date:20140124

Sorry if I have so many questions. I just really need to finish this. When I
try to follow this

"In the .mdp file used for the minimizations, add a line "define =
-DSTRONG_POSRES" to make use of these new position restraints. Then, simply
follow the InflateGRO instructions (contained in the script itself), a
procedure that is easily scripted. Scale the lipid positions by a factor of
4:

perl inflategro.pl system.gro 4 DPPC 14 system_inflated.gro 5 area.dat"

I typed the command there is an error

Can't open perl script "inflategro.pl": No such file or directory

How can I have this file???

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Re: [gmx-users] Question Re. KALP-15 in DPPC tutorial




On 1/24/14, 11:21 PM, jhosamelly wrote:


Thanks Justin. I fixed the problem earlier but when I got to

"2. Pack the lipids around the protein

The easiest method I have found so far for packing lipids around an embedded
protein is the InflateGRO methodology (ref), available here. First,
concatenate the protein and bilayer structure files:

cat KALP_newbox.gro dppc128_whole.gro > system.gro

Remove unnecessary lines (the box vectors from the KALP structure, the
header information from the DPPC structure) and update the second line of
the coordinate file (total number of atoms) accordingly."

I don't know what file to edit. Remove unnecessary lines in what file?


In system.gro.  If you study the file format and examine what you have created, 
you will see that there is extraneous stuff that will break the file format.


-Justin

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Re: [gmx-users] Question Re. KALP-15 in DPPC tutorial


Thanks Justin. I fixed the problem earlier but when I got to 

"2. Pack the lipids around the protein

The easiest method I have found so far for packing lipids around an embedded
protein is the InflateGRO methodology (ref), available here. First,
concatenate the protein and bilayer structure files:

cat KALP_newbox.gro dppc128_whole.gro > system.gro

Remove unnecessary lines (the box vectors from the KALP structure, the
header information from the DPPC structure) and update the second line of
the coordinate file (total number of atoms) accordingly."

I don't know what file to edit. Remove unnecessary lines in what file?
Thanks
BTW, I just saw that you are the one who made this tutorial! Thank you for
that. :) Such a great help.

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Re: [gmx-users] Question Re. KALP-15 in DPPC tutorial




On 1/24/14, 10:44 PM, jhosamelly wrote:

""
"Non-bonded interactions involving atom type HW are also present; since
these
are all zero you can delete these lines as well, or otherwise rename HW as H
to
be consistent with the GROMOS96 53A6 naming convention. If you do not rename
these lines or remove them, grompp will later fail with a fatal error."

-Justin
""
Yes I deleted that already. I got that fatal error.



Clearly something is left over that you didn't properly get rid of.  grep is 
your friend here.


-Justin

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Department of Pharmaceutical Sciences
School of Pharmacy
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Re: [gmx-users] Question Re. KALP-15 in DPPC tutorial

""
"Non-bonded interactions involving atom type HW are also present; since
these
are all zero you can delete these lines as well, or otherwise rename HW as H
to
be consistent with the GROMOS96 53A6 naming convention. If you do not rename
these lines or remove them, grompp will later fail with a fatal error."

-Justin
""
Yes I deleted that already. I got that fatal error.

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Re: [gmx-users] Question Re. KALP-15 in DPPC tutorial

On 1/24/14, 10:30 PM, jhosamelly wrote:

I'm now doing the GROMACS tutorial KALP-15 in DPPC

I followed everything that is said needed to be changed in the topol.top,
lipid.itp, ffbonded.itp, ffnonbonded.itp . Or at least I think so.

http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/02_topology.html

I copied the [atom type] section from the tutorial, since as what it says
the one from lipid.itp lacks atm.no. column, to the ffnonbonded.itp.

I copied [ nonbond_params ] from the lipid.itp, except the section ";;
parameters for lipid-GROMOS interactions." , to the [ nonbond_params ] at
ffnonbonded.itp.

I copied [ pairtypes ] from lipid.ito to [ pairtypes ] at ffnonbonded.itp.

I copied the [ dihedraltypes ] from lipid.itp to the ffbonded.itp

but the when I tried to follow this

"We have already aligned the KALP peptide using editconf. The bilayer lies
in the x-y plane, with the normal along the z-axis. Convert the dppc128.pdb
to .gro format with editconf and remove the initial periodicity. The latter
step is easily accomplished through the use of trjconv:"

the command I used is editconf -f dppc128.pdb -o dppc128.gro

I don't know how to "remove the initial periodicity" so I continued and
typed the next command

There are multiple steps in this process; it encompasses most of the second
entitled "1. Orient the protein and membrane."

"(1) Generate a .tpr file for a DPPC-only system using grompp. You can use
any valid .mdp file and a topology corresponding to pure DPPC. An example
.mdp file can be found here and such a topology can be found here. Note how
simple the topology is. It includes dppc.itp and spc.itp to read parameters
for DPPC and water; it's that simple! Run grompp:

grompp -f minim.mdp -c dppc128.gro -p topol_dppc.top -o em.tpr"

I get fatal error

Fatal error:
Unknown atomtype HW

From
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/02_topology.html:

"Non-bonded interactions involving atom type HW are also present; since these
are all zero you can delete these lines as well, or otherwise rename HW as H to
be consistent with the GROMOS96 53A6 naming convention. If you do not rename
these lines or remove them, grompp will later fail with a fatal error."

