[gmx-users] Re:Re:trr file
hj zou
hjzou at iris3.simm.ac.cn
Wed Dec 29 02:54:20 CET 2004
Dear parinald,
Thank you for your suggestions. But no velocity is available if there is no
trr file. So the new tpr file produced from 'tpbconv' will have no velocith which is
not what I want.
======= 2004-12-28 11:05:00 you wrote£º=======
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>Today's Topics:
>
> 1. Re: trr file (parinald at unsl.edu.ar)
> 2. CYS deprotonated! (Alberto Malvezzi)
> 3. Re: CYS deprotonated! (David van der Spoel)
> 4. Re: coulombtype selection (Jian Zou)
> 5. Re: coulombtype selection (David)
> 6. How to compute covariance? (Semen Esilevsky)
> 7. gromacs Website offline (Florian Haberl)
> 8. Re: gromacs Website offline (David van der Spoel)
>
>
>----------------------------------------------------------------------
>
>Message: 1
>Date: Mon, 27 Dec 2004 11:26:56 -0300 (ARGSL-ST)
>From: parinald at unsl.edu.ar
>Subject: Re: [gmx-users] trr file
>To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
>Message-ID:
> <8280.200.70.107.157.1104157616.squirrel at inter17.unsl.edu.ar>
>Content-Type: text/plain;charset=iso-8859-1
>
>use tpbconv.
>
>> Dear gmx-users£¬
>> I moved the trr file to another directory by mistake while the mdrun
>> simulation is still running. How can I let mdrun produce the trr file
>> again? If I stop the mdrun,
>> then I will lose the velocity which makes me unable to continue the
>> simulation.
>> Thank you in advance.
>>
>> Best regard,
>>
>> ***********************************************
>> Hanjun Zou
>> 555 Zu Chong Zhi Road, Zhangjiang Hi-Tech Park
>> Drug Discovery and Design Center
>> Shanghai Institute of Meteria Medica
>> Chinese Academy of Sciences
>> Shanghai 201203, China
>> Tel£º +86-21-50806600-1201
>> E-mail: hjzou at mail.shcnc.ac.cn
>> ***********************************************
>>
>>
>>
>> _______________________________________________
>> gmx-users mailing list
>> gmx-users at gromacs.org
>> http://www.gromacs.org/mailman/listinfo/gmx-users
>> Please don't post (un)subscribe requests to the list. Use the
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>
>
>
>------------------------------
>
>Message: 2
>Date: Mon, 27 Dec 2004 14:28:33 -0200
>From: Alberto Malvezzi <malvezzi at iq.usp.br>
>Subject: [gmx-users] CYS deprotonated!
>To: gmx-users at gromacs.org
>Message-ID: <41D03831.1040504 at iq.usp.br>
>Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>Dear all,
>I have a depronated CYS in my protein.
>Is there a way to tell this to gromacs?
>Has anyone done this before?
>Thank You
>Alberto Malvezzi
>Universidade de São Paulo
>Brazil
>
>On Thu, Dec 16, 2004 at 03:54:44PM +0000, Osmany Guirola Cruz wrote:
> > >>
> > Does not work :-( , my problem is this i have a peptide C-XXXXXXX-C (not
> > ciclic) but
> > i dont want CYSH in mi gro file(i want it deprotonated and in the rtp
> > files i found CYS1
> > and CYS2). i probed pdb2gmx -ss and pdb2gmx -ss -inter and does not work
> > always pdb2gmx
> > put CYSH.
>
>i have a topology for a deprotonated cys, made from some quantum
>calculations a while ago. it's best that you contact me off-list.
>it will require some searching through my archives...
>
>Marc
>--
>Marc Lensink http://www.biochem.oulu.fi/~lensink/
>SCMBB, Université Libre de Bruxelles lensink at scmbb.ulb.ac.be
>Boulevard du Triomphe - CP 263, B-1050 Brussels, Belgium
>tel: +32 2 650 5411 secr: +32 2 650 2013 fax: +32 2 650 5425
>
>
>
>------------------------------
>
>Message: 3
>Date: Mon, 27 Dec 2004 18:59:51 +0100
>From: David van der Spoel <spoel at xray.bmc.uu.se>
>Subject: Re: [gmx-users] CYS deprotonated!
>To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>Message-ID: <1104170391.3427.0.camel at vangogh>
>Content-Type: text/plain; charset=UTF-8
>
>On Mon, 2004-12-27 at 14:28 -0200, Alberto Malvezzi wrote:
>> Dear all,
>> I have a depronated CYS in my protein.
>> Is there a way to tell this to gromacs?
>check recent mailing lists.
>> Has anyone done this before?
