<br><br><blockquote>hai justin,<br><br>ya i am working on actual KALP tutorial only<br><br>http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/index.html<br><br>and i am using the pdb file which is given in the website. This is the first time i am doing MD simulation <br>for transmembrane proteins before using the protein of my interest i tried it with the peptide given the tutorial.<br><br>hereby i am attaching the .mdp file which i am using <br><br><pre>; minim.mdp - used as input into grompp to generate em.tpr<br>; Parameters describing what to do, when to stop and what to save<br>integrator        = steep                Algorithm (steep = steepest descent minimization)<br>emtol                = 1000.0         Stop minimization when the maximum force < 1000.0 kJ/mol/nm<br>emstep = 0.01 ; Energy step size<br>nsteps                = 50000                 Maximum number of (minimization) steps to perform<br><br>; Parameters describing how to find the neighbors of each atom and ho
w to calculate the interactions<br>nstlist                = 1                Frequency to update the neighbor list and long range forces<br>ns_type                = grid                Method to determine neighbor list (simple, grid)<br>rlist                = 1.2                Cut-off for making neighbor list (short range forces)<br>coulombtype        = PME                Treatment of long range electrostatic interactions<br>rcoulomb        = 1.2                Short-range electrostatic cut-off<br>rvdw                = 1.2                Short-range Van der Waals cut-off<br>pbc                = xyz                 Periodic Boundary Conditions (yes/no)<br></pre><br>thank you<br><br>with regards,<br>N.Hema Dhevi<br><br><br><br><br>---------- Original message ----------<br>From:gmx-users-request@gromacs.org< gmx-users-request@gromacs.org ><br>Date: 30 Nov 09 19:38:18<br>Subject: gmx-users Digest, Vol 67, Issue 150<br>To: gmx-users@gromacs.org<br><br>Send gmx-users mailing list submissions to<br>
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Today's Topics:<br>
<br>
1. Re: Re: How to make carbon nanotube infinite? (Justin A. Lemkul)<br>
2. trjconv -pbc cluster with rhombic dodecahedron box<br>
(chris.neale@utoronto.ca)<br>
3. Re: gmx-users Digest, memory allocation error (Justin A. Lemkul)<br>
4. amber force field in Gromacs (servaas)<br>
5. Survey: 3 minutes of your time (Pieter van 't Hof)<br>
6. Survey: 3 minutes of your time (Pieter van 't Hof)<br>
<br>
<br>
----------------------------------------------------------------------<br>
<br>
Message: 1<br>
Date: Mon, 30 Nov 2009 08:05:45 -0500<br>
From: "Justin A. Lemkul" <jalemkul@vt.edu><br>
Subject: Re: [gmx-users] Re: How to make carbon nanotube infinite?<br>
To: Discussion list for GROMACS users <gmx-users@gromacs.org><br>
Message-ID: <4B13C329.1090301@vt.edu><br>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed<br>
<br>
<br>
<br>
Cun Zhang wrote:<br>
> hi, Justin. Thank you for your meticulous and patient explanation !<br>
> <br>
> Before I see this post, I misunderstood the meaning of sharing bonds.<br>
> I thought note only the bonds,but also the angles and the dihedrals<br>
> should be added to top file.<br>
<br>
I see now that I should have been more careful in my explanation. It is better <br>
stated that *bonded parameters* should extend across periodic boundaries, not <br>
just bonds. But the same principle applies.<br>
<br>
> <br>
> It was so complicated to deal manually that I wrote that script.<br>
> <br>
<br>
That's sensible, but I didn't understand what your scripting was doing with <br>
renumbering and all that. Just add the appropriate parameters to the .top, <br>
given the numbering in the coordinate file.<br>
<br>
> I will read the doucment you mentioned carefully .<br>
<br>