-Justin

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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

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[gmx-users] Question Re. KALP-15 in DPPC tutorial

I'm now doing the GROMACS tutorial KALP-15 in DPPC

I followed everything that is said needed to be changed in the topol.top,
lipid.itp, ffbonded.itp, ffnonbonded.itp . Or at least I think so.

http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/02_topology.html

I copied the [atom type] section from the tutorial, since as what it says
the one from lipid.itp lacks atm.no. column, to the ffnonbonded.itp.

I copied [ nonbond_params ] from the lipid.itp, except the section ";;
parameters for lipid-GROMOS interactions." , to the [ nonbond_params ] at
ffnonbonded.itp.

I copied [ pairtypes ] from lipid.ito to [ pairtypes ] at ffnonbonded.itp.

I copied the [ dihedraltypes ] from lipid.itp to the ffbonded.itp

but the when I tried to follow this

the command I used is editconf -f dppc128.pdb -o dppc128.gro

I don't know how to "remove the initial periodicity" so I continued and
typed the next command

grompp -f minim.mdp -c dppc128.gro -p topol_dppc.top -o em.tpr"

I get fatal error

Fatal error:
Unknown atomtype HW

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Re: [gmx-users] Pull code vs. manual pull for umbrella sampling




On 1/24/14, 3:50 PM, shivangi nangia wrote:

Dear Justin,

Okay, so I have multiple configurations of protein and bi-layer system (30
initial configurations) at varied distances (in steps of 0.05 nm).

The protein has been moved away with respect to its COM.
So I have "manually" pulled the protein away from the bi-layer instead of using
the pull code.

I have run MD simulations for each of these configurations.

I need to use g_wham to calculate the PMF and for that I need the pullx.xvg 
files.



It won't be possible.  What you did wasn't umbrella sampling, it was just MD. 
If there is no restraint potential applied during the simulations in each of the 
sampling windows, there's nothing to de-bias to reconstruct a free energy profile.


You can generate the configurations in any manner you like (manually or by using 
the pull code), but the umbrella sampling itself requires the use of the pull code.


-Justin

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==

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Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
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Baltimore, MD 21201

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Re: [gmx-users] Pull code vs. manual pull for umbrella sampling

Dear Justin,

Okay, so I have multiple configurations of protein and bi-layer system (30
initial configurations) at varied distances (in steps of 0.05 nm).

The protein has been moved away with respect to its COM.
So I have "manually" pulled the protein away from the bi-layer instead of
using the pull code.

I have run MD simulations for each of these configurations.

I need to use g_wham to calculate the PMF and for that I need the pullx.xvg
files.

Thanks,
sxn

Shivangi Nangia, Ph. D
Postdoctoral Research Associate
Department of Molecular and Cell Biology
University of Connecticut

On Fri, Jan 24, 2014 at 3:38 PM, Justin Lemkul  wrote:

>
>
> On 1/24/14, 2:34 PM, shivangi nangia wrote:
>
>> Hello,
>>
>> I wish to perform umbrella sampling without using the pull code.
>> I have varied starting configurations for protein-bilayer.
>>
>> Is there any advantage(s) of doing a manual pull versus the pull code or
>> vice-versa?
>> What is the reason to do it with pull force?
>>
>>
> I think you need to provide more detail on what you are doing or are
> planning to do.  What is manual pulling?
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> 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
>
> ==
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> Gromacs Users mailing list
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> * 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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Re: [gmx-users] Rerun error




On 1/24/14, 1:56 PM, Shima Arasteh wrote:






On Friday, January 24, 2014 9:09 PM, Shima Arasteh 
 wrote:
I tried
trjconv -f md_0_1.trr -s md_0_1.tpr -split 1000 -o md_0_1_new.trr

My system does not recognize the md_0_1.trr file. oh... :-(
Would you please help me?



Providing a single command does not help much.  What does "does not recognize" 
mean?  What is the *exact* error?  How was md_0_1.trr generated in the first 
place and how does it relate to the other files shown in the commands below?


-Justin




Sincerely,
Shima




On Friday, January 24, 2014 8:23 PM, Mark Abraham  
wrote:

You're using unix split? That could work for .trr under the right conditions, 
but apparently it is not. trjconv has a million different ways to split 
trajectories, so try them. Also chekc that your file system can handle files 
bigger than 2GB at all.

Mark



On Fri, Jan 24, 2014 at 5:40 PM, Shima Arasteh  
wrote:

Making a new folder didn't solve my problem unfortunately.


The commands I ran are these:
1.Split files larger than 2G
split -b 2097152000  md_0_1.trr -d

The output files are:
x00
x01
x02
.
.
.
x10


Then:
2.grompp -f md.mdp -c npt_6.gro -t npt_6.cpt -p topol.top -o md_rerun_0.tpr -n 
index.ndx
3.mdrun -rerun x00.trr -s md_rerun_0.tpr -e md_rerun_0.edr -o md_rerun_0.trr -v






Sincerely,
Shima



From: Mark Abraham 
To: Shima Arasteh 
Cc: "gmx-us...@gromacs.org" 
Sent: Friday, January 24, 2014 7:19 PM

Subject: Re: [gmx-users] Rerun error



So there's nothing in it. Maybe mdrun over-write it according to Christian's 
theory, but since we don't know what your commands were, we're guessing... The 
extra 30 seconds of copy-pasting your commands from your terminal would have 
led to an answer by now!

