[gmx-users] Re: gmx-users Digest, Vol 97, Issue 6

niaz poorgholami poorgholami at gmail.com
Tue May 1 19:44:42 CEST 2012 

Dear Justin
the results of EM was:
Steepest Descents converged to Fmax < 1000 in 77 steps
Potential Energy  = -3.6802272e+05
Maximum force     =  8.9652832e+02 on atom 1556
Norm of force     =  1.1512711e+02
 thank you for your concern

On Tue, May 1, 2012 at 9:33 PM,  <gmx-users-request at gromacs.org> wrote:
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> Today's Topics:
>
>   1. Re: POPC: ff53a6 and CHARMM36 formats (Justin A. Lemkul)
>   2. Re: segmentation fault during equilibration (Justin A. Lemkul)
>   3. Re: minimum distance between periodic images does not     aggree
>      with box dimensions (Tsjerk Wassenaar)
>   4. saltbridges newbie question (Denis Kazakiewicz)
>   5. Re: disre and posres together? (Mark Abraham)
>   6. Re: saltbridges newbie question (Peter C. Lai)
>   7. Re: saltbridges newbie question (Denis Kazakiewicz)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Tue, 01 May 2012 08:16:14 -0400
> From: "Justin A. Lemkul" <jalemkul at vt.edu>
> Subject: Re: [gmx-users] POPC: ff53a6 and CHARMM36 formats
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4F9FD40E.5070404 at vt.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>
>
> On 5/1/12 8:05 AM, Ángel Piñeiro wrote:
>> I guess there are better solutions but an alternative is to map your bilayer to
>> MARTINI (http://md.chem.rug.nl/cgmartini/) and then to use SUGAR-PIE
>> (http://smmb.usc.es/sugarpie/sugarpie.php) to go to from MARTINI to all-atom
>> CHARMM36.
>>
>
> Even simpler would be to fix the offending atom names and build a suitable .hdb
> entry (if one does not already exist) and produce the topology with pdb2gmx.  I
> would think it would then be far easier to preserve the original configurations
> of the lipids, rather than changing the resolution back and forth.
>
> -Justin
>
>> Hope it helps,
>>
>> Ángel.
>>
>>
>> On Tue, 2012-05-01 at 17:25 +0530, Anirban Ghosh wrote:
>>> Hi ALL,
>>>
>>>
>>> I have a equilibrated POPC bilayer (100 ns run) that I have run using GROMOS
>>> ff53a6 FF. Now, I wish to use this POPC bilayer for a new simulation using
>>> CHARMM36 FF in GROAMCS 4.5.5. There are differences in atom naming conventions
>>> (N, P, C, O) between this two FFs as a result of which pdb2gmx gives error.
>>> Can these atom names (hydrogens can be ignored) of my equilibrated POPC
>>> bilayer be changed manually and then used with CHARMM36 FF? Thanks a lot in
>>> advance.
>>>
>>>
>>>
>>>
>>> Regards,
>>>
>>>
>>> Anirban
>>> --
>>> gmx-users mailing listgmx-users at gromacs.org  <mailto:gmx-users at gromacs.org>
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>>
>>
>>
>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
>
>
> ------------------------------
>
> Message: 2
> Date: Tue, 01 May 2012 08:42:26 -0400
> From: "Justin A. Lemkul" <jalemkul at vt.edu>
> Subject: Re: [gmx-users] segmentation fault during equilibration
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4F9FDA32.6010502 at vt.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>
>
> On 5/1/12 7:19 AM, niaz poorgholami wrote:
>> Dear gmx users,
>> I am simulating a system including carbon nanotube(a finite
>> one)+water+surfactant and so far I have done these things:
>> 1.I generated the topology of CNT ( opls force field) by this command:
>> g_x2top -f cnt.pdf -o cnt.top -nopairs -nexcl 3 -name CNT
>> 2.I used TopolGen to produce topology of surfactant and I calculated
>> the charges of atomes by the RESP method and checked the
>> atomtypes to make sure that they make sence as well.so I changed some
>> atomtypes according to the opls.
>> 3.I build a topol.top file that contains topolgy of CNT+surfactant.
>> 4.I created the initial configuration for the CNT+surfactant by means
>> of packmol.
>> 5.I used editconf and genbox with these command:
>> editconf -f CNTSUR.pdb -o newbox.gro -d 0.7 -bt cubic
>
> Unrelated to the crash, but if your longest cutoff is 1.4 nm, setting a
> solute-box distance of 0.7 nm will lead to trouble if you ever use NPT.  With
> just a small fluctuation in box dimension, you can easily violate the minimum
> image convention.
