > > > is it a true way?
> > > > >
> > > > >
> > > > > tnx for your responding ;-)
> > > > > --
> > > > > 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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> > or
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> > > > >
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[gmx-users] Cannot write trajectory frame

[masoud keramati]

Hello and happy new year!

i have seen this issue in archive,
the problem is with .trr size that can not reach more than 2GB and i think
that is my problem too.
my question is ,can i write .trr file with another file name and then
finally append them?
is it a true way?


tnx for your responding ;-)
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Re: [gmx-users] Cannot write trajectory frame

[masoud keramati]

yes that's true .. and i'm searching for a way to remove this limitation
but ,what you mean by "get a real one" ?

On Sun, Jan 3, 2016 at 2:02 PM, Mark Abraham <mark.j.abra...@gmail.com>
wrote:

> Hi,
>
> As you've read in the archive, this depends solely on your file system. Get
> a real one! :-)
>
> Mark
>
> On Sun, 3 Jan 2016 11:17 masoud keramati <keramati.ma3...@gmail.com>
> wrote:
>
> > Hello and happy new year!
> >
> > i have seen this issue in archive,
> > the problem is with .trr size that can not reach more than 2GB and i
> think
> > that is my problem too.
> > my question is ,can i write .trr file with another file name and then
> > finally append them?
> > is it a true way?
> >
> >
> > tnx for your responding ;-)
> > --
> > Gromacs Users mailing list
> >
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> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
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Re: [gmx-users] Extending simulations

[masoud keramati]

sorry with my question

is it true that for extending simulation use the following code?

gmx grompp -f md.mdp -c md.gro -t md.trr -p topol.top -o md2.tpr
gmx mdrun -deffnm md2

*md.gro and md.trr is files for first run

On 12/22/15, Justin Lemkul  wrote:
>
>
> On 12/21/15 7:00 PM, Soumya Lipsa Rath wrote:
>> Dear Mark and Chandan,
>>
>> Thank you so much for the information. I was indeed using a wrong tpr
>> file.
>> I will include the -cpi state.cpt flag during the tpbconv step.
>>
>
> You don't need -cpi with tpbconv, only in mdrun.
>
> -Justin
>
>> Thanks,
>>
>> Soumya
>>
>> On Mon, Dec 21, 2015 at 12:30 PM, Soumya Lipsa Rath
>> >> wrote:
>>
>>> Dear Gromacs users,
>>>
>>> I am trying to extend my simulation for 200ns by using:
>>>
>>> tpbconv_mpi -s topol.tpr -extend 20 -o topol2.tpr
>>> mdrun_mpi -s topol2.tpr -cpi state.cpt -append -maxwarn 5 >&
>>> grompp_output.log
>>>
>>> However, my simulation has only extended for 50ns. Am I doing something
>>> wrong?
>>>
>>> Thanks,
>>>
>>> Soumya
>>>
>
> --
> ==
>
> 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] high temperature molecular dynamics

[masoud keramati]

Hi to all

is there any guide for high temperature molecular dynamics simulation?
i want to use this method for unfolding process.

thank for your respond :-)
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Re: [gmx-users] high temperature molecular dynamics

[masoud keramati]

tnx dear David


On 12/22/15, David van der Spoel <sp...@xray.bmc.uu.se> wrote:
> On 22/12/15 10:58, masoud keramati wrote:
>> Hi to all
>>
>> is there any guide for high temperature molecular dynamics simulation?
>> i want to use this method for unfolding process.
>>
>> thank for your respond :-)
>>
> Just increase the temperature. You may need to reduce the time step though.
>
>
> --
> David van der Spoel, Ph.D., Professor of Biology
> Dept. of Cell & Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone:+46184714205.
> sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
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[gmx-users] Writing checkpoint

[masoud keramati]

hi to all

in the mdrun log file i see "Writing checkpoint, step 47840 at Tue Dec
 8 18:42:52 2015".
what means of this Writing checkpoint?
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Re: [gmx-users] Writing checkpoint

[masoud keramati]

can i run  gromacs  in parallel using two different computers?