Mark



On Fri, Jan 24, 2014 at 4:19 PM, Shima Arasteh  
wrote:

Last frame -1 time0.000


# Atoms  -1
Last frame -1 time0.000


Item#frames Timestep (ps)
Step 0
Time 0
Lambda   0
Coords   0
Velocities   0
Forces   0
Box  0





Sincerely,
Shima




From: Mark Abraham 
To: Discussion list for GROMACS users ; Shima Arasteh 

Sent: Friday, January 24, 2014 6:43 PM
Subject: Re: [gmx-users] Rerun error




What does gmxcheck say about this files?

Mark



On Fri, Jan 24, 2014 at 3:49 PM, Shima Arasteh  
wrote:

Hi,


I had a large .trr file, tried to do rerun on it. First I used split command 
and made 10 new .trr files with 2G in size. Then ran rerun on the first 2G.trr, 
but this does not work for the rest of trr files and I get the error:
The number of atoms in trajectory (-1) doesn't match the input file.

Would you please give me any suggestions?
Thanks in advance



Sincerely,
Shima
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==

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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

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Re: [gmx-users] Pull code vs. manual pull for umbrella sampling




On 1/24/14, 2:34 PM, shivangi nangia wrote:

Hello,

I wish to perform umbrella sampling without using the pull code.
I have varied starting configurations for protein-bilayer.

Is there any advantage(s) of doing a manual pull versus the pull code or
vice-versa?
What is the reason to do it with pull force?



I think you need to provide more detail on what you are doing or are planning to 
do.  What is manual pulling?


-Justin

--
==

Justin A. Lemkul, Ph.D.
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

==
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[gmx-users] Pull code vs. manual pull for umbrella sampling

Hello,

I wish to perform umbrella sampling without using the pull code.
I have varied starting configurations for protein-bilayer.

Is there any advantage(s) of doing a manual pull versus the pull code or
vice-versa?
What is the reason to do it with pull force?

Thanks,
sxn
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Re: [gmx-users] Rerun error






On Friday, January 24, 2014 9:09 PM, Shima Arasteh 
 wrote:
I tried 
trjconv -f md_0_1.trr -s md_0_1.tpr -split 1000 -o md_0_1_new.trr

My system does not recognize the md_0_1.trr file. oh... :-(
Would you please help me?



Sincerely,
Shima




On Friday, January 24, 2014 8:23 PM, Mark Abraham  
wrote:

You're using unix split? That could work for .trr under the right conditions, 
but apparently it is not. trjconv has a million different ways to split 
trajectories, so try them. Also chekc that your file system can handle files 
bigger than 2GB at all.

Mark



On Fri, Jan 24, 2014 at 5:40 PM, Shima Arasteh  
wrote:

Making a new folder didn't solve my problem unfortunately.
>
>The commands I ran are these:
>1.Split files larger than 2G
>split -b 2097152000  md_0_1.trr -d
>
>The output files are:
>x00
>x01
>x02
>.
>.
>.
>x10
>
>
>Then:
>2.grompp -f md.mdp -c npt_6.gro -t npt_6.cpt -p topol.top -o md_rerun_0.tpr -n 
>index.ndx
>3.mdrun -rerun x00.trr -s md_rerun_0.tpr -e md_rerun_0.edr -o md_rerun_0.trr -v
>
>
>
>
>
>
>Sincerely,
>Shima
>
>
>
>From: Mark Abraham 
>To: Shima Arasteh 
>Cc: "gmx-us...@gromacs.org" 
>Sent: Friday, January 24, 2014 7:19 PM
>
>Subject: Re: [gmx-users] Rerun error
>
>
>
>So there's nothing in it. Maybe mdrun over-write it according to Christian's 
>theory, but since we don't know what your commands were, we're guessing... The 
>extra 30 seconds of copy-pasting your commands from your terminal would have 
>led to an answer by now!
>
>Mark
>
>
>
>On Fri, Jan 24, 2014 at 4:19 PM, Shima Arasteh  
>wrote:
>
>Last frame -1 time    0.000   
>>
>># Atoms  -1
>>Last frame -1 time    0.000   
>>
>>
>>Item    #frames Timestep (ps)
>>Step 0
>>Time 0
>>Lambda   0
>>Coords   0
>>Velocities   0
>>Forces   0
>>Box  0
>>
>>
>>
>>
>>
>>Sincerely,
>>Shima
>>
>>
>>
>>
>>From: Mark Abraham 
>>To: Discussion list for GROMACS users ; Shima Arasteh 
>>
>>Sent: Friday, January 24, 2014 6:43 PM
>>Subject: Re: [gmx-users] Rerun error
>>
>>
>>
>>
>>What does gmxcheck say about this files?
>>
>>Mark
>>
>>
>>
>>On Fri, Jan 24, 2014 at 3:49 PM, Shima Arasteh  
>>wrote:
>>
>>Hi,
>>>
>>>I had a large .trr file, tried to do rerun on it. First I used split command 
>>>and made 10 new .trr files with 2G in size. Then ran rerun on the first 
>>>2G.trr, but this does not work for the rest of trr files and I get the error:
>>>The number of atoms in trajectory (-1) doesn't match the input file.
>>>
>>>Would you please give me any suggestions?
>>>Thanks in advance
>>>
>>>
>>>
>>>Sincerely,
>>>Shima 
>>>--
>>>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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>>>mail to gmx-users-requ...@gromacs.org.
>>> 
>> 
> 
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Re: [gmx-users] pullx and pullf

Is there any advantage(s) of doing a manual pull versus the pull code or
vice-versa?

