Subject: [gmx-users] [ dummies 2] or [ virtual_sites 2] not works.
Gerrit Groenhof
ggroenh at gwdg.de
Fri Jan 22 22:53:13 CET 2010
Hi,
Add the LA to the atoms block in the ff*nb.itp, using zero for all parameters. Check out for instance how the MW sites of water are listed.
LA 0 0.0 0.000 A 0.0 0.0
Gerrit
>
> Date: Fri, 22 Jan 2010 23:22:30 +0900
> From: "yoochan,myung" <myc14 at kangwon.ac.kr>
> Subject: [gmx-users] [ dummies 2] or [ virtual_sites 2] not works.
> To: gmx-users at gromacs.org
> Message-ID: <40B2AEDA-8F01-4D91-AE44-2886F2401400 at kangwon.ac.kr>
> Content-Type: text/plain; charset=us-ascii
>
> Hi.
>
> I'm on QM/MM simulation (gromacs-gaussian03).
>
> I exactly followed under reference, but I could't success.
> http://wwwuser.gwdg.de/~ggroenh/EMBO2004/html/qmmmvacuum.html#top
>
>
>
> I checked presence of two LA atoms in [ atoms] of TOP file.
>
> Also, I checked under [ dummies 2] and [ constraints ]in Top file.
> (I think, [ dummies 2] = [ virtual_sites 2] but, [ virtual_sites 2] in 4.x.x Gromacs, [ dummies 2] in 3.x.x)
>
> [ dummies 2]
> 1279 906 904 1 0.72
> 1280 938 936 1 0.72
>
> [ constraints ]
> 906 904 2 0.153
> 938 936 2 0.153
>
>
> And then, I did GROMPP, I got this error message.
> (In reference, there is a "run.scr " step which is multiple GROMPP and MDRUN running scripts.)
>
> 'Atom type "LA" not found'
>
>
> I think grompp doesn't recognize atom "LA" on [ atoms ] as dummies.
>
> Any suggestions?
>
>
> Regards.
>
> yoochan,
>
> ------------------------------
>
> Message: 2
> Date: Fri, 22 Jan 2010 13:02:50 -0500
> From: nishap.patel at utoronto.ca
> Subject: [gmx-users] cut-off
> To: gmx-users at gromacs.org
> Message-ID: <20100122130250.y57ap287284ooo0o at webmail.utoronto.ca>
> Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes";
> format="flowed"
>
> Hello,
>
> I wanted to know, if say my box is 30A (cubic) and if I set my
> cut-off lengths i.e. rvdw-switch = 0.8 and rvdw =0.9 , does that mean,
> the simulation will cut-0ff at 9A? Should I be changing that to 1.5nm
> (to get half the box cut-off)? I am a little confused about that.
>
> Thanks.
>
> Nisha Patel
>
>
>
>
> ------------------------------
>
> Message: 3
> Date: Fri, 22 Jan 2010 13:10:29 -0500
> From: "Justin A. Lemkul" <jalemkul at vt.edu>
> Subject: Re: [gmx-users] cut-off
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4B59EA15.50508 at vt.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>
>
> nishap.patel at utoronto.ca wrote:
>> Hello,
>>
>> I wanted to know, if say my box is 30A (cubic) and if I set my
>> cut-off lengths i.e. rvdw-switch = 0.8 and rvdw =0.9 , does that mean,
>> the simulation will cut-0ff at 9A? Should I be changing that to 1.5nm
>> (to get half the box cut-off)? I am a little confused about that.
>>
>
> Setting rvdw = 0.9 means that van der Waals interactions beyond 0.9 nm are zero.
> It has no effect on, for example, Coulombic interactions.
