Re: [gmx-users] 3D pressure profile of a bilayer
On Tue, Sep 6, 2011 at 10:07 PM, Shou-Chuang Yang wrote: > Dear gmx-users, > > Could anyone help me with the calculation of 3D pressure profile in a > function of y? > I used the provided gromacs-4.0.2_localpressure for my calculatioin. It > calculate > the 3D pressure profile as a function of z (the default setting of bilayer > normal > is z-direction). > > In my case, I have a bilayer which rotate at the first few nano second run > and remained normal to y-directiona for the rest. How can I obtain a 3D > pressure analysis > along the y-direction? > Couldnt you rotate your box so that the bilayer is in z dir ? > I really appreciated your help! > > Thanks, > Joanne > -- > > > -- > gmx-users mailing listgmx-users@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-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users mailing listgmx-users@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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] 3D pressure profile of a bilayer
On Wed, Sep 7, 2011 at 12:11 AM, Amit Choubey wrote: > > > On Tue, Sep 6, 2011 at 10:07 PM, Shou-Chuang Yang wrote: > >> Dear gmx-users, >> >> Could anyone help me with the calculation of 3D pressure profile in a >> function of y? >> I used the provided gromacs-4.0.2_localpressure for my calculatioin. It >> calculate >> the 3D pressure profile as a function of z (the default setting of bilayer >> normal >> is z-direction). >> >> In my case, I have a bilayer which rotate at the first few nano second run >> and remained normal to y-directiona for the rest. How can I obtain a 3D >> pressure analysis >> along the y-direction? >> > Couldnt you rotate your box so that the bilayer is in z dir ? > The local pressure analysis need to read the trajectory file with both positions and velocities. I thought of rotate my system and rerun it for the last 600 ns ( I am using MARTINI), but since I am also doing semiisotropic coupling, I cannot "rotate" the pressure coupling directions. Another way I tried is to modify the output .trr into another .trr which y and z columns printed out reversely as well as the Vy and Vz columns. Thinking that maybe the analysis code will read my "originally y coordinates" as "z coordinates". What I got was segmentation fault. I am not sure whether it will work out eventually. > I really appreciated your help! >> >> Thanks, >> Joanne >> -- >> >> >> -- >> gmx-users mailing listgmx-users@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-requ...@gromacs.org. >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> > > > -- > gmx-users mailing listgmx-users@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-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- Shou-Chuang Yang Master’s Candidate Department of Chemical Engineering and Materials Science University of California, Davis Phone: 1-646-639-4240 -- gmx-users mailing listgmx-users@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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] 3D pressure profile of a bilayer
On Wed, Sep 7, 2011 at 12:30 AM, Shou-Chuang Yang wrote: > > > On Wed, Sep 7, 2011 at 12:11 AM, Amit Choubey wrote: > >> >> >> On Tue, Sep 6, 2011 at 10:07 PM, Shou-Chuang Yang wrote: >> >>> Dear gmx-users, >>> >>> Could anyone help me with the calculation of 3D pressure profile in a >>> function of y? >>> I used the provided gromacs-4.0.2_localpressure for my calculatioin. It >>> calculate >>> the 3D pressure profile as a function of z (the default setting of >>> bilayer normal >>> is z-direction). >>> >>> In my case, I have a bilayer which rotate at the first few nano second >>> run >>> and remained normal to y-directiona for the rest. How can I obtain a 3D >>> pressure analysis >>> along the y-direction? >>> >> Couldnt you rotate your box so that the bilayer is in z dir ? >> > > The local pressure analysis need to read the trajectory file with both > positions and velocities. > I thought of rotate my system and rerun it for the last 600 ns ( I am using > MARTINI), but since > I am also doing semiisotropic coupling, I cannot "rotate" the pressure > coupling directions. > > Another way I tried is to modify the output .trr into another .trr which y > and z columns printed out > reversely as well as the Vy and Vz columns. Thinking that maybe the > analysis code will read my > "originally y coordinates" as "z coordinates". What I got was segmentation > fault. > Why do you get a segmentation fault if you swap the y and z coordinates,velocity columns? Another way around is to change the simple_localpres_analysis.c code. If you look into it there is a loop that runs over boxes in z direction to calculate pressure tensor in z direction. You could change it to y. > I am not sure whether it will work out eventually. > >> I really appreciated your help! >>> >>> Thanks, >>> Joanne >>> -- >>> >>> >>> -- >>> gmx-users mailing listgmx-users@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-requ...