Shivangi Nangia, Ph. D
Postdoctoral Research Associate
Department of Molecular and Cell Biology
University of Connecticut


On Fri, Jan 24, 2014 at 1:22 PM, Justin Lemkul  wrote:

>
>
> On 1/24/14, 1:21 PM, shivangi nangia wrote:
>
>> Is there a way around to generate similar data as in pullx/pullf.xvg
>> files (from
>> just md runs) without using the pull code.
>>
>>
> pullf.xvg contains pulling forces from the harmonic spring.  If you didn't
> apply any biasing potential, there is no force to report.  The pullx.xvg
> file simply reports the distance between the reference and pulled group;
> you can obtain the same information from g_dist.
>
> -Justin
>
>
>>
>>
>> Shivangi Nangia, Ph. D
>> Postdoctoral Research Associate
>> Department of Molecular and Cell Biology
>> University of Connecticut
>>
>>
>> On Fri, Jan 24, 2014 at 1:00 PM, Justin Lemkul > > wrote:
>>
>>
>>
>> On 1/24/14, 12:50 PM, shivangi nangia wrote:
>>
>> Hello,
>>
>> I am running a umbrella sampling but not using the pull code.
>>
>> I have various starting configurations for a protein-bilayer
>> system.
>> I am performing md runs for each configuration separately.
>>
>> In order to use g_wham I need pullx/pullf .xvg files.
>>
>> I have tried these commands:
>>
>> 1) mdrun_mpi -s nocard1.tpr -px ( to run the md simulation),
>> pullx.xvg is
>> not generated
>>
>> 2) Post md run
>>
>> mdrun_mpi -s nocard1.tpr -cpi nocard1_moved.cpt -rerun
>> nocard1_moved.xtc -px
>>
>> pullx.xvg is still not generated.
>>
>>
>> You will not get these output files unless you are using the pull
>> code.
>>
>> -Justin
>>
>> --
>> ==__
>>
>>
>> Justin A. Lemkul, Ph.D.
>> 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@outerbanks.umaryland.__edu
>>  | (410) 706-7441
>> 
>>
>> ==__
>>
>> --
>> 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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>> _gmx-users
>> 
>> or send
>> a mail to gmx-users-requ...@gromacs.org > gromacs.org>.
>>
>>
>>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> 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
>
> ==
> --
> 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] pullx and pullf




On 1/24/14, 1:21 PM, shivangi nangia wrote:

Is there a way around to generate similar data as in pullx/pullf.xvg files (from
just md runs) without using the pull code.



pullf.xvg contains pulling forces from the harmonic spring.  If you didn't apply 
any biasing potential, there is no force to report.  The pullx.xvg file simply 
reports the distance between the reference and pulled group; you can obtain the 
same information from g_dist.


-Justin





Shivangi Nangia, Ph. D
Postdoctoral Research Associate
Department of Molecular and Cell Biology
University of Connecticut


On Fri, Jan 24, 2014 at 1:00 PM, Justin Lemkul mailto:jalem...@vt.edu>> wrote:



On 1/24/14, 12:50 PM, shivangi nangia wrote:

Hello,

I am running a umbrella sampling but not using the pull code.

I have various starting configurations for a protein-bilayer system.
I am performing md runs for each configuration separately.

In order to use g_wham I need pullx/pullf .xvg files.

I have tried these commands:

1) mdrun_mpi -s nocard1.tpr -px ( to run the md simulation), pullx.xvg 
is
not generated

2) Post md run

mdrun_mpi -s nocard1.tpr -cpi nocard1_moved.cpt -rerun 
nocard1_moved.xtc -px

pullx.xvg is still not generated.


You will not get these output files unless you are using the pull code.

-Justin

--
==__

Justin A. Lemkul, Ph.D.
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@outerbanks.umaryland.__edu
 | (410) 706-7441


==__
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--
==

Justin A. Lemkul, Ph.D.
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

==
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Re: [gmx-users] pullx and pullf

Is there a way around to generate similar data as in pullx/pullf.xvg files
(from just md runs) without using the pull code.

Shivangi Nangia, Ph. D
Postdoctoral Research Associate
Department of Molecular and Cell Biology
University of Connecticut

On Fri, Jan 24, 2014 at 1:00 PM, Justin Lemkul  wrote:

>
>
> On 1/24/14, 12:50 PM, shivangi nangia wrote:
>
>> Hello,
>>
>> I am running a umbrella sampling but not using the pull code.
>>
>> I have various starting configurations for a protein-bilayer system.
>> I am performing md runs for each configuration separately.
>>
>> In order to use g_wham I need pullx/pullf .xvg files.
>>
>> I have tried these commands:
>>
>> 1) mdrun_mpi -s nocard1.tpr -px ( to run the md simulation), pullx.xvg is
>> not generated
>>
>> 2) Post md run
>>
>> mdrun_mpi -s nocard1.tpr -cpi nocard1_moved.cpt -rerun nocard1_moved.xtc
>> -px
>>
>> pullx.xvg is still not generated.
>>
>>
> You will not get these output files unless you are using the pull code.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> 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
>
> ==
> --
> 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] Problems with mdrun (version 4.6.5) and CPU-type: Xeon E5472

2014-01-24 Thread Teemu Murtola

Please try setting GMX_DISTRIBUTABLE_BUILD=ON for CMake and see whether
that fixes the problem.