The CNT how-to was painstakingly assembled by Chris Stiles a few years ago after <br>
many conversations like this one. He has done a nice service by assembling the <br>
tutorial. I believe it applies to version 3.3.3, but many of the principles are <br>
the same. Remember, as I suggested before, that x2top from the 3.3.3 <br>
distribution works with the -pbc option, which does all of the complicated work <br>
for you. Not a bad option for your initial topology generation.<br>
<br>
> And I will fix these notes and warnings as grompp and mdrun suggest.<br>
> <br>
<br>
Good idea :)<br>
<br>
-Justin<br>
<br>
-- <br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]vt.edu | (540) 231-9080<br>
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin<br>
<br>
========================================<br>
<br>
<br>
------------------------------<br>
<br>
Message: 2<br>
Date: Mon, 30 Nov 2009 08:18:42 -0500<br>
From: chris.neale@utoronto.ca<br>
Subject: [gmx-users] trjconv -pbc cluster with rhombic dodecahedron<br>
        box<br>
To: gmx-users@gromacs.org<br>
Message-ID: <20091130081842.9t05l0tg2ogwoc80@webmail.utoronto.ca><br>
Content-Type: text/plain;        charset=ISO-8859-1;        DelSp="Yes";<br>
        format="flowed"<br>
<br>
Hi Daniel, what Tsjerk has suggested is really the only way to go <br>
here. If your cluster is not whole in the first frame, you can do it <br>
this way:<br>
<br>
1. use trjconv -pbc cluster to make your cluster whole in a frame near <br>
the start of your trajectory. If the first frame enters the infinite <br>
loop, then try the second frame, etc.<br>
<br>
2. Make a new .tpr based on this clustered .gro<br>
<br>
3. run trjconv -pbc nojump<br>
<br>
Chris.<br>
<br>
--- original message ---<br>
<br>
Hi Daniel,<br>
<br>
This doesn't exactly answer your question, but if your vesicle is<br>
whole at the start, can't you better keep it that way using -pbc<br>
nojump? If necessary, you can also recenter afterwards.<br>
<br>
Hope it helps,<br>
<br>
Tsjerk<br>
<br>
On Mon, Nov 30, 2009 at 12:24 PM, Daniel Parton<br>
<daniel.parton@bioch.ox.ac.uk> wrote:<br>
<br>
[Hide Quoted Text]<br>
Hi,<br>
<br>
I am running a coarse-grained simulation of a lipid vesicle (~70,000<br>
particles), using a rhombic dodecahedron box to limit the amount of solvent<br>
I require. The vesicle (unsurprisingly) moves over the periodic boundaries<br>
during the simulation. Various analyses I am conducting require the vesicle<br>
to be whole, so I have been trying to use trjconv with the -pbc cluster<br>
option, selecting the lipids as the group to be clustered. I am only<br>
interested in the lipid behaviour, so I am using a trajectory with only the<br>
lipids included. However, at certain frames, the program seems to enter an<br>
infinite loop, producing many lines of the following sort of information:<br>
<br>
...<br>
COM: 12.445 5.934 15.354 iter = 2359<br>
COM: 12.675 6.135 3.094 iter = 2360<br>
COM: 12.455 5.934 15.368 iter = 2361<br>
COM: 12.686 6.131 3.116 iter = 2362<br>
COM: 12.454 5.945 15.396 iter = 2363<br>
COM: 12.720 6.168 3.176 iter = 2364<br>
COM: 12.461 5.947 15.435 iter = 2365<br>
COM: 12.731 6.174 3.221 iter = 2366<br>
COM: 12.468 5.945 15.475 iter = 2367<br>
COM: 12.723 6.172 3.247 iter = 2368<br>
...<br>
<br>
This is using gromacs version 3.2.1, as with any later version I have tried<br>
(3.3.3, 4.0.4, 4.0.5), trjconv -pbc clust won't work at all, even with<br>
cubic simulation boxes. I have successfully used version 3.2.1 many times<br>
for this purpose when dealing with cubic simulation boxes.<br>
<br>
I have tried many different ways to get this to work, such as converting to<br>
the compact representation before clustering. Also, the frame where the<br>
program is the first one where a lipid has moved over a periodic boundary,<br>
when the system is viewed as the compact representation. The same behaviour<br>