@gromacs.org. >>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>> >> >> >> -- >> gmx-users mailing listgmx-users@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-requ...@gromacs.org. >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> > > > > -- > Shou-Chuang Yang > Master’s Candidate > Department of Chemical Engineering and Materials Science > University of California, Davis > Phone: 1-646-639-4240 > > > -- > gmx-users mailing listgmx-users@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-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users mailing listgmx-users@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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: Antw: Re: Re: [gmx-users] constant PH simulations
There is no problem in being wrong. The problem is that he wants to be wrong. At least 4 different researchers gave constructive input and this subject keeps hitting the same key. I've always been told that worse than not knowing, is not wanting to know. Still, I apologize for my outburst. Best regards, On Wed, Sep 7, 2011 at 1:54 AM, Mark Abraham wrote: > On 7/09/2011 3:53 AM, João Henriques wrote: >> >> I guess someone has been living in a cave for the past decade or so... > > Please keep contributions to the mailing list constructive :-) Everyone's > been wrong before! > > Mark > -- > gmx-users mailing list gmx-users@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-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- João Henriques -- gmx-users mailing listgmx-users@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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: Force a gromacs tool to write step-by-step a result in a result in a xvg file
Hi Florian, I have followed your suggestion below and used a pdb file instead of a xtc file and it works!!! Thank you very much for the info. A bientot Stephane -- Message: 3 Date: Tue, 06 Sep 2011 12:26:34 +0200 From: Dommert Florian Subject: Re: [gmx-users] Force a gromacs tool to write step-by-step a result in a xvg file To: Discussion list for GROMACS users Message-ID: <1315304794.2757.18.camel@fermi> Content-Type: text/plain; charset="utf-8" Hi, I would suggest you extract the single snapshot from your xtc file and then run the analysis tool on the single snapshot file. /Flo On Tue, 2011-09-06 at 12:12 +0200, intra\sa175950 wrote: > Dear All > > > > I use the g_clustersize to examine the cluster decay vs. time during > the aggregation process of glycolipids into a micelle with the > following command: > > > > $WORKDIR/gromacs-4.5.3/bin/g_clustsize_mpi -f *.xtc -s run_1.tpr -mc > bDM-AMBER99SB-ILDN-Self_b_cluster.xvg -nc > bDM-AMBER99SB-ILDN-Self_b_N_cluster.xvg -b 102000 -e 102000 -dt 4 -tu > ps -n index.ndx > > > > Unfortunately, the program stops with the following error after > several steps > > > > - > > > > Program g_clustsize_mpi, VERSION 4.5.3 > > Source code file: matio.c, line: 561 > > > > Fatal error: > > Lo: 0.00, Mid: 1.00, Hi: 1.00 > > - > > > > I know that this error comes because I have in my system only one cluster of constant size in my system. > > > > Unfortunately, when this error appears g_clustsize_mpi stops and no > results for the preceding steps are written in the corresponding xvg > files. So it is possible to force g_clustersize (and any others > gromacs tools) to write step-by-step a calculation in a *.xvg file. > > > > Thank you in advance for your help > > > > Stephane > > > -- > gmx-users mailing listgmx-users@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-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Florian Dommert Dipl. - Phys. Institute for Computational Physics University Stuttgart Pfaffenwaldring 27 70569 Stuttgart EMail: domm...@icp.uni-stuttgart.de Homepage: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert Tel.: +49 - (0)711 - 68563613 Fax.: +49 - (0)711 - 68563658 -- next part -- A non-text attachment was scrubbed... Name: not available Type: application/pgp-signature Size: 198 bytes Desc: This is a digitally signed message part Url : http://lists.gromacs.org/pipermail/gmx-users/attachments/20110906/7b985230/a ttachment-0001.bin -- -- gmx-users mailing listgmx-users@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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Antw: Re: Antw: Re: Re: [gmx-users] constant PH simulations