On Fri, Jan 24, 2014 at 6:18 PM, Thomas Schlesier wrote:

> Hi all,
> I am having problems with GROMACS 4.6.5 and one type of CPU on our cluster
> (other CPU-types make no problems). GROMACS was always compiled on the
> master, which uses a different CPU-type (see below at the beginning of the
> 'md.log'-file).
>
> For the CPU type (partial output from 'cat /proc/cpuinfo'):
> vendor_id   : GenuineIntel
> cpu family  : 6
> model   : 23
> model name  : Intel(R) Xeon(R) CPU   E5472  @ 3.00GHz
> stepping: 6
> cpu MHz : 3000.186
> cache size  : 6144 KB
>
> 'grompp' 'g_rdf' and 'pdb2gmx' all work fine, only 'mdrun' gives problems
> (so I think only 'mdrun' is affected).
>
> Error message is:
> Illegal instruction
> and i get a 'core dump'. (Didn't looked into the dumped file, since i only
> know i can do this with 'gdb' but have absolute no idea how 'gdb' works and
> for what i should look).
>
> Last lines of the 'md.log' file before the crash (energy minimization of a
> small water box with cut-offs):
>
> Removing pbc first time
>
>  PLEASE READ AND CITE THE FOLLOWING REFERENCE 
> S. Miyamoto and P. A. Kollman
> SETTLE: An Analytical Version of the SHAKE and RATTLE Algorithms for Rigid
> Water Models
> J. Comp. Chem. 13 (1992) pp. 952-962
>   --- Thank You ---  
>
> So, i get the impression, that the preparation for the simulation is
> success full, and the crash happens when the actual simulation starts.
>
> The same simulation works with gromacs 4.0.7 and 4.5.5 (on the same
> machine). So I thought SSE4.1 or the internal MPI-stuff from gromacs 4.6.5
> produces the problem.
> So i compiled gromacs 4.6.5 with
> -DGMX_CPU_ACCELERATION=SSE2 (or) None
> and without any MPI support (and then running only a serial calculation).
> Also tried for FFT the internal 'fftpack' (thought maybe the FFT part
> might be the problem - for this i also ran the simulation without PME and
> only plain cut-offs).
>
> But the error still occurs in every case :(
>
> I tried the compilation with two different compilers:
> Intel:
> icc (ICC) 12.1.2 2028
> Copyright (C) 1985-2011 Intel Corporation.  All rights reserved.
> and GNU:
> gcc (GCC) 4.6.4 20120511 (prerelease)
> Copyright (C) 2011 Free Software Foundation, Inc.
> but i makes no difference.
>
>
> To give some more information:
>
> Beginning of the 'md.log'-file:
>
> Log file opened on Fri Jan 24 16:40:34 2014
> Host: tc-3-12.local  pid: 6755  nodeid: 0  nnodes:  1
> Gromacs version:VERSION 4.6.5
> Precision:  single
> Memory model:   64 bit
> MPI library:none
> OpenMP support: disabled
> GPU support:disabled
> invsqrt routine:gmx_software_invsqrt(x)
> CPU acceleration:   SSE4.1
> FFT library:fftpack (built-in)
> Large file support: enabled
> RDTSCP usage:   enabled
> Built on:   Fr 24. Jan 16:26:42 CET 2014
> Built by:   schl...@dirac.chemie.uni-mainz.de [CMAKE]
> Build OS/arch:  Linux 2.6.18-238.19.1.el5 x86_64
> Build CPU vendor:   GenuineIntel
> Build CPU brand:Intel(R) Xeon(R) CPU   X5670  @ 2.93GHz
> Build CPU family:   6   Model: 44   Stepping: 1
> Build CPU features: apic clfsh cmov cx8 cx16 htt lahf_lm mmx msr
> nonstop_tsc pcid pdcm pdpe1gb popcnt pse rdtscp sse2 sse3 sse4.1 sse4.2
> ssse3
> C compiler: /share/apps/gcc/gcc-4.6.4_20120511/bin/gcc GNU gcc
> (GCC) 4.6.4 20120511 (prerelease)
> C compiler flags:   -msse4.1-Wextra -Wno-missing-field-initializers
> -Wno-sign-compare -Wall -Wno-unused -Wunused-value -Wno-unknown-pragmas
> -fomit-frame-pointer -funroll-all-loops -fexcess-precision=fast  -O3
> -DNDEBUG
>
> cmake-command for compilation (used for the last build):
> (here i'm using line breaks to make it easier to read):
>
> cmake
> -DCMAKE_C_COMPILER=/share/apps/gcc/gcc-4.6.4_20120511/bin/gcc
> -DCMAKE_CXX_COMPILER=/share/apps/gcc/gcc-4.6.4_20120511/bin/g++
> -DGMX_BUILD_OWN_FFTW=OFF
> -DCMAKE_INSTALL_PREFIX=/scrcluster/schlesi/bug465 -DBUILD_SHARED_LIBS=OFF
> -DGMX_PREFER_STATIC_LIBS=ON
> -DGMX_CPU_ACCELERATION=SSE4.1
> -DGMX_MPI_IN_PLACE=OFF
> -DGMX_OPENMP=OFF
> -DGMX_THREAD_MPI=OFF
> -DGMX_MPI=OFF
> -DGMX_FFT_LIBRARY=fftpack
> ..
> (Sidenote: the 'GMX_MPI_IN_PLACE' isn't used - cmake tells me this).
>
> Till now i havn't tried to compile GROMACS on any of the problematic
> machines, but i can try this on monday.
>
>
> 
>
> Has anyone any idea (for solving, or to better trace the error)? Since i'm
> at the end with my knowledge (actually i'm quite happy that i came so far,
> since about this 'hardcore' computer stuff my knowledge is very limited).
> If someone needs more informations (or the core dumped file), just tell me.
>
> Greetings (and wish you a nice weekend)
> Thomas
> --
> Gromacs Users mailing list

Re: [gmx-users] pullx and pullf




On 1/24/14, 12:50 PM, shivangi nangia wrote:

Hello,

I am running a umbrella sampling but not using the pull code.

