[gmx-users] gromacs.org_gmx-users Digest, Vol 129, Issue 4
asasa qsqs
sanaz_dr_m at yahoo.com
Fri Jan 2 17:12:21 CET 2015
Dear justin,
I want to calculate the electrostatic potential of pure DPPC with this command "g_potential -f md.trr -s md.tpr -n dppc.ndx -sl 70 -o electrostatic.xvg" but i gave negative value for it that is not in agreement with another simulations. content of electrostatic.xvg is :
# This file was
created Fri Jan 2 06:59:44 2015
# by the following command:
# g_potential -f md.trr -n dppc.ndx -s md.tpr -d z -sl 70 -o electrostatic.xvg
#
# g_potential is part of G R O M A C S:
#
# Gromacs Runs On Most of All Computer Systems
#
@ title "Electrostatic
Potential"
@ xaxis label "Box (nm)"
@ yaxis label "Potential (V)"
@TYPE xy
@ view 0.15, 0.15, 0.75, 0.85
@ legend on
@ legend box on
@ legend loctype view
@ legend 0.78, 0.8
@ legend length 2
@ s0 legend "DPPC"
0 -0
0.1020072937011719 -2.567502819917437e-07
0.2040145874023437 -5.135005644617221e-06
0.3060218811035156 -4.947257004377959e-05
0.4080291748046875 -0.0003370328865105846
0.5100364685058594 -0.001842456075442605
0.6120437622070312 -0.008000900456833342
0.7140510559082031 -0.0277002585097313
0.816058349609375 -0.07850842775718628
0.9180656433105469 -0.1869234659171869
1.020072937011719 -0.3819110421478191
1.122080230712891 -0.6821675855578936
1.224087524414062 -1.084356581618383
1.326094818115234 -1.563908413892375
1.428102111816406 -2.088089675203653
1.530109405517578 -2.622860581236976
1.63211669921875 -3.136185314266401
1.734123992919922 -3.600551094919505
1.836131286621094 -3.988238825132194
1.938138580322265 -4.278617107110116
2.040145874023438 -4.469604973139271
2.142153167724609 -4.577608951258815
2.244160461425781 -4.629402873791392
2.346167755126953 -4.649992367693026
2.448175048828125 -4.656826483858561
2.550182342529297 -4.658976705591106
2.652189636230469 -4.659532283703276
2.75419692993164 -4.659610386590746
2.856204223632812 -4.659623050260158
2.958211517333984 -4.659629776578899
3.060218811035156 -4.659632940486518
3.162226104736328 -4.659633456656731
3.2642333984375 -4.659633732123568
3.366240692138672 -4.659634007590405
3.468247985839843 -4.659634283057242
3.570255279541016 -4.65963455852408
3.672262573242187 -4.659634737709559
3.774269866943359 -4.659634242925521
3.876277160644531 -4.659632143452044
3.978284454345703 -4.659629867461843
4.080291748046875 -4.659672875799365
4.182299041748046 -4.659850308951451
4.284306335449219 -4.659936339019628
4.386313629150391 -4.659331951664936
4.488320922851562 -4.65658309018609
4.590328216552734 -4.646515258536495
4.692335510253906 -4.616826878885218
4.794342803955078 -4.546972187682989
4.896350097656249 -4.411449918083245
4.998357391357422 -4.187652974057762
5.100364685058594 -3.86655691142704
5.202371978759765 -3.456370989402685
5.304379272460937 -2.974261936074294
5.406386566162109 -2.443137155357121
5.508393859863281 -1.894504652441843
5.610401153564453 -1.367078174976005
5.712408447265624 -0.9023050100298249
5.814415740966797 -0.5323573575841695
5.916423034667968 -0.2692219366920132
6.01843032836914 -0.1047745876335641
6.120437622070312 -0.01593955616386777
6.222444915771484 0.02507844662681752
6.324452209472656 0.04088049050993046
6.426459503173827 0.04582596098146221
6.528466796875 0.04705941609406363
6.630474090576172 0.04729255605812091
6.732481384277343 0.0473236335498442
6.834488677978515 0.04732571430656037
6.936495971679687 0.04732516337288611
7.038503265380859 0.04732461243921186
would you please help me what must i do for obtaining the correct value according to another simulations?