At first I would like to say that I deeply apologize for the cave-like things I have said. I again say, that this was not the field I am deeply involved. >From Gerrit I got a banana. For this guy, I am a cave-man. Thanks, for being such ready for open discussion. I did not tell that I do not want to be wrong. Questions, which are included in my doubts: Generalized forces and averages for H+ interchange ? Comparison with titration experiments ? Is there any experimental evidence for the rates of interchange ? Are simulation-times or the periods of interchange at any time realistic? Are equilibria sampled well, with such interchanges, or are there jumps in free energy by this interchange ? Why is there no free H+ ? Thanks for your kind and very constructive criticisms. I would appreciate, if this so-called discussion will find an end. I am deeply depressed about such comments and I will not take part in any users-discussion in the future. It makes no sense, because talking like this expresses the way on how science is done today. Repelling that person, who does not walk the common way. And: Maybe I have lived in a cave, but someone like you, who answers in such a way, IS A CAVEMAN ! >>> João Henriques 07.09.11 11.30 Uhr >>> There is no problem in being wrong. The problem is that he wants to be wrong. At least 4 different researchers gave constructive input and this subject keeps hitting the same key. I've always been told that worse than not knowing, is not wanting to know. Still, I apologize for my outburst. Best regards, On Wed, Sep 7, 2011 at 1:54 AM, Mark Abraham wrote: > On 7/09/2011 3:53 AM, João Henriques wrote: >> >> I guess someone has been living in a cave for the past decade or so... > > Please keep contributions to the mailing list constructive :-) Everyone's > been wrong before! > > Mark > -- > gmx-users mailing listgmx-users@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-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- João Henriques -- gmx-users mailing listgmx-users@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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: Re: Antw: Re: Re: [gmx-users] constant PH simulations
http://www.gromacs.org/Documentation/How-tos/Constant_pH_Simulation On 7 September 2011 11:01, Emanuel Peter < emanuel.pe...@chemie.uni-regensburg.de> wrote: > At first I would like to say that I deeply apologize for > the cave-like things I have said. I again say, that this > was not the field I am deeply involved. > From Gerrit I got a banana. > For this guy, I am a cave-man. > > Thanks, for being such ready for open discussion. > > I did not tell that I do not want to be wrong. > Questions, which are included in my doubts: > > Generalized forces and averages for H+ interchange ? > Comparison with titration experiments ? > Is there any experimental evidence for the rates of > interchange ? > Are simulation-times or the periods of interchange at > any time realistic? > Are equilibria sampled well, with such interchanges, > or are there jumps in free energy by this interchange ? > Why is there no free H+ ? > > Thanks for your kind and very constructive criticisms. > > I would appreciate, if this so-called discussion will > find an end. > I am deeply depressed about such comments and > I will not take part in any users-discussion in the future. > It makes no sense, because talking like this expresses > the way on how science is done today. Repelling that > person, who does not walk the common way. > And: > > Maybe I have lived in a cave, but someone like you, who answers in > such a way, IS A CAVEMAN ! > > >>> João Henriques 07.09.11 11.30 Uhr >>> > > There is no problem in being wrong. The problem is that he wants to be > wrong. At least 4 different researchers gave constructive input and > this subject keeps hitting the same key. I've always been told that > worse than not knowing, is not wanting to know. > > Still, I apologize for my outburst. > > Best regards, > > On Wed, Sep 7, 2011 at 1:54 AM, Mark Abraham > wrote: > > On 7/09/2011 3:53 AM, João Henriques wrote: > >> > >> I guess someone has been living in a cave for the past decade or so... > > > > Please keep contributions to the mailing list constructive :-) Everyone's > > been wrong before! > > > > Mark > > -- > > gmx-users mailing list gmx-users@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-requ...@gromacs.org. > > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > -- > João Henriques > -- > gmx-users mailing list gmx-users@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-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > -- > gmx-users mailing listgmx-users@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-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- Diogo Vila Viçosa, MSc in Biochemistry Faculty of Science of the University of Lisbon Department of Chemistry and Biochemistry C8 Building, Room 8.5.47 Campo Grande, 1749-016 Lisbon, Portugal E-mail: diogo.vic...@fc.ul.pt http://intheochem.fc.ul.pt/members/diogovv.html -- gmx-users mailing listgmx-users@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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: Re: Antw: Re: Re: [gmx-users] constant PH simulations