I have various starting configurations for a protein-bilayer system.
I am performing md runs for each configuration separately.

In order to use g_wham I need pullx/pullf .xvg files.

I have tried these commands:

1) mdrun_mpi -s nocard1.tpr -px ( to run the md simulation), pullx.xvg is
not generated

2) Post md run

mdrun_mpi -s nocard1.tpr -cpi nocard1_moved.cpt -rerun nocard1_moved.xtc -px

pullx.xvg is still not generated.



You will not get these output files unless you are using the pull code.

-Justin

--
==

Justin A. Lemkul, Ph.D.
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

==
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[gmx-users] pullx and pullf

Hello,

I am running a umbrella sampling but not using the pull code.

I have various starting configurations for a protein-bilayer system.
I am performing md runs for each configuration separately.

In order to use g_wham I need pullx/pullf .xvg files.

I have tried these commands:

1) mdrun_mpi -s nocard1.tpr -px ( to run the md simulation), pullx.xvg is
not generated

2) Post md run

mdrun_mpi -s nocard1.tpr -cpi nocard1_moved.cpt -rerun nocard1_moved.xtc -px

pullx.xvg is still not generated.


Kindly help.


Thanks,

sxn
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Re: [gmx-users] Rerun error

I tried 
trjconv -f md_0_1.trr -s md_0_1.tpr -split 1000 -o md_0_1_new.trr

My system does not recognize the md_0_1.trr file. oh... :-(






Sincerely,
Shima



On Friday, January 24, 2014 8:23 PM, Mark Abraham  
wrote:

You're using unix split? That could work for .trr under the right conditions, 
but apparently it is not. trjconv has a million different ways to split 
trajectories, so try them. Also chekc that your file system can handle files 
bigger than 2GB at all.

Mark



On Fri, Jan 24, 2014 at 5:40 PM, Shima Arasteh  
wrote:

Making a new folder didn't solve my problem unfortunately.
>
>The commands I ran are these:
>1.Split files larger than 2G
>split -b 2097152000  md_0_1.trr -d
>
>The output files are:
>x00
>x01
>x02
>.
>.
>.
>x10
>
>
>Then:
>2.grompp -f md.mdp -c npt_6.gro -t npt_6.cpt -p topol.top -o md_rerun_0.tpr -n 
>index.ndx
>3.mdrun -rerun x00.trr -s md_rerun_0.tpr -e md_rerun_0.edr -o md_rerun_0.trr -v
>
>
>
>
>
>
>Sincerely,
>Shima
>
>
>
>From: Mark Abraham 
>To: Shima Arasteh 
>Cc: "gmx-us...@gromacs.org" 
>Sent: Friday, January 24, 2014 7:19 PM
>
>Subject: Re: [gmx-users] Rerun error
>
>
>
>So there's nothing in it. Maybe mdrun over-write it according to Christian's 
>theory, but since we don't know what your commands were, we're guessing... The 
>extra 30 seconds of copy-pasting your commands from your terminal would have 
>led to an answer by now!
>
>Mark
>
>
>
>On Fri, Jan 24, 2014 at 4:19 PM, Shima Arasteh  
>wrote:
>
>Last frame -1 time    0.000   
>>
>># Atoms  -1
>>Last frame -1 time    0.000   
>>
>>
>>Item    #frames Timestep (ps)
>>Step 0
>>Time 0
>>Lambda   0
>>Coords   0
>>Velocities   0
>>Forces   0
>>Box  0
>>
>>
>>
>>
>>
>>Sincerely,
>>Shima
>>
>>
>>
>>
>>From: Mark Abraham 
>>To: Discussion list for GROMACS users ; Shima Arasteh 
>>
>>Sent: Friday, January 24, 2014 6:43 PM
>>Subject: Re: [gmx-users] Rerun error
>>
>>
>>
>>
>>What does gmxcheck say about this files?
>>
>>Mark
>>
>>
>>
>>On Fri, Jan 24, 2014 at 3:49 PM, Shima Arasteh  
>>wrote:
>>
>>Hi,
>>>
>>>I had a large .trr file, tried to do rerun on it. First I used split command 
>>>and made 10 new .trr files with 2G in size. Then ran rerun on the first 
>>>2G.trr, but this does not work for the rest of trr files and I get the error:
>>>The number of atoms in trajectory (-1) doesn't match the input file.
>>>
>>>Would you please give me any suggestions?
>>>Thanks in advance
>>>
>>>
>>>
>>>Sincerely,
>>>Shima 
>>>--
>>>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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[gmx-users] Problems with mdrun (version 4.6.5) and CPU-type: Xeon E5472

2014-01-24 Thread Thomas Schlesier


Hi all,
I am having problems with GROMACS 4.6.5 and one type of CPU on our 
cluster (other CPU-types make no problems). GROMACS was always compiled 
on the master, which uses a different CPU-type (see below at the 
beginning of the 'md.log'-file).