occurs when that frame is dumped out as a .gro file and the program is run<br>
on that file only.<br>
<br>
Does anyone have any idea how to get this to work? Any help would be much<br>
appreciated! Please let me know if you need more information about my<br>
simulation set-up.<br>
<br>
Daniel Parton<br>
<br>
<br>
<br>
<br>
<br>
------------------------------<br>
<br>
Message: 3<br>
Date: Mon, 30 Nov 2009 08:38:21 -0500<br>
From: "Justin A. Lemkul" <jalemkul@vt.edu><br>
Subject: Re: [gmx-users] gmx-users Digest, memory allocation error<br>
To: "Gromacs Users' List" <gmx-users@gromacs.org><br>
Message-ID: <4B13CACD.2020908@vt.edu><br>
Content-Type: text/plain; charset=UTF-8; format=flowed<br>
<br>
<br>
<br>
hema dhevi wrote:<br>
> <br>
> hi justin,<br>
> <br>
> thanks for your reply<br>
> <br>
> Totally I have 6126 atoms (residues + DPPC ) I am using the same pdb file<br>
> and lipid pdb (DPPC-128) which is given in the KAPL tutorial.<br>
> <br>
<br>
OK, just to clarify - are you working on the actual KALP tutorial when this <br>
error comes up, or are you working on your own system? I am not 100% clear from <br>
what you've described. Your previous message said you had some bacterial <br>
protein, and now you're talking about the KALP system.<br>
<br>
Can you post the .mdp file you're using?<br>
<br>
-Justin<br>
<br>
> E ven tried it without adding any solvents to it, I am getting the same <br>
> error (memory allocation).<br>
> <br>
> My system has 15.6 GB free space its a HP workstation with 2GB RAM.<br>
> <br>
> looking for ur reply at the earliest.<br>
> <br>
> Thanks in advance<br>
> <br>
> with regards,<br>
> N.Hema Dhevi<br>
> <br>
> <br>
> ---------- Original message ----------<br>
> From:Justin A. Lemkul< jalemkul@vt.edu ><br>
> Date: 29 Nov 09 02:49:42<br>
> Subject: Re: [gmx-users] gmx-users Digest, memory allocation error<br>
> To: hema dhevi , Discussion list for GROMACS users<br>
> <br>
> <br>
> <br>
> hema dhevi wrote:<br>
> > Dear all,<br>
> ><br>
> > I am doing MD simulation for a bacterial inner transmembrane protein.<br>
> > I need to know which unit of lipid molecule i should take for<br>
> building<br>
> > the lipid bilayer.<br>
> ><br>
> > I made a trial run with DPPC. I was referring KAPL tutorial for my<br>
> > simulation. I made all the alteration in the topology file and in<br>
> the<br>
> > itp file, as it is mentioned in the<br>
> > tutorial but i wouldnt run after inflategro step ie during grompp<br>
> i am<br>
> > getting memory allocation error.<br>
> ><br>
> > Hereby I am attaching the erro r msg i got from grompp<br>
> ><br>
> ><br>
> > grompp -f ion.mdp -c system.pdb -p topol_protein.top -o ions.tpr<br>
> ><br>
> ><br>
> > Program grompp, VERSION 3.3.3<br>
> > Source code file: smalloc.c, line: 137<br>
> ><br>
> > Fatal error:<br>
> > realloc for nnb->a[i][nre] (103103576 bytes, file topexcl.c, line<br>
> 101,<br>
> > nnb->a[i][nre]=0x0x33b3c3a0)<br>
> > ----------------------<br>
> ><br>
> > "Can't You Make This Thing Go Faster ?" (Black Crowes)<br>
> ><br>
> > : Cannot allocate memory<br>
> > Program grompp, VERSION 4.0.5<br>
> > Source code file: smalloc.c , line: 179<br>
> ><br>
> > Fatal error:<br>
> > Not enough memory.<br>
> > Failed to realloc 244312864 bytes for nnb->a[i][nre],<br>
> > nnb->a[i][nre]=0x22deb4d8 (called from file topexcl.c, line 102)<br>
> > -----------------------------<br>
> > --------------------------<br>
> ><br>
> > "It's Against the Rules" (Pulp Fiction)<br>
> > : Cannot allocate memory<br>
> ><br>
> ><br>
> > I think i didnt made any error in file preparation and alteration of<br>
> > .itp and .top file. Because I tried it with 2 DPPC molecule it was<br>
> > working fine. when i am trying with the whole set of 128 molecules of<br>
> > DPPC i am facing this problem. Is this a problem something related to<br>