Why don't you read the papers associated with the link everyone keeps sending you!!! Stop it with the autistic behavior. http://www.gromacs.org/Documentation/How-tos/Constant_pH_Simulation Here is the main paper regarding the CpH-MD method I'm currently using: http://jcp.aip.org/resource/1/jcpsa6/v117/i9/p4184_s1 Here's a tip: searching google scholar a little before emailing everyone in the list should prove useful. Cheers, On Wed, Sep 7, 2011 at 11:01 AM, Emanuel Peter wrote: > At first I would like to say that I deeply apologize for > the cave-like things I have said. I again say, that this > was not the field I am deeply involved. > From Gerrit I got a banana. > For this guy, I am a cave-man. > > Thanks, for being such ready for open discussion. > > I did not tell that I do not want to be wrong. > Questions, which are included in my doubts: > > Generalized forces and averages for H+ interchange ? > Comparison with titration experiments ? > Is there any experimental evidence for the rates of > interchange ? > Are simulation-times or the periods of interchange at > any time realistic? > Are equilibria sampled well, with such interchanges, > or are there jumps in free energy by this interchange ? > Why is there no free H+ ? > > Thanks for your kind and very constructive criticisms. > > I would appreciate, if this so-called discussion will > find an end. > I am deeply depressed about such comments and > I will not take part in any users-discussion in the future. > It makes no sense, because talking like this expresses > the way on how science is done today. Repelling that > person, who does not walk the common way. > And: > > Maybe I have lived in a cave, but someone like you, who answers in > such a way, IS A CAVEMAN ! > João Henriques 07.09.11 11.30 Uhr >>> > There is no problem in being wrong. The problem is that he wants to be > wrong. At least 4 different researchers gave constructive input and > this subject keeps hitting the same key. I've always been told that > worse than not knowing, is not wanting to know. > > Still, I apologize for my outburst. > > Best regards, > > On Wed, Sep 7, 2011 at 1:54 AM, Mark Abraham > wrote: >> On 7/09/2011 3:53 AM, João Henriques wrote: >>> >>> I guess someone has been living in a cave for the past decade or so... >> >> Please keep contributions to the mailing list constructive :-) Everyone's >> been wrong before! >> >> Mark >> -- >> gmx-users mailing list gmx-users@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-requ...@gromacs.org. >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> > > > > -- > João Henriques > -- > gmx-users mailing list gmx-users@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-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > -- > gmx-users mailing list gmx-users@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-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- João Henriques -- gmx-users mailing listgmx-users@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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Antw: Re: Re: Antw: Re: Re: [gmx-users] constant PH simulations
SMA. >>> João Henriques 07.09.11 13.09 Uhr >>> Why don't you read the papers associated with the link everyone keeps sending you!!! Stop it with the autistic behavior. http://www.gromacs.org/Documentation/How-tos/Constant_pH_Simulation Here is the main paper regarding the CpH-MD method I'm currently using: http://jcp.aip.org/resource/1/jcpsa6/v117/i9/p4184_s1 Here's a tip: searching google scholar a little before emailing everyone in the list should prove useful. Cheers, On Wed, Sep 7, 2011 at 11:01 AM, Emanuel Peter wrote: > At first I would like to say that I deeply apologize for > the cave-like things I have said. I again say, that this > was not the field I am deeply involved. > From Gerrit I got a banana. > For this guy, I am a cave-man. > > Thanks, for being such ready for open discussion. > > I did not tell that I do not want to be wrong. > Questions, which are included in my doubts: > > Generalized forces and averages for H+ interchange ? > Comparison