>> Thank You
>> Alberto Malvezzi
>> Universidade de São Paulo
>> Brazil
>>
>> On Thu, Dec 16, 2004 at 03:54:44PM +0000, Osmany Guirola Cruz wrote:
>> > >>
>> > Does not work :-( , my problem is this i have a peptide C-XXXXXXX-C (not
>> > ciclic) but
>> > i dont want CYSH in mi gro file(i want it deprotonated and in the rtp
>> > files i found CYS1
>> > and CYS2). i probed pdb2gmx -ss and pdb2gmx -ss -inter and does not work
>> > always pdb2gmx
>> > put CYSH.
>>
>> i have a topology for a deprotonated cys, made from some quantum
>> calculations a while ago. it's best that you contact me off-list.
>> it will require some searching through my archives...
>>
>> Marc
>--
>David.
>________________________________________________________________________
>David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
>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://xray.bmc.uu.se/~spoel
>++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>
>
>
>
>------------------------------
>
>Message: 4
>Date: Tue, 28 Dec 2004 14:55:32 +0800
>From: "Jian Zou" <zouj01 at mails.tsinghua.edu.cn>
>Subject: Re: [gmx-users] coulombtype selection
>To: "gmx-users" <gmx-users at gromacs.org>
>Message-ID: <304216541.23743 at mails.tsinghua.edu.cn>
>Content-Type: text/plain; format=flowed; charset="Windows-1252";
> reply-type=original
>
>Prof. Spoel,
>
>From: David van der Spoel <spoel at xray.bmc.uu.se>
>Subject: Re: [gmx-users] coulombtype selection
>To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>Message-ID: <1103616643.9622.0.camel at vangogh>
>Content-Type: text/plain
>
>On Tue, 2004-12-21 at 09:26 +0200, Kay Gottschalk wrote:
>>> I think for DNA you should use PME.
>> Yes, but you can definitely change the cut/offs to 0.9/1.4 for vdw and 0.9
>> for Coulomb.
>> That will speed up a factor of 8.
>OK, PME should be used for my case.
>
>I tried this cutoff but the simulation failed due to "pressure scaling more
>than 1".
>I also tried 1.0/1.5 for vdw and 1.0 for coulomb, failed again due to the
>same reason.
>When I change the cutoff to 1.0/2.0 for vdw and 1.0 for coulomb, the
>simulation runs.
>Should I do further EM or PR before MD if I still want to reduce the cutoff
>to save time? Or I should remove P coupling?
>
>Thanks a lot in advance.
>
>
>Regards,
>
>Jian Zou
>
>
>
>------------------------------
>
>Message: 5
>Date: Tue, 28 Dec 2004 08:51:17 +0100
>From: David <spoel at xray.bmc.uu.se>
>Subject: Re: [gmx-users] coulombtype selection
>To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>Message-ID: <1104220277.3912.0.camel at h42n2fls34o1123.telia.com>
>Content-Type: text/plain
>
>On Tue, 2004-12-28 at 14:55 +0800, Jian Zou wrote:
>> Prof. Spoel,
>>
>> From: David van der Spoel <spoel at xray.bmc.uu.se>
>> Subject: Re: [gmx-users] coulombtype selection
>> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>> Message-ID: <1103616643.9622.0.camel at vangogh>
>> Content-Type: text/plain
>>
>> On Tue, 2004-12-21 at 09:26 +0200, Kay Gottschalk wrote:
>> >> I think for DNA you should use PME.
>> > Yes, but you can definitely change the cut/offs to 0.9/1.4 for vdw and 0.9
>> > for Coulomb.
>> > That will speed up a factor of 8.
>> OK, PME should be used for my case.
>>
>> I tried this cutoff but the simulation failed due to "pressure scaling more
>> than 1".
>> I also tried 1.0/1.5 for vdw and 1.0 for coulomb, failed again due to the
>> same reason.
>> When I change the cutoff to 1.0/2.0 for vdw and 1.0 for coulomb, the
>> simulation runs.
>> Should I do further EM or PR before MD if I still want to reduce the cutoff
>> to save time? Or I should remove P coupling?
>First check your starting structure and topology, second increase tau_p
>to e.g. 5 ps and check the compressibility (should be roughly 5e-5).
>>
>> Thanks a lot in advance.
>>
>>
>> Regards,
>>
>> Jian Zou
>>
>> _______________________________________________
>> gmx-users mailing list
>> gmx-users at gromacs.org
>> http://www.gromacs.org/mailman/listinfo/gmx-users
>> Please don't post (un)subscribe requests to the list. Use the
>> www interface or send it to gmx-users-request at gromacs.org.
>--
>David.