> > Memory of system if so what is the requirement for making this run<br>
> > possible.<br>
> ><br>
> <br>
> How many atoms are in your system? How much memory do you have<br>
> available on the<br>
> machine you're using? The general solutions can be found here:<br>
> <br>
> http://www.gromacs.org/Documentation/Errors#Cannot_allocate_memory<br>
> <br>
> -Justin<br>
> <br>
> > I got struck up in my work I am highly in need of ur help...<br>
> ><br>
> ><br>
> > Thanks in advance< /span><br>
> ><br>
> > with regards,<br>
> > N.Hema Dhevi<br>
> ><br>
> <br>
> -- <br>
> ========================================<br>
> <br>
> Justin A. Lemkul<br>
> Ph.D. Candidate<br>
> ICTAS Doctoral Scholar<br>
> Department of Biochemistry<br>
> Virginia Tech<br>
> Blacksburg, VA<br>
> jalemkul[at]vt.edu | (540) 231-9080<br>
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin<br>
> <br>
> ========================================<br>
> <br>
<br>
-- <br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]vt.edu | (540) 231-9080<br>
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin<br>
<br>
========================================<br>
<br>
<br>
------------------------------<br>
<br>
Message: 4<br>
Date: Mon, 30 Nov 2009 14:29:56 +0100<br>
From: servaas <servaas.michielssens@student.kuleuven.be><br>
Subject: [gmx-users] amber force field in Gromacs<br>
To: "gmx-users@gromacs.org" <gmx-users@gromacs.org><br>
Message-ID: <1259587796.12957.18.camel@boltzmann><br>
Content-Type: text/plain<br>
<br>
Hello,<br>
<br>
I tried using the amber force field in GROMACS. I proceeded as follows:<br>
Determined my parameters with RED/ANTECHAMBER/tleap converted them with amb2gmx.pl <br>
(or with acpypi, problem is the same) to gromacs coordinate and topology files. It concerns a modified nucleotide. I minimized with steepest descent, everything was fine. <br>
When I tried running a simulation in single precision with this .mdp file (only nucleotide without solvent):<br>
<br>
integrator = md<br>
<br>
dt = 0.002<br>
nsteps = 250000<br>
nstcomm = 1<br>
<br>
;output<br>
nstxout = 1<br>
nstvout = 1<br>
nstfout = 0<br>
nstlog = 500<br>
nstenergy = 1<br>
<br>
nstlist = 10<br>
ns_type = grid<br>
rlist = 1.2<br>
coulombtype = PME<br>
rcoulomb = 1.2<br>
vdwtype = cut-off<br>
rvdw = 1.2<br>
<br>
fourierspacing = 0.12<br>
pme_order = 4<br>
ewald_rtol = 1e-5<br>
<br>
;constraints<br>
constraints = all-bonds<br>
<br>
<br>
; temperature coupling is on<br>
Tcoupl = v-rescale<br>
tau_t = 0.1<br>
tc-grps = system<br>
ref_t = 300<br>
<br>
pcoupl = no<br>
<br>
I get LINCS errors and eventually a crash. Now I tried running the same simulation with the same force field parameters in amber and everything was fine. <br>
I also ran the calculation in GROMACS with double precision here again everything was fine... I also tried running a small nucleic acid fragment (so no modified parameters here) <br>
that I created in tleap and converted to GROMACS again this crashes with lincs errors in GROMACS. When I look at the trajectories it is the O4' of the ribose who clashes with the O3'. <br>
<br>
The fact that I still get this problem with non modified amber parameters makes me thing there is something wrong with my .mdp file to run with amber FF, any suggestions?<br>
Strange also that double precision seems to work just fine....<br>
<br>
<br>
<br>
------------------------------<br>
<br>
Message: 5<br>
Date: Mon, 30 Nov 2009 14:49:12 +0100<br>
From: Pieter van 't Hof <pieter.van.t.hof@logica.com><br>
Subject: [gmx-users] Survey: 3 minutes of your time<br>
To: gmx-users@gromacs.org<br>
Message-ID: <1259588952.16011.27.camel@docktop><br>
Content-Type: text/plain<br>
<br>
Hello,<br>
<br>
My name is Pieter van 't Hof. As part of my Master thesis in computer<br>
science I am currently extending Gromacs and VMD to visualize short<br>