>
> Most force fields have defined cutoffs that should be used in order to be
> consistent with the original derivation of the parameter set, so it is generally
> inadvisable to make ad hoc changes to the cutoffs in order to meet some
> arbitrary criterion. The minimum image convention specifies that your longest
> cutoff must always be less than half the smallest box vector. If you set up a
> system with a cutoff equal to exactly one half of a box vector, if that box
> vector decreases even slightly (i.e., under the influence of pressure coupling),
> then you will be calculating spurious forces.
>
> -Justin
>
>> Thanks.
>>
>> Nisha Patel
>>
>>
>
> --
> ========================================
>
> 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: 4
> Date: Fri, 22 Jan 2010 13:20:06 -0500
> From: nishap.patel at utoronto.ca
> Subject: Re: [gmx-users] cut-off
> To: gmx-users at gromacs.org
> Message-ID: <20100122132006.3azbohlydcw4co04 at webmail.utoronto.ca>
> Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes";
> format="flowed"
>
> I see what you mean, so say if I am doing RDF, the values beyond 9A
> would be bogus?
>
>
> Quoting "Justin A. Lemkul" <jalemkul at vt.edu>:
>
>>
>>
>> nishap.patel at utoronto.ca wrote:
>>> Hello,
>>>
>>> I wanted to know, if say my box is 30A (cubic) and if I set my
>>> cut-off lengths i.e. rvdw-switch = 0.8 and rvdw =0.9 , does that
>>> mean, the simulation will cut-0ff at 9A? Should I be changing that
>>> to 1.5nm (to get half the box cut-off)? I am a little confused
>>> about that.
>>>
>>
>> Setting rvdw = 0.9 means that van der Waals interactions beyond 0.9 nm
>> are zero. It has no effect on, for example, Coulombic interactions.
>>
>> Most force fields have defined cutoffs that should be used in order to
>> be consistent with the original derivation of the parameter set, so it
>> is generally inadvisable to make ad hoc changes to the cutoffs in order
>> to meet some arbitrary criterion. The minimum image convention
>> specifies that your longest cutoff must always be less than half the
>> smallest box vector. If you set up a system with a cutoff equal to
>> exactly one half of a box vector, if that box vector decreases even
>> slightly (i.e., under the influence of pressure coupling), then you
>> will be calculating spurious forces.
>>
>> -Justin
>>
>>> Thanks.
>>>
>>> Nisha Patel
>>>
>>>
>>
>> --
>> ========================================
>>
>> 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
>>
>> ========================================
>> --
>> 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/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/mailing_lists/users.php
>
>
>
> Nisha Patel
> MSc Candidate
> Leslie Dan Faculty of Pharmacy
> Department of Pharmaceutical Sciences
> 144 College Street
> Room 1172
> Toronto, ON
> M5S 3M2
> Canada
> Telephone: 416-978-1536
>
>
>
> ------------------------------
>
> Message: 5
> Date: Fri, 22 Jan 2010 13:32:55 -0500
> From: "Justin A. Lemkul" <jalemkul at vt.edu>
> Subject: Re: [gmx-users] cut-off
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4B59EF57.9010502 at vt.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>
>
> nishap.patel at utoronto.ca wrote:
>> I see what you mean, so say if I am doing RDF, the values beyond 9A
>> would be bogus?
>>
>
> To a large extent, probably, but I don't think that I can say that absolutely
> without context. For example, you've only shown us rvdw, what about rcoulomb?
> If it is longer for some reason, then this value will also influence the RDF.
> Long-range electrostatics (i.e., PME) may have some effect as well, but I don't
> really have much detailed experience in doing that sort of thing.
>
> There is a nice section in the manual about RDF calculation, as well as an
> example RDF plot for SPC water that should give you an idea of what to expect,
> in general.
>
> -Justin
>
>>
>> Quoting "Justin A. Lemkul" <jalemkul at vt.edu>:
>>
>>>
>>>
>>> nishap.patel at utoronto.ca wrote:
>>>> Hello,
>>>>
>>>> I wanted to know, if say my box is 30A (cubic) and if I set my
>>>> cut-off lengths i.e. rvdw-switch = 0.8 and rvdw =0.9 , does that
>>>> mean, the simulation will cut-0ff at 9A? Should I be changing that
>>>> to 1.5nm (to get half the box cut-off)? I am a little confused about
>>>> that.