with titration experiments ? > Is there any experimental evidence for the rates of > interchange ? > Are simulation-times or the periods of interchange at > any time realistic? > Are equilibria sampled well, with such interchanges, > or are there jumps in free energy by this interchange ? > Why is there no free H+ ? > > Thanks for your kind and very constructive criticisms. > > I would appreciate, if this so-called discussion will > find an end. > I am deeply depressed about such comments and > I will not take part in any users-discussion in the future. > It makes no sense, because talking like this expresses > the way on how science is done today. Repelling that > person, who does not walk the common way. > And: > > Maybe I have lived in a cave, but someone like you, who answers in > such a way, IS A CAVEMAN ! > João Henriques 07.09.11 11.30 Uhr >>> > There is no problem in being wrong. The problem is that he wants to be > wrong. At least 4 different researchers gave constructive input and > this subject keeps hitting the same key. I've always been told that > worse than not knowing, is not wanting to know. > > Still, I apologize for my outburst. > > Best regards, > > On Wed, Sep 7, 2011 at 1:54 AM, Mark Abraham > wrote: >> On 7/09/2011 3:53 AM, João Henriques wrote: >>> >>> I guess someone has been living in a cave for the past decade or so... >> >> Please keep contributions to the mailing list constructive :-) Everyone's >> been wrong before! >> >> Mark >> -- >> gmx-users mailing list gmx-users@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-requ...@gromacs.org. >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> > > > > -- > João Henriques > -- > gmx-users mailing list gmx-users@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-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > -- > gmx-users mailing listgmx-users@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-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- João Henriques -- gmx-users mailing listgmx-users@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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: gromacs doubts
Please keep all Gromacs-related correspondence on the gmx-users list. I am not a private tutor. karthick wrote: sir iam karthick using gromacs for academic purpose.i had run protein-ligand complex based on your lyzozyme tutorial.further i want to about DGbind value..i heard g_lie command is used for that purpose but i dont know how to use it..please help me in this regardthanks in advance I have no experience with g_lie. There are various methods for calculating free energy, such as TI or BAR (for which there is also a tutorial), umbrella sampling, etc. -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 -- gmx-users mailing listgmx-users@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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] constant PH simulations
> > Message: 1 > Date: Wed, 07 Sep 2011 12:01:00 +0200 > From: "Emanuel Peter" > Subject: Antw: Re: Antw: Re: Re: [gmx-users] constant PH simulations > To: > Message-ID: <4e675cfc02f100014...@gwsmtp1.uni-regensburg.de> > Content-Type: text/plain; charset="iso-8859-1" > > At first I would like to say that I deeply apologize for > the cave-like things I have said. I again say, that this > was not the field I am deeply involved. >> From Gerrit I got a banana. > For this guy, I am a cave-man. No, a monkey, just like you signed one of your earlier mails. The questions you raise are all unaswered, but extremely relevant. Futher open discussion is highly appreciated. > > Generalized forces and averages for H+ interchange ? The idea is that the protons are degrees of freedom. Protons can thus appear "spontaneously" on titrating sites. The driving force is the thermodynamic force: DG/Dl. More details can be foudn in the papers By Charly Brooks, JAna Khandogin and ourselves. > Comparison with titration experiments ? Not many of these around, but these will be crucial to establish the validty of the different approaches. > Is there any experimental evidence for the rates of > interchange ? NMR maybe. > Are simulation-times or the periods of interchange at > any time realistic? Probably not. > Are equilibria sampled well, with such interchanges, > or are there jumps in free energy by this interchange ? No the system follows the underlying free energy landscape always. THerefore there are no jumps, as one may habe in MC approaches. However, the price one pays is that one does sample intermediate state, in which the proton is only partially there. > Why is there no free H+ ? That would give an enormous sampling problem. Furthermore, the properties of MM hydroniom are very different from real hydronium Hope this adds to the discussion. Gerrit -- gmx-users mailing listgmx-users@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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Permeability coefficient
