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Re: run-cpt-md.inp
rmv #383 11/18/04 08:24 PM
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Thank you for all yours answers and patience.

Re: run-cpt-md.inp
lennart #384 02/24/05 05:53 AM
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Dear all ,
I used the script to caculate the density (water + protein) , and find the final density = 0.212099 .
It's not reasonable . The density (water + protein)
should be near 1 (g/cc) .
yeng tseng

http://165.112.184.13/ubbthreads/showflat.php?Cat=0&Number=4274&an=0&page=0
"
scalar mass stat
set m ?STOT
calc rho = 1.66 * @M / ?VOLU
"

Re: run-cpt-md.inp
label #385 02/24/05 09:01 AM
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lennart Online Content OP
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Yes you seem to have too little water in you system. How big is your protein? How many water molecules do you have? What does your box look like (edgelengths)?


Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden
run-cpt-md.inp cubic system & shell ? shth
lennart #386 11/30/06 04:24 PM
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below given output results

calc XSIZ = INT( ?XMAX - ?XMIN + 16)
RDCMND substituted energy or value "?XMAX" to "20.1479"
RDCMND substituted energy or value "?XMIN" to "-18.9459"
Evaluating: INT(20.1479--18.9459+16)
Parameter: XSIZ <- "55"

CHARMM> calc YSIZ = INT( ?YMAX - ?YMIN + 16)
RDCMND substituted energy or value "?YMAX" to "13.4203"
RDCMND substituted energy or value "?YMIN" to "-12.5572"
Evaluating: INT(13.4203--12.5572+16)
Parameter: YSIZ <- "41"

CHARMM> calc ZSIZ = INT( ?ZMAX - ?ZMIN + 16)
RDCMND substituted energy or value "?ZMAX" to "11.4326"
RDCMND substituted energy or value "?ZMIN" to "-13.2873"
Evaluating: INT(11.4326--13.2873+16)
Parameter: ZSIZ <- "40"

orthogonal lattice of protein +water has a size of 55 41 40angs, how could i find total thickness of the water shell
i wish to extract the system protein +water at different thickness?(commands like show shth ? show shell?)

inorder to chnage the existing script as a cubic system , besides size of the protein i added different integers to find the uniform size of cubic crystal

calc XSIZ = INT( ?XMAX - ?XMIN + 2)
RDCMND substituted energy or value "?XMAX" to "20.1479"
RDCMND substituted energy or value "?XMIN" to "-18.9459"
Evaluating: INT(20.1479--18.9459+2)
Parameter: XSIZ <- "40"

CHARMM> calc YSIZ = INT( ?YMAX - ?YMIN + 15)
RDCMND substituted energy or value "?YMAX" to "13.4203"
RDCMND substituted energy or value "?YMIN" to "-12.5572"
Evaluating: INT(13.4203--12.5572+15)
Parameter: YSIZ <- "40"

CHARMM> calc ZSIZ = INT( ?ZMAX - ?ZMIN + 16)
RDCMND substituted energy or value "?ZMAX" to "11.4326"
RDCMND substituted energy or value "?ZMIN" to "-13.2873"
Evaluating: INT(11.4326--13.2873+16)
Parameter: ZSIZ <- "40"

!now i defined the uniform size
crystal define cubic @xsize @ysize@zsize 90 90 90
crystal facility cutoff 14.0
is this is the way of doing cubic steup?

Re: run-cpt-md.inp cubic system & shell ? shth
prakash #387 11/30/06 04:50 PM
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lennart Online Content OP
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"coor stat sele protein end" will give you the dimensions of your protein, and
"coor stat" will give the total dimensions. This may help you figure out the thickness of your "water shell" (at least along the x,y,z axes).

If you know that you want a 40x40x40 cubic box all the CALC commands are unnecesary. This suffices:
crystal define cubic 40.0 40.0 40.0 90.0 90.0 90.0
crystal build cutoff 20.0
If your cube is packed with atoms a shorter cutoff can be used; the important fact is that you want 26 images for a cubic system.

Use the POST function of the forums for new posts, not the REPLY.


Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden
Re: run-cpt-md.inp
tnc #388 10/04/07 12:25 PM
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I was using run-cpt-md.inp script, But since ORTH is not recommended I substituted it with another isotropic shape viz OCTA

but I encountered following error:-


CHARMM> ! setup Periodic Boundary Conditions
CHARMM> ! Here we have to use the crystal facility
CHARMM> ! Variables XSIZ,YSIZ, and ZSIZ have already been defined
CHARMM> crystal define OCTAhedral @XSIZ @YSIZ @ZSIZ 109.47 109.47 109.47
Parameter: XSIZ -> "65.0"
Parameter: YSIZ -> "65.0"
Parameter: ZSIZ -> "65.0"
XTLSYM> DIFF,RSMALL 0.3053E-02 0.1000E-09
XTLSYM> XTLTYP=OCTA
XTLABC: 62.546656 -12.508314 62.546656 -12.508314 -12.508314 62.546656

***** LEVEL -4 WARNING FROM <XTLSYM> *****
***** Shape matrix symmetry is not conserved
******************************************
BOMLEV ( -2) IS REACHED - TERMINATING. WRNLEV IS 5

Can someone suggest what went wrong? I am attaching my output script.

Attached Files
15779-run-cpt-md_old.txt (0 Bytes, 661 downloads)
Last edited by vbrahma; 10/04/07 12:33 PM.

Vijaya Brahma Research Scholar Institute of MIcrobial Technology India
Re: run-cpt-md.inp
vbrahma #389 10/04/07 12:43 PM
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lennart Online Content OP
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For the TO you need all the digits in for the angle (see setup-truncatd-octahedron.str). I find the RHDO more robust to use in this respect.


Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden
Re: run-cpt-md.inp
lennart #390 10/04/07 07:43 PM
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Thanks.. I am using RHDO and i am not facing any problem now!


Vijaya Brahma Research Scholar Institute of MIcrobial Technology India
Re: run-cpt-md.inp
lennart #391 05/22/08 03:27 PM
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Dear Lennart,

I have a question regarding the temperature control in this script. I can't see neither BERE nor NOSE nor HOOVER keywords. Yet you use "ichecw 1" and "iasors 1".

Does it mean that the temperature is controlled by scaling the velocities when temperatures lies outside TWINDH\L?

Thank you very much.

Re: run-cpt-md.inp
joseph #392 05/22/08 03:33 PM
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lennart Online Content OP
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Yes - from dynamc.doc:
ICHECW 1 The option for checking to see if the average temperature
of the system lies within the allotted temperature window
(between FINALT+TWINDH and FINALT+TWINDL) every
IEQFRQ steps.

For a well behaved system the temperature is usually quite stable and this simple scheme seldom interferes to rescale velocities (if at all); if it has t do many rescaling it works in a similar way as a Berendsen thermostat.


Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden
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