>>>>
>>>
>>> Setting rvdw = 0.9 means that van der Waals interactions beyond 0.9 nm
>>> are zero. It has no effect on, for example, Coulombic interactions.
>>>
>>> Most force fields have defined cutoffs that should be used in order to
>>> be consistent with the original derivation of the parameter set, so it
>>> is generally inadvisable to make ad hoc changes to the cutoffs in order
>>> to meet some arbitrary criterion. The minimum image convention
>>> specifies that your longest cutoff must always be less than half the
>>> smallest box vector. If you set up a system with a cutoff equal to
>>> exactly one half of a box vector, if that box vector decreases even
>>> slightly (i.e., under the influence of pressure coupling), then you
>>> will be calculating spurious forces.
>>>
>>> -Justin
>>>
>>>> Thanks.
>>>>
>>>> Nisha Patel
>>>>
>>>>
>>>
>>> --
>>> ========================================
>>>
>>> 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
>>>
>>> ========================================
>>> --
>>> 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/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/mailing_lists/users.php
>>
>>
>>
>> Nisha Patel
>> MSc Candidate
>> Leslie Dan Faculty of Pharmacy
>> Department of Pharmaceutical Sciences
>> 144 College Street
>> Room 1172
>> Toronto, ON
>> M5S 3M2
>> Canada
>> Telephone: 416-978-1536
>>
>
> --
> ========================================
>
> 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: 6
> Date: Sat, 23 Jan 2010 03:11:32 +0700
> From: akram gorji <lotus6150 at gmail.com>
> Subject: [gmx-users] question
> To: gmx-users at gromacs.org
> Message-ID:
> <891238761001221211n5ecbbf80r51780dd4756997bc at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hi,I want to simulate a finite nono-tubes.Does nonotube be flexible or
> rigid?which is better?thanks
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> ------------------------------
>
> Message: 7
> Date: Fri, 22 Jan 2010 21:25:36 +0100
> From: David van der Spoel <spoel at xray.bmc.uu.se>
> Subject: Re: [gmx-users] question
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4B5A09C0.2070906 at xray.bmc.uu.se>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> On 1/22/10 9:11 PM, akram gorji wrote:
>> Hi,I want to simulate a finite nono-tubes.Does nonotube be flexible or
>> rigid?which is better?thanks
>>
> Do you mean nano tubes?
>
> Try some literature search. Quite a bit has been done on this topic,
> also with GROMACS.
>
> --
> David.
> ________________________________________________________________________
> David van der Spoel, PhD, Professor of Biology
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596, 75124 Uppsala, Sweden
> phone: 46 18 471 4205 fax: 46 18 511 755
> spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>
>
> ------------------------------
>
> Message: 8
> Date: Fri, 22 Jan 2010 14:28:27 -0700