On 12/8/15, Justin Lemkul <jalem...@vt.edu> wrote:
>
>
> On 12/8/15 10:17 AM, masoud keramati wrote:
>> hi to all
>>
>> in the mdrun log file i see "Writing checkpoint, step 47840 at Tue Dec
>>   8 18:42:52 2015".
>> what means of this Writing checkpoint?
>>
>
> mdrun is writing a checkpoint file. You can use it to extend the run,
> restart
> after a power outage, etc.
>
> -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] Writing checkpoint

[masoud keramati]

ok

tnx  for ur respond

On 12/8/15, Justin Lemkul <jalem...@vt.edu> wrote:
>
>
> On 12/8/15 11:36 AM, masoud keramati wrote:
>> can i run  gromacs  in parallel using two different computers?
>>
>
> I think you should spend some time reading the manual, website, mailing list
>
> archive, and published GROMACS papers.
>
> -Justin
>
>> On 12/8/15, Justin Lemkul <jalem...@vt.edu> wrote:
>>>
>>>
>>> On 12/8/15 10:17 AM, masoud keramati wrote:
>>>> hi to all
>>>>
>>>> in the mdrun log file i see "Writing checkpoint, step 47840 at Tue Dec
>>>>8 18:42:52 2015".
>>>> what means of this Writing checkpoint?
>>>>
>>>
>>> mdrun is writing a checkpoint file. You can use it to extend the run,
>>> restart
>>> after a power outage, etc.
>>>
>>> -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
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>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
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[gmx-users] LINCS WARNING

[masoud keramati]

Hi to all dear gmx users

during the Energy Minimization i got this warning in first few steps
after step 20
"step 20: Water molecule starting at atom 34209 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate."

but after 3021 steps it was converged to Fmax < 1000.

then i start the Equilibration and in the zero to 4 steps i got this:
"Step 0, time 0 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.018591, max 0.374857 (between atoms 2409 and 2411)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length"

in the step 5i got this and mdrun was terminate.
" Water molecule starting at atom 32146 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.

WARNING: Listed nonbonded interaction between particles 2312 and 2326
at distance 4211.247 which is larger than the table limit 2.034 nm.

This is likely either a 1,4 interaction, or a listed interaction inside
a smaller molecule you are decoupling during a free energy calculation.
Since interactions at distances beyond the table cannot be computed,
they are skipped until they are inside the table limit again. You will
only see this message once, even if it occurs for several interactions.

IMPORTANT: This should not happen in a stable simulation, so there is
probably something wrong with your system. Only change the table-extension
distance in the mdp file if you are really sure that is the reason.


Segmentation fault (core dumped)"

my Equilibration is:

define  = -DPOSRES  ; position restrain the protein
; Run parameters
integrator  = md; leap-frog integrator
nsteps  = 5 ; 2 * 5 = 100 ps
dt  = 0.002 ; 2 fs
; Output control
nstxout = 500   ; save coordinates every 1.0 ps
nstvout = 500   ; save velocities every 1.0 ps
nstenergy   = 500   ; save energies every 1.0 ps
nstlog  = 500   ; update log file every 1.0 ps
; Bond parameters
continuation= no; first dynamics run
constraint_algorithm= lincs ; holonomic constraints
constraints = all-bonds ; all bonds (even heavy atom-H
bonds) constrained
lincs_iter  = 1 ; accuracy of LINCS
lincs_order = 4 ; also related to accuracy
; Neighborsearching
cutoff-scheme   = Verlet
ns_type = grid  ; search neighboring grid cells
nstlist = 10; 20 fs, largely irrelevant with Verlet
rcoulomb= 1.0   ; short-range electrostatic cutoff (in 
nm)
rvdw= 1.2   ; short-range van der Waals cutoff (in 
nm)
; Electrostatics
coulombtype = PME   ; Particle Mesh Ewald for long-range 
electrostatics
pme_order   = 4 ; cubic interpolation
fourierspacing  = 0.135 ; grid spacing for FFT
; Temperature coupling is on
tcoupl  = nose-hoover   ; modified Berendsen thermostat
tc-grps = system; two coupling groups - more accurate
tau_t   = 0.1 0.1   ; time constant, in ps
ref_t   = 300 300   ; reference temperature, one for each 
group, in K
; Pressure coupling is off
pcoupl  = no; no pressure coupling in NVT
; Periodic boundary conditions
pbc = xyz   ; 3-D PBC
; Dispersion correction
DispCorr= EnerPres  ; account for cut-off vdW scheme
; Velocity generation
gen_vel = yes   ; assign velocities from Maxwell distribution
gen_temp= 300   ; temperature for Maxwell distribution
gen_seed= -1; generate a random seed