For the CPU type (partial output from 'cat /proc/cpuinfo'):
vendor_id   : GenuineIntel
cpu family  : 6
model   : 23
model name  : Intel(R) Xeon(R) CPU   E5472  @ 3.00GHz
stepping: 6
cpu MHz : 3000.186
cache size  : 6144 KB

'grompp' 'g_rdf' and 'pdb2gmx' all work fine, only 'mdrun' gives 
problems (so I think only 'mdrun' is affected).


Error message is:
Illegal instruction
and i get a 'core dump'. (Didn't looked into the dumped file, since i 
only know i can do this with 'gdb' but have absolute no idea how 'gdb' 
works and for what i should look).


Last lines of the 'md.log' file before the crash (energy minimization of 
a small water box with cut-offs):


Removing pbc first time

 PLEASE READ AND CITE THE FOLLOWING REFERENCE 
S. Miyamoto and P. A. Kollman
SETTLE: An Analytical Version of the SHAKE and RATTLE Algorithms for Rigid
Water Models
J. Comp. Chem. 13 (1992) pp. 952-962
  --- Thank You ---  

So, i get the impression, that the preparation for the simulation is 
success full, and the crash happens when the actual simulation starts.


The same simulation works with gromacs 4.0.7 and 4.5.5 (on the same 
machine). So I thought SSE4.1 or the internal MPI-stuff from gromacs 
4.6.5 produces the problem.

So i compiled gromacs 4.6.5 with
-DGMX_CPU_ACCELERATION=SSE2 (or) None
and without any MPI support (and then running only a serial calculation).
Also tried for FFT the internal 'fftpack' (thought maybe the FFT part 
might be the problem - for this i also ran the simulation without PME 
and only plain cut-offs).


But the error still occurs in every case :(

I tried the compilation with two different compilers:
Intel:
icc (ICC) 12.1.2 2028
Copyright (C) 1985-2011 Intel Corporation.  All rights reserved.
and GNU:
gcc (GCC) 4.6.4 20120511 (prerelease)
Copyright (C) 2011 Free Software Foundation, Inc.
but i makes no difference.


To give some more information:

Beginning of the 'md.log'-file:

Log file opened on Fri Jan 24 16:40:34 2014
Host: tc-3-12.local  pid: 6755  nodeid: 0  nnodes:  1
Gromacs version:VERSION 4.6.5
Precision:  single
Memory model:   64 bit
MPI library:none
OpenMP support: disabled
GPU support:disabled
invsqrt routine:gmx_software_invsqrt(x)
CPU acceleration:   SSE4.1
FFT library:fftpack (built-in)
Large file support: enabled
RDTSCP usage:   enabled
Built on:   Fr 24. Jan 16:26:42 CET 2014
Built by:   schl...@dirac.chemie.uni-mainz.de [CMAKE]
Build OS/arch:  Linux 2.6.18-238.19.1.el5 x86_64
Build CPU vendor:   GenuineIntel
Build CPU brand:Intel(R) Xeon(R) CPU   X5670  @ 2.93GHz
Build CPU family:   6   Model: 44   Stepping: 1
Build CPU features: apic clfsh cmov cx8 cx16 htt lahf_lm mmx msr 
nonstop_tsc pcid pdcm pdpe1gb popcnt pse rdtscp sse2 sse3 sse4.1 sse4.2 
ssse3
C compiler: /share/apps/gcc/gcc-4.6.4_20120511/bin/gcc GNU gcc 
(GCC) 4.6.4 20120511 (prerelease)
C compiler flags:   -msse4.1-Wextra -Wno-missing-field-initializers 
-Wno-sign-compare -Wall -Wno-unused -Wunused-value -Wno-unknown-pragmas 
  -fomit-frame-pointer -funroll-all-loops -fexcess-precision=fast  -O3 
-DNDEBUG


cmake-command for compilation (used for the last build):
(here i'm using line breaks to make it easier to read):

cmake
-DCMAKE_C_COMPILER=/share/apps/gcc/gcc-4.6.4_20120511/bin/gcc 
-DCMAKE_CXX_COMPILER=/share/apps/gcc/gcc-4.6.4_20120511/bin/g++ 
-DGMX_BUILD_OWN_FFTW=OFF

-DCMAKE_INSTALL_PREFIX=/scrcluster/schlesi/bug465 -DBUILD_SHARED_LIBS=OFF
-DGMX_PREFER_STATIC_LIBS=ON
-DGMX_CPU_ACCELERATION=SSE4.1
-DGMX_MPI_IN_PLACE=OFF
-DGMX_OPENMP=OFF
-DGMX_THREAD_MPI=OFF
-DGMX_MPI=OFF
-DGMX_FFT_LIBRARY=fftpack
..
(Sidenote: the 'GMX_MPI_IN_PLACE' isn't used - cmake tells me this).

Till now i havn't tried to compile GROMACS on any of the problematic 
machines, but i can try this on monday.





Has anyone any idea (for solving, or to better trace the error)? Since 
i'm at the end with my knowledge (actually i'm quite happy that i came 
so far, since about this 'hardcore' computer stuff my knowledge is very 
limited).

If someone needs more informations (or the core dumped file), just tell me.