> From: Jose Tusell <jrta1981 at gmail.com>
> Subject: [gmx-users] diketopiperazine
> To: gmx-users at gromacs.org
> Message-ID:
> <d0c164c71001221328q2151c25cn7615012f91304daa at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hi,
>
> I'm trying to construct diketopiperazine with gromacs. The problem that I
> have right now is forming the bond that unites the C and N termi to make the
> cyclic peptide. I tried using specbond.dat but so far I've been
> unsucessful. Here is my specbond.dat file and pdb file:
>
> specbond.dat
> 8
> CYS SG 1 CYS SG 1 0.2 CYS2 CYS2
> CYS SG 1 HEME FE 2 0.25 CYS2 HEME
> CYS SG 1 HEME CAB 1 0.18 CYS2 HEME
> CYS SG 1 HEME CAC 1 0.18 CYS2 HEME
> HIS NE2 1 HEME FE 1 0.2 HIS1 HEME
> MET SD 1 HEME FE 1 0.24 MET HEME
> CYM SG 1 CYM SG 1 0.2 CYS2 CYS2
> TRP N 1 HISH C 1 0.2 TRP HISH
>
> whdikp.pdb
> REMARK S 14 x 14 mn oif
> ATOM 1 N TRP 1 -0.813 0.594 1.164
> ATOM 2 H TRP 1 -0.249 1.064 1.843
> ATOM 3 CA TRP 1 -0.264 -0.210 0.004
> ATOM 4 HA TRP 1 0.855 -0.244 0.066
> ATOM 5 CB TRP 1 -0.633 0.484 -1.321
> ATOM 6 HB1 TRP 1 -1.672 0.344 -1.531
> ATOM 7 HB2 TRP 1 -0.408 1.528 -1.262
> ATOM 8 CG TRP 1 0.205 -0.166 -2.397
> ATOM 9 CD1 TRP 1 0.227 -1.464 -2.727
> ATOM 10 HD1 TRP 1 -0.407 -2.173 -2.195
> ATOM 11 CD2 TRP 1 1.119 0.455 -3.258
> ATOM 12 NE1 TRP 1 1.166 -1.607 -3.796
> ATOM 13 HE1 TRP 1 1.401 -2.473 -4.259
> ATOM 14 CE2 TRP 1 1.673 -0.432 -4.078
> ATOM 15 CE3 TRP 1 1.485 1.803 -3.344
> ATOM 16 HE3 TRP 1 1.065 2.575 -2.699
> ATOM 17 CZ2 TRP 1 2.626 -0.117 -5.054
> ATOM 18 HZ2 TRP 1 3.035 -0.902 -5.690
> ATOM 19 CZ3 TRP 1 2.444 2.145 -4.320
> ATOM 20 HZ3 TRP 1 2.741 3.190 -4.402
> ATOM 21 CH2 TRP 1 2.990 1.222 -5.140
> ATOM 22 HH2 TRP 1 3.727 1.540 -5.878
> ATOM 23 C TRP 1 -0.816 -1.621 0.004
> ATOM 24 O TRP 1 -0.072 -2.712 0.004
> ATOM 25 N HISH 2 -2.331 -1.621 0.004
> ATOM 26 H HISH 2 -2.895 -2.093 -0.674
> ATOM 27 CA HISH 2 -2.881 -0.816 1.162
> ATOM 28 HA HISH 2 -4.000 -0.781 1.098
> ATOM 29 CB HISH 2 -2.516 -1.510 2.488
> ATOM 30 HB1 HISH 2 -1.564 -1.990 2.400
> ATOM 31 HB2 HISH 2 -2.494 -0.794 3.283
> ATOM 32 CG HISH 2 -3.591 -2.538 2.747
> ATOM 33 ND1 HISH 2 -3.867 -3.560 1.846
> ATOM 34 HD1 HISH 2 -3.399 -3.715 0.964
> ATOM 35 CD2 HISH 2 -4.447 -2.700 3.792
> ATOM 36 HD2 HISH 2 -4.608 -2.157 4.723
> ATOM 37 CE1 HISH 2 -4.846 -4.291 2.344
> ATOM 38 HE1 HISH 2 -5.219 -5.152 1.791
> ATOM 39 NE2 HISH 2 -5.203 -3.793 3.502
> ATOM 40 HE2 HISH 2 -5.932 -4.166 4.093
> ATOM 41 C HISH 2 -2.329 0.595 1.164
> ATOM 42 O HISH 2 -3.089 1.710 1.164
>
> Thanks for any suggestions,
>
> Jose Tusell
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>
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>
> End of gmx-users Digest, Vol 69, Issue 110
> ******************************************
--
Gerrit Groenhof
MPI biophysical chemistry
Goettingen
Germany
http://wwwuser.gwdg.de/~ggroenh/
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