>________________________________________________________________________
>David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
>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://xray.bmc.uu.se/~spoel
>++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>
>
>
>------------------------------
>
>Message: 6
>Date: Tue, 28 Dec 2004 00:28:14 -0800 (PST)
>From: Semen Esilevsky <yesint4 at yahoo.com>
>Subject: [gmx-users] How to compute covariance?
>To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>Message-ID: <20041228082814.67384.qmail at web40522.mail.yahoo.com>
>Content-Type: text/plain; charset=us-ascii
>
>Dear gmx users,
>I'm sorry for stupid question, but I can't find the
>answer for two days :(
>The problem is how to compute the correlation (or
>covariance) of two particular atoms using the
>MDtrajectory. I just need a correct equation for this
>(not the program, which does this).
>If I have the atoms i and j I'd rather compute the
>covariance between them as
>
>cov_ij = <(xi-xi_mean)*(xj-xj_mean)> +
> <(yi-yi_mean)*(yj-yj_mean)> +
> <(zi-zi_mean)*(zj-zj_mean)>
>
>But I'm confused about the "off-diagonal" averages
>like
><(xi-xi_mean)*(zj-zj_mean)>. Do I have to include them
>or not and how?
>
>Thank you in advance for help!
>
>Semen
>
>
>
>__________________________________
>Do you Yahoo!?
>Jazz up your holiday email with celebrity designs. Learn more.
>http://celebrity.mail.yahoo.com
>
>
>------------------------------
>
>Message: 7
>Date: Tue, 28 Dec 2004 09:40:00 +0100
>From: Florian Haberl <Florian.Haberl at chemie.uni-erlangen.de>
>Subject: [gmx-users] gromacs Website offline
>To: "gmx-users" <gmx-users at gromacs.org>
>Message-ID: <200412280940.00143.Florian.Haberl at chemie.uni-erlangen.de>
>Content-Type: text/plain; charset="us-ascii"
>
>Hi
>
>i think www.gromacs.org is offline, same as i tried struktbio205.bmc.uu.se
>
>My browser said:
>
>An error occured while loading http://www.gromacs.org/:
>
>
>Could not connect to host www.gromacs.org
>
>traceroute looks ok
>
>[quote]
>traceroute www.gromacs.org
>traceroute to struktbio205.bmc.uu.se (130.238.41.205), 30 hops max, 38 byte
>packets
> 1 reliant.gate.uni-erlangen.de (131.188.30.8) 1.214 ms 0.263 ms 0.194 ms
> 2 botany-bay.gate.uni-erlangen.de (131.188.20.109) 0.282 ms 0.238 ms
>0.213 ms
> 3 enterprise.gate.uni-erlangen.de (131.188.20.102) 0.259 ms 0.249 ms
>0.226 ms
> 4 excelsior.gate.uni-erlangen.de (131.188.5.1) 0.559 ms 0.469 ms 0.421 ms
> 5 ar-erlangen1.g-win.dfn.de (188.1.36.1) 0.274 ms 0.255 ms 0.214 ms
> 6 cr-erlangen1-ge5-0.g-win.dfn.de (188.1.72.1) 0.327 ms 0.265 ms 0.236 ms
> 7 cr-leipzig1-po5-2.g-win.dfn.de (188.1.18.46) 4.857 ms 4.609 ms 4.697 ms
> 8 cr-frankfurt1-po10-0.g-win.dfn.de (188.1.18.189) 11.007 ms 11.163 ms
>10.999 ms
> 9 dfn.de1.de.geant.net (62.40.105.1) 11.236 ms 11.288 ms 11.305 ms
>10 de1-2.de2.de.geant.net (62.40.96.53) 11.245 ms 11.254 ms 11.214 ms
>11 de.se1.se.geant.net (62.40.96.66) 33.107 ms 80.518 ms 33.069 ms
>12 sw-gw.nordu.net (62.40.103.118) 33.148 ms 33.117 ms 33.086 ms
>13 stockholm2-POS6-0.sunet.se (193.10.252.178) 33.353 ms 83.039 ms 61.552
>ms
>14 uppsala2-POS0.sunet.se (130.242.82.34) 64.271 ms 34.535 ms 34.345 ms
>15 uu1-SRP1.sunet.se (130.242.85.163) 34.324 ms 34.501 ms 34.291 ms
>16 uulokalt1-FE1.sunet.se (130.242.88.2) 34.826 ms 35.007 ms 34.545 ms
>17 130.238.6.226 (130.238.6.226) 35.928 ms 35.482 ms 35.413 ms
>18 struktbio205.bmc.uu.se (130.238.41.205) 35.563 ms 35.545 ms 35.101 ms
>
>[/quote]
>
>Greetings,
>
>Florian
>
>
>--
>-------------------------------------------------------------------------------
> Florian Haberl Universitaet Erlangen/
> Computer-Chemie-Centrum Nuernberg
> Naegelsbachstr. 25
> D-91052 Erlangen
> Mailto: florian.haberl AT chemie.uni-erlangen.de
> -------------------------------------------------------------------------------
>
>
>
>------------------------------
>
>Message: 8
>Date: Tue, 28 Dec 2004 11:10:09 +0100
>From: David van der Spoel <spoel at xray.bmc.uu.se>
>Subject: Re: [gmx-users] gromacs Website offline
>To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>Message-ID: <1104228609.3425.3.camel at vangogh>
>Content-Type: text/plain
>
>On Tue, 2004-12-28 at 09:40 +0100, Florian Haberl wrote:
>> Hi
>>
>> i think www.gromacs.org is offline, same as i tried struktbio205.bmc.uu.se
>>
>> My browser said:
>>
>> An error occured while loading http://www.gromacs.org/:
>>
>>
>fixed. thanks for the message.