range Lennard Jones potentials and Coulomb forces during interactive<br>
molecular dynamics simulations. In order to choose a representation<br>
method which is suitable for the most people, I designed a little survey<br>
with 7 multiple choice questions. <br>
<br>
If some of you (preferably people who use Gromacs mainly for<br>
protein-ligand interactions) would fill-in this survey, it is greatly<br>
appreciated.<br>
<br>
Thank you very much in advance.<br>
<br>
<br>
Sincerely,<br>
<br>
Pieter van 't Hof<br>
Utrecht University, The Netherlands<br>
<br>
<br>
Please help Logica to respect the environment by not printing this email / Pour contribuer comme Logica au respect de l'environnement, merci de ne pas imprimer ce mail / Bitte drucken Sie diese Nachricht nicht aus und helfen Sie so Logica dabei, die Umwelt zu schützen. / Por favor ajude a Logica a respeitar o ambiente nao imprimindo este correio electronico.<br>
<br>
<br>
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This e-mail and any attachment is for authorised use by the intended recipient(s) only. It may contain proprietary material, confidential information and/or be subject to legal privilege. It should not be copied, disclosed to, retained or used by, any other party. If you are not an intended recipient then please promptly delete this e-mail and any attachment and all copies and inform the sender. Thank you.<br>
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------------------------------<br>
<br>
Message: 6<br>
Date: Mon, 30 Nov 2009 14:52:21 +0100<br>
From: Pieter van 't Hof <pieter.van.t.hof@logica.com><br>
Subject: [gmx-users] Survey: 3 minutes of your time<br>
To: gmx-users@gromacs.org<br>
Message-ID: <1259589141.16011.29.camel@docktop><br>
Content-Type: text/plain<br>
<br>
Hello,<br>
<br>
My name is Pieter van 't Hof. As part of my Master thesis in computer<br>
science I am currently extending Gromacs and VMD to visualize short<br>
range Lennard Jones potentials and Coulomb forces during interactive<br>
molecular dynamics simulations. In order to choose a representation<br>
method which is suitable for the most people, I designed a little survey<br>
with 7 multiple choice questions. <br>
<br>
If some of you (preferably people who use Gromacs mainly for<br>
protein-ligand interactions) would fill-in this survey, it is greatly<br>
appreciated.<br>
<br>
The survey is located at http://www.thesistools.com/?qid=95789<br>
<br>
Thank you very much in advance.<br>
<br>
<br>
Sincerely,<br>
<br>
Pieter van 't Hof<br>
Utrecht University, The Netherlands<br>
<br>
<br>
Please help Logica to respect the environment by not printing this email / Pour contribuer comme Logica au respect de l'environnement, merci de ne pas imprimer ce mail / Bitte drucken Sie diese Nachricht nicht aus und helfen Sie so Logica dabei, die Umwelt zu schützen. / Por favor ajude a Logica a respeitar o ambiente nao imprimindo este correio electronico.<br>
<br>
<br>
<br>
This e-mail and any attachment is for authorised use by the intended recipient(s) only. It may contain proprietary material, confidential information and/or be subject to legal privilege. It should not be copied, disclosed to, retained or used by, any other party. If you are not an intended recipient then please promptly delete this e-mail and any attachment and all copies and inform the sender. Thank you.<br>
<br>
<br>
<br>
<br>
------------------------------<br>
<br>
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End of gmx-users Digest, Vol 67, Issue 150<br>
******************************************</pieter.van.t.hof@logica.com></pieter.van.t.hof@logica.com></gmx-users@gromacs.org></servaas.michielssens@student.kuleuven.be></gmx-users@gromacs.org></jalemkul@vt.edu></daniel.parton@bioch.ox.ac.uk></gmx-users@gromacs.org></jalemkul@vt.edu></blockquote>