Greetings (and wish you a nice weekend)
Thomas
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Re: [gmx-users] Changing temperature and pressure in lipid bilayer simulation.




On 1/23/14, 7:16 PM, jhosamelly wrote:

Thank you for your reply. I appreciate it. I'm reading the sections on the 
manual you said. I came across that before already but I don't really know how 
to apply it. LOL. I'll try to figure it out.

About the extraction of water from the bilayer. What I mean is, in a bilayer we 
know that the top part is water, the middle is the lipid and the bottom part is 
also water. What I wanna do is extract most of the water from the bilayer and 
the only thing left is the lipid (and maybe some water). Thanks.



Such a task can be accomplished with g_select, trjconv, or a script of your own 
creation.


-Justin

--
==

Justin A. Lemkul, Ph.D.
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

==
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Re: [gmx-users] Rerun error

2014-01-24 Thread Mark Abraham

So there's nothing in it. Maybe mdrun over-write it according to
Christian's theory, but since we don't know what your commands were, we're
guessing... The extra 30 seconds of copy-pasting your commands from your
terminal would have led to an answer by now!

Mark

On Fri, Jan 24, 2014 at 4:19 PM, Shima Arasteh
wrote:

> Last frame -1 time0.000
>
> # Atoms  -1
> Last frame -1 time0.000
>
>
> Item#frames Timestep (ps)
> Step 0
> Time 0
> Lambda   0
> Coords   0
> Velocities   0
> Forces   0
> Box  0
>
>
>
>
>
> Sincerely,
> Shima
>
>
> 
> From: Mark Abraham 
> To: Discussion list for GROMACS users ; Shima
> Arasteh 
> Sent: Friday, January 24, 2014 6:43 PM
> Subject: Re: [gmx-users] Rerun error
>
>
>
> What does gmxcheck say about this files?
>
> Mark
>
>
>
> On Fri, Jan 24, 2014 at 3:49 PM, Shima Arasteh <
> shima_arasteh2...@yahoo.com> wrote:
>
> Hi,
> >
> >I had a large .trr file, tried to do rerun on it. First I used split
> command and made 10 new .trr files with 2G in size. Then ran rerun on the
> first 2G.trr, but this does not work for the rest of trr files and I get
> the error:
> >The number of atoms in trajectory (-1) doesn't match the input file.
> >
> >Would you please give me any suggestions?
> >Thanks in advance
> >
> >
> >
> >Sincerely,
> >Shima
> >--
> >Gromacs Users mailing list
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> >* 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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Re: [gmx-users] Rerun error

Last frame -1 time    0.000   

# Atoms  -1
Last frame -1 time    0.000   


Item    #frames Timestep (ps)
Step 0
Time 0
Lambda   0
Coords   0
Velocities   0
Forces   0
Box  0





Sincerely,
Shima



From: Mark Abraham 
To: Discussion list for GROMACS users ; Shima Arasteh 
 
Sent: Friday, January 24, 2014 6:43 PM
Subject: Re: [gmx-users] Rerun error



What does gmxcheck say about this files?

Mark



On Fri, Jan 24, 2014 at 3:49 PM, Shima Arasteh  
wrote:

Hi,
>
>I had a large .trr file, tried to do rerun on it. First I used split command 
>and made 10 new .trr files with 2G in size. Then ran rerun on the first 
>2G.trr, but this does not work for the rest of trr files and I get the error:
>The number of atoms in trajectory (-1) doesn't match the input file.
>
>Would you please give me any suggestions?
>Thanks in advance
>
>
>
>Sincerely,
>Shima 
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Re: [gmx-users] Rerun error

2014-01-24 Thread Christian Wennberg

Try moving the trajectory to a separate folder from the one you are 
running the rerun from and then use --rerun /newfolder/traj.trr.
Mdrun creates a new traj.trr when doing rerun and then tries to read 
this instead of the one you supply from the start if they both are to be 
named traj.trr


/Christian

On 2014-01-24 15:49, Shima Arasteh wrote:

Hi,

I had a large .trr file, tried to do rerun on it. First I used split command 
and made 10 new .trr files with 2G in size. Then ran rerun on the first 2G.trr, 
but this does not work for the rest of trr files and I get the error:
The number of atoms in trajectory (-1) doesn't match the input file.

Would you please give me any suggestions?
Thanks in advance



Sincerely,
Shima


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Re: [gmx-users] reseed

2014-01-24 Thread Mark Abraham

No, see gen-vel in .mdp settings.

Mark

On Fri, Jan 24, 2014 at 3:30 PM, Jacopo Sgrignani  wrote:

> Dear all
> I would like to run multiple independent simulations reassigning starting
> velocities,
> does the -reseed option work only in REMD or also for standard MD?
>
> thanks
>
> Jacopo
>
>
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Re: [gmx-users] Rerun error

2014-01-24 Thread Mark Abraham

What does gmxcheck say about this files?

Mark

On Fri, Jan 24, 2014 at 3:49 PM, Shima Arasteh
wrote:

> Hi,
>
> I had a large .trr file, tried to do rerun on it. First I used split
> command and made 10 new .trr files with 2G in size. Then ran rerun on the
> first 2G.trr, but this does not work for the rest of trr files and I get
> the error:
> The number of atoms in trajectory (-1) doesn't match the input file.
>
> Would you please give me any suggestions?
> Thanks in advance
>
>
>
> Sincerely,
> Shima
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> posting!
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[gmx-users] Rerun error