tnx for your help
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Re: [gmx-users] combine two pdb files

[masoud keramati]

yes it's true.
thank you all

On Sat, Nov 28, 2015 at 3:31 PM, Peter Stern <peter.st...@weizmann.ac.il>
wrote:

> Probably.  So follow Chandan Choudhury's suggestion to use editconf -resnr
> 1 to reorder the residue numbers too and then it should work.
>
> 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 masoud
> keramati
> Sent: Saturday, November 28, 2015 1:12 PM
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] combine two pdb files
>
> hi
>
> yes that's right. but it's renuber atoms not residues.
> is the same residue number make an error?
>
> tnx : )
>
> On Sat, Nov 28, 2015 at 1:57 AM, Peter Stern <peter.st...@weizmann.ac.il>
> wrote:
>
> > AFAIK pdb2gmx doesn't care about the atom numbers in your pdb file
> > since in any case it reorders them and renumbers them after adding
> > hydrogen atoms.  Did you try it?
> >
> > Regards,
> > Peter
> >
> > Sent from my iPad
> >
> > > On 27 בנוב׳ 2015, at 22:28, masoud keramati
> > > <keramati.ma3...@gmail.com>
> > wrote:
> > >
> > > Hello
> > >
> > > I want to simulate two proteins and need to combine these two pdb
> > > files
> > in
> > > one.
> > > important thing is the atom number. if combine with cat command it
> > > gives
> > a
> > > file that contain two atom with the same atom and residue number
> > > that
> > will
> > > make an error in simulation.
> > > is there exist any way to combine these two pdb files to solve this
> > problem?
> > > I mean if first pdb finish with atom number n and residue number m
> > > then next pdb is start with atom number n+1 and residue number m+1.
> > >
> > > tnx
> > > --
> > > Gromacs Users mailing list
> > >
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> > posting!
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> > > or
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> > --
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Re: [gmx-users] combine two pdb files

[masoud keramati]

hi

yes that's right. but it's renuber atoms not residues.
is the same residue number make an error?

tnx : )

On Sat, Nov 28, 2015 at 1:57 AM, Peter Stern <peter.st...@weizmann.ac.il>
wrote:

> AFAIK pdb2gmx doesn't care about the atom numbers in your pdb file since
> in any case it reorders them and renumbers them after adding hydrogen
> atoms.  Did you try it?
>
> Regards,
> Peter
>
> Sent from my iPad
>
> > On 27 בנוב׳ 2015, at 22:28, masoud keramati <keramati.ma3...@gmail.com>
> wrote:
> >
> > Hello
> >
> > I want to simulate two proteins and need to combine these two pdb files
> in
> > one.
> > important thing is the atom number. if combine with cat command it gives
> a
> > file that contain two atom with the same atom and residue number that
> will
> > make an error in simulation.
> > is there exist any way to combine these two pdb files to solve this
> problem?
> > I mean if first pdb finish with atom number n and residue number m then
> > next pdb is start with atom number n+1 and residue number m+1.
> >
> > tnx
> > --
> > 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.
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[gmx-users] combine two pdb files

[masoud keramati]

Hello

I want to simulate two proteins and need to combine these two pdb files in
one.
important thing is the atom number. if combine with cat command it gives a
file that contain two atom with the same atom and residue number that will
make an error in simulation.
is there exist any way to combine these two pdb files to solve this problem?
I mean if first pdb finish with atom number n and residue number m then
next pdb is start with atom number n+1 and residue number m+1.

tnx
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