Dear friends, I am using the GROMACS-4.5.3 for molecular dynamics as described by* Justin Lemkul in Tutorial 2: KALP15 in DPPC. *I want to calculate the Permeability Coefficient for Ligand in DPPC so please help me. -- Manoj Kumar Gadhwal (M. Pharma), PhD Schloar, Prin. K. M. Kundnani College of Pharmacy, Colaba, Mumbai-05. Cont. No. +91 9769051866 -- gmx-users mailing listgmx-users@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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Bad water removal
Hi, I have generated a membrane protein complex and then added a waterbox using Gromacs,but instead of being at the outer surfaces of lipid membrane,water spreads all around the membrane. How to make appropriate water box?am I doing a simple mistake? Please help this beginner. Thanks in advance. Madhumita Das -- gmx-users mailing listgmx-users@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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Permeability coefficient
manoj gadhwal wrote: Dear friends, I am using the GROMACS-4.5.3 for molecular dynamics as described by* Justin Lemkul in Tutorial 2: KALP15 in DPPC. *I want to calculate the Permeability Coefficient for Ligand in DPPC so please help me. I briefly looked up this term and it sounds like you need a diffusion constant (which you can get with g_msd) and a partitioning coefficient (which is harder to get, but can be obtained from free energy calculations). -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 -- gmx-users mailing listgmx-users@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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Bad water removal
madhumita das wrote: Hi, I have generated a membrane protein complex and then added a waterbox using Gromacs,but instead of being at the outer surfaces of lipid membrane,water spreads all around the membrane. How to make appropriate water box?am I doing a simple mistake? If you've got water all around the membrane, then your box dimensions are probably set incorrectly. Please see the following tutorial; it addresses this issue and others: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/index.html -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 -- gmx-users mailing listgmx-users@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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Trajectory viewing by freeing a part
Hi, While viewing a trajectory I am trying to see how a particular part or group is behaving, while keeping the rest frozen (I dont want them to move). For example, in a two domain protein keeping one domain frozen and seeing the other domain movement or in a protein ligand complex keeing the protein frozen and seeing the movement of the ligand. I tried -center in trjconv and selected the group that I need to center. Any other suggestions? Thanks and Regards, Raghu -- gmx-users mailing listgmx-users@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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Trajectory viewing by freeing a part
Ragothaman Yennamalli wrote: Hi, While viewing a trajectory I am trying to see how a particular part or group is behaving, while keeping the rest frozen (I dont want them to move). For example, in a two domain protein keeping one domain frozen and seeing the other domain movement or in a protein ligand complex keeing the protein frozen and seeing the movement of the ligand. I tried -center in trjconv and selected the group that I need to center. Any other suggestions? Use trjconv -fit rot+trans with a custom index group of whatever you'd like to keep (somewhat) fixed. You cannot fix any group's position with trjconv; you can only remove periodicity and to least-squares fitting to get a smooth trajectory. -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 -- gmx-users mailing listgmx-users@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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Trajectory viewing by freeing a part
On 8/09/2011 3:55 AM, Justin A. Lemkul wrote: Ragothaman Yennamalli wrote: Hi, While viewing a trajectory I am trying to see how a particular part or group is behaving, while keeping the rest frozen (I dont want them to move). For example, in a two domain protein keeping one domain frozen and seeing the other domain movement or in a protein ligand complex keeing the protein frozen and seeing the movement of