>
>> genbox -cp newbox.gro -cs spc216.gro -p topol.top -o solv.gro
>> 6.I run grompp and genion for adding the ions:
>> grompp -f em.mdp -c solv.gro -p topol.top -o ions.tpr
>> genion -s ions.tpr -p topol.top -o solv_ions.gro -nname BR -nn 28
>> 7.I run grompp again for energy minimization:
>> grompp -f em_real.mdp -c solv_ions.gro -p topol.top -o em.tpr
>> mdrun -deffnm em
>> the em_real.mdp file contains:
>> ; Parameters describing what to do, when to stop and what to save
>> integrator    = steep         ; Algorithm (steep = steepest descent minimization)
>> emtol         = 1000.0        ; Stop minimization when the maximum force<  10.0 kJ/mol
>> emstep          = 0.01          ; Energy step size
>> nsteps                = 70000         ; Maximum number of (minimization) steps to perform
>> energygrps    = UNK LIG       ; Which energy group(s) to write to disk
>>
>> ; Parameters describing how to find the neighbors of each atom and how
>> to calculate the interactions
>> nstlist               = 1                 ; Frequency to update the neighbor list and long range forces
>> ns_type               = grid          ; Method to determine neighbor list (simple, grid)
>> rlist         = 0.9           ; Cut-off for making neighbor list (short range forces)
>> coulombtype   = PME           ; Treatment of long range electrostatic interactions
>> rcoulomb      = 0.9           ; long range electrostatic cut-off
>> rvdw          = 1.4           ; Periodic Boundary Conditions (yes/no)
>> pbc           = xyz           ; Periodic Boundary Conditions (yes/no)
>>
>
> What was the outcome of EM?  What were your values for Fmax and Epot?
>
>> 8.then I made an index file for CNT and surfactant and used genrestr
>> to restraint the CNT and surfactant during equilibration.
>> 9.I run grompp and mdrun with these command:grompp -f nvt.mdp -c
>> em.gro -p topol.top -o nvt.tpr -n index.ndx
>>                                              mdrun -deffnm nvt
>> and after passing 42900 of 50000 steps, segmentation fault occured.I
>> checked the log file but it did not contain any errors and I also used
>> VMD to see trajetory but I did not see anything wrong.
>> I would be pleased if anyone could help me how to fix this.
>
> We need to see your complete .mdp file for the NVT run.  As of now, there is no
> indication of what is wrong.
>
> -Justin
>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
>
>
> ------------------------------
>
> Message: 3
> Date: Tue, 1 May 2012 14:59:56 +0200
> From: Tsjerk Wassenaar <tsjerkw at gmail.com>
> Subject: Re: [gmx-users] minimum distance between periodic images does
>        not     aggree with box dimensions
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID:
>        <CABzE1SjRk2CM_Z1y1ddQWVSPwDukjEu3ox636A-fkRQ2b7YS2Q at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Hi Thomas,
>
> The rhombic dodecahedron is built as a rectangular brick, which makes
> it easy to fill with a rectangular bricklet of water. Now, for the
> smaller distances the short edge of the rectangular brick is smaller
> than the diameter of the particle, and it is represented fragmented.
> Best way to get acquainted with this stuff is drawing a circle, and a
> hexagon around it. Then tesselate a patch of space and draw the
> corresponding rectangular cell. Try to translate the rectangle such
> that the whole circle fits in. Good luck! :p
>
> For the other thing, notice that the distance reported is close to a
> bond length. Before checking the distances between periodic images,
> make sure that the solute not fragmented...
>
> Cheers,
>
> Tsjerk
>
> On Mon, Apr 30, 2012 at 4:38 PM, Thomas Evangelidis <tevang3 at gmail.com> wrote:
>>
>> Dear GROMACS users,
>>
>> I have a nanoparticle (perfect sphere) and want to enclose it into a rhombic
>> dodecahedron. For this purpose I use the following command lines
>>
>> editconf_d4.5.5 -f nano.gro -bt dodecahedron -d 1 -c -o nano_box.gro
>> grompp_d4.5.5 -f em.mdp -c nano_box.gro -p nano.top -o nano_box_EM.tpr
>> mdrun_d4.5.5 -v -deffnm nano_box_EM
>>
>> echo 0 | trjconv_d4.5.5 -pbc mol -ur compact -f nano_box_EM.trr -s
>> nano_box_EM.tpr -o nano_em_dodecahedron.xtc
>> echo 2 | g_mindist_d4.5.5 -f nano_em_dodecahedron.xtc -s nano_box_EM.tpr -pi
>> -od nano_mindist.xvg
>>
>> The first paradox is that the nanoparticle is fragmented in the dodecahedron
>> representation for -d (editconf option) less that 1 nm. The second paradox
>> is that the minimum distance between periodic images for -d 0.5, 1, 2, 3 is
>> 0.183, 0.237, 4.171 and 6.167 nm respectively. The last two distances are
>> close to the expected values but the first two are far from them. I would
>> expect ~1 and ~2 nm for -d 0.5 and 1 respectively, since by definition with
>> option -d and dodecahedron, the dimensions are set to the diameter of the
>> system (largest distance between atoms) plus twice the speciï¬ ed distance.