>
>
>> Could not connect to host www.gromacs.org
>>
>> traceroute looks ok
>>
>> [quote]
>> traceroute www.gromacs.org
>> traceroute to struktbio205.bmc.uu.se (130.238.41.205), 30 hops max, 38 byte
>> packets
>> 1 reliant.gate.uni-erlangen.de (131.188.30.8) 1.214 ms 0.263 ms 0.194 ms
>> 2 botany-bay.gate.uni-erlangen.de (131.188.20.109) 0.282 ms 0.238 ms
>> 0.213 ms
>> 3 enterprise.gate.uni-erlangen.de (131.188.20.102) 0.259 ms 0.249 ms
>> 0.226 ms
>> 4 excelsior.gate.uni-erlangen.de (131.188.5.1) 0.559 ms 0.469 ms 0.421 ms
>> 5 ar-erlangen1.g-win.dfn.de (188.1.36.1) 0.274 ms 0.255 ms 0.214 ms
>> 6 cr-erlangen1-ge5-0.g-win.dfn.de (188.1.72.1) 0.327 ms 0.265 ms 0.236 ms
>> 7 cr-leipzig1-po5-2.g-win.dfn.de (188.1.18.46) 4.857 ms 4.609 ms 4.697 ms
>> 8 cr-frankfurt1-po10-0.g-win.dfn.de (188.1.18.189) 11.007 ms 11.163 ms
>> 10.999 ms
>> 9 dfn.de1.de.geant.net (62.40.105.1) 11.236 ms 11.288 ms 11.305 ms
>> 10 de1-2.de2.de.geant.net (62.40.96.53) 11.245 ms 11.254 ms 11.214 ms
>> 11 de.se1.se.geant.net (62.40.96.66) 33.107 ms 80.518 ms 33.069 ms
>> 12 sw-gw.nordu.net (62.40.103.118) 33.148 ms 33.117 ms 33.086 ms
>> 13 stockholm2-POS6-0.sunet.se (193.10.252.178) 33.353 ms 83.039 ms 61.552
>> ms
>> 14 uppsala2-POS0.sunet.se (130.242.82.34) 64.271 ms 34.535 ms 34.345 ms
>> 15 uu1-SRP1.sunet.se (130.242.85.163) 34.324 ms 34.501 ms 34.291 ms
>> 16 uulokalt1-FE1.sunet.se (130.242.88.2) 34.826 ms 35.007 ms 34.545 ms
>> 17 130.238.6.226 (130.238.6.226) 35.928 ms 35.482 ms 35.413 ms
>> 18 struktbio205.bmc.uu.se (130.238.41.205) 35.563 ms 35.545 ms 35.101 ms
>>
>> [/quote]
>>
>> Greetings,
>>
>> Florian
>>
>>
>--
>David.
>________________________________________________________________________
>David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
>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://xray.bmc.uu.se/~spoel
>++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>
>
>
>
>------------------------------
>
>_______________________________________________
>gmx-users mailing list
>gmx-users at gromacs.org
>http://www.gromacs.org/mailman/listinfo/gmx-users
>
>
>End of gmx-users Digest, Vol 8, Issue 52
>****************************************
= = = = = = = = = = = = = = = = = = = =
************************************************
Hanjun Zou
555 Zu Chong Zhi Road, Zhangjiang Hi-Tech Park
Drug Discovery and Design Center
Shanghai Institute of Meteria Medica
Chinese Academy of Sciences
Shanghai 201203, China
Tel£º +86-21-50806600-1201
E-mail: hjzou at mail.shcnc.ac.cn
************************************************
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