Regards,
Mrs.Mahdavi
On Thursday, January 1, 2015 6:14 PM, "gromacs.org_gmx-users-request at maillist.sys.kth.se" <gromacs.org_gmx-users-request at maillist.sys.kth.se> wrote:
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Today's Topics:
1. Re: atom freezing (mah maz)
2. Re: atom freezing (Justin Lemkul)
3. Re: atom freezing (mah maz)
4. Re: Restarting crashed simulation (bharat gupta)
5. Re: g_select syntax unavailable in GROMACS 5.0 and 5.0.1
(Kester Wong)
----------------------------------------------------------------------
Message: 1
Date: Thu, 1 Jan 2015 22:07:33 +0330
From: mah maz <mahmaz71 at gmail.com>
To: gromacs.org_gmx-users at maillist.sys.kth.se
Subject: Re: [gmx-users] atom freezing
Message-ID:
<CAJp4d_sL1h859QFxkUUQnZwfu4afk1+dh8tv9pR23cRELujgDA at mail.gmail.com>
Content-Type: text/plain; charset=UTF-8
Thanks Justin! I tried the freezegrps and freezedim but it needed the name
of the groups. As I said in my system only one type of atom is defined.
Should I put the desired atoms in a different group and freeze them? Any
other ways to call the atoms by their numbers?
Regars,
Mah
On Thu, Jan 1, 2015 at 9:06 PM, mah maz <mahmaz71 at gmail.com> wrote:
> Dear all,
>
> I want to have different situations for different atoms in my system. In
> the .mdp file how can I freez some of the atoms? ( I dont have residues in
> the system; 3 kinds of atoms are present just by one atom type name) Is it
> possible to assign different situations to some of the atoms by writing
> atom numbers?
>
> thank you!
>
------------------------------
Message: 2
Date: Thu, 01 Jan 2015 13:38:36 -0500
From: Justin Lemkul <jalemkul at vt.edu>
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] atom freezing
Message-ID: <54A5942C.9090007 at vt.edu>
Content-Type: text/plain; charset=windows-1252; format=flowed
On 1/1/15 1:37 PM, mah maz wrote:
> Thanks Justin! I tried the freezegrps and freezedim but it needed the name
> of the groups. As I said in my system only one type of atom is defined.
> Should I put the desired atoms in a different group and freeze them? Any
> other ways to call the atoms by their numbers?
Index groups are the only method. The group concept is described in depth in
the manual. Read about make_ndx.
-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
jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
==================================================
------------------------------
Message: 3
Date: Thu, 1 Jan 2015 22:19:22 +0330
From: mah maz <mahmaz71 at gmail.com>
To: gromacs.org_gmx-users at maillist.sys.kth.se
Subject: Re: [gmx-users] atom freezing
Message-ID:
<CAJp4d_uuaibgGY3f6aWdf0CciJJCaTU9ZKUdpoxiJoP78nomQw at mail.gmail.com>
Content-Type: text/plain; charset=UTF-8
Dear Justin,
Thank you for your help!
Cheers,
Mah
On Thu, Jan 1, 2015 at 10:07 PM, mah maz <mahmaz71 at gmail.com> wrote:
> Thanks Justin! I tried the freezegrps and freezedim but it needed the name
> of the groups. As I said in my system only one type of atom is defined.
> Should I put the desired atoms in a different group and freeze them? Any
> other ways to call the atoms by their numbers?
> Regars,
> Mah
>
> On Thu, Jan 1, 2015 at 9:06 PM, mah maz <mahmaz71 at gmail.com> wrote:
>
>> Dear all,
>>
>> I want to have different situations for different atoms in my system. In
>> the .mdp file how can I freez some of the atoms? ( I dont have residues in
>> the system; 3 kinds of atoms are present just by one atom type name) Is it
>> possible to assign different situations to some of the atoms by writing
>> atom numbers?
>>
>> thank you!
>>
>
>
------------------------------
Message: 4
Date: Fri, 2 Jan 2015 08:17:14 +0900
From: bharat gupta <bharat.85.monu at gmail.com>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Subject: Re: [gmx-users] Restarting crashed simulation
Message-ID:
<CAAh+zSXktpvh6H4vv46RxgxVVYwTEA0MKnu2pkgwyyy+v3-88g at mail.gmail.com>
Content-Type: text/plain; charset=UTF-8
Hi,
My simulation stopped because of power outage and I restarted it using the
command:
mpirun -np 32 mdrun_mpi -cpi mdrun.cpt -s mdrun.cpt
It shows correctly the restarting time point, however the mdrun.log is not
getting updated and I don't know how to verify whether the simulation is
being continued or not ?
--
*Best Regards*
Bharat
------------------------------
Message: 5
Date: Fri, 2 Jan 2015 11:12:54 +0900
From: Kester Wong <Kester2014 at ibs.re.kr>
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] g_select syntax unavailable in GROMACS 5.0
and 5.0.1
Message-ID: <Mime4j.41a1.382861a4eacd7697.14aa86aba84 at ibs.re.kr>
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