>> Can anyone explain what's happening?
>>
>> Thanks in advance.
>> Thomas
>>
>>
>>
>> --
>>
>> ======================================================================
>>
>> Thomas Evangelidis
>>
>> PhD student
>>
>> Biomedical Research Foundation, Academy of Athens
>>
>> 4 Soranou Ephessiou , 115 27 Athens, Greece
>>
>> email: tevang at bioacademy.gr
>>
>>           tevang3 at gmail.com
>>
>>
>> website: https://sites.google.com/site/thomasevangelidishomepage/
>>
>>
>>
>>
>> --
>> gmx-users mailing list    gmx-users at gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>> Please don't post (un)subscribe requests to the list. Use the
>> www interface or send it to gmx-users-request at gromacs.org.
>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
>
> post-doctoral researcher
> Molecular Dynamics Group
> * Groningen Institute for Biomolecular Research and Biotechnology
> * Zernike Institute for Advanced Materials
> University of Groningen
> The Netherlands
>
>
> ------------------------------
>
> Message: 4
> Date: Tue, 01 May 2012 15:08:24 +0200
> From: Denis Kazakiewicz <d.kazakiewicz at gmail.com>
> Subject: [gmx-users] saltbridges newbie question
> To: gmx-users at gromacs.org
> Message-ID: <4F9FE048.9060601 at gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hello
> Would you please give a hint or reference about how to interpret salt
> bridge analysis graphs (output of g_saltbr command)?
> Thank you
>
> Denis
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> ------------------------------
>
> Message: 5
> Date: Wed, 02 May 2012 00:19:44 +1000
> From: Mark Abraham <Mark.Abraham at anu.edu.au>
> Subject: Re: [gmx-users] disre and posres together?
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4F9FF100.2090106 at anu.edu.au>
> Content-Type: text/plain; charset="iso-8859-1"
>
> On 1/05/2012 4:58 PM, Banafsheh Mehrazma wrote:
>> Dear all;
>> I am wondering if we can use both disre and POSRES in .mdp file together?
>
> Yes, this is a routine procedure for equilibrating while preserving an
> initial structure for some reason.
>
>> To be more perspective,  is it correct to add all these below in the
>> *.mdp file?
>> ..........................................
>> define= -DPOSRES
>> disre             = simple
>> disre-weighting   = equal
>> disre-mixed       = no
>> disre-fc          = 1000
>> disre-tau         = 0
>> .........................................
>>
>
> That looks fine.
>
> Mark
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> ------------------------------
>
> Message: 6
> Date: Tue, 1 May 2012 11:50:55 -0500
> From: "Peter C. Lai" <pcl at uab.edu>
> Subject: Re: [gmx-users] saltbridges newbie question
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <20120501165054.GB94109 at cesium.hyperfine.info>
> Content-Type: text/plain; charset="us-ascii"
>
> If you use -sep it should just be distance over time of a given charged pair.
>
> The only functional difference between g_saltbr and g_dist is that g_saltbr
> tries to be intelligent and preselects the pairs for you...
>
> On 2012-05-01 03:08:24PM +0200, Denis Kazakiewicz wrote:
>> Hello
>> Would you please give a hint or reference about how to interpret salt
>> bridge analysis graphs (output of g_saltbr command)?
>> Thank you
>>
>> Denis
>
>> --
>> gmx-users mailing list    gmx-users at gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
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>
>
> --
> ==================================================================
> Peter C. Lai                    | University of Alabama-Birmingham
> Programmer/Analyst              | KAUL 752A
> Genetics, Div. of Research      | 705 South 20th Street
> pcl at uab.edu                     | Birmingham AL 35294-4461
> (205) 690-0808                  |
> ==================================================================
>
>
>
> ------------------------------
>
> Message: 7
> Date: Tue, 01 May 2012 19:02:30 +0200
> From: Denis Kazakiewicz <d.kazakiewicz at gmail.com>
> Subject: Re: [gmx-users] saltbridges newbie question
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4FA01726.8030502 at gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Thank you indeed
> Apologize for a silly question
> On 01.05.2012 18:50, Peter C. Lai wrote:
>> If you use -sep it should just be distance over time of a given charged pair.
>>
>> The only functional difference between g_saltbr and g_dist is that g_saltbr
>> tries to be intelligent and preselects the pairs for you...
>>
>> On 2012-05-01 03:08:24PM +0200, Denis Kazakiewicz wrote:
>>> Hello
>>> Would you please give a hint or reference about how to interpret salt
>>> bridge analysis graphs (output of g_saltbr command)?
>>> Thank you
>>>
>>> Denis
>>> --
>>> gmx-users mailing list    gmx-users at gromacs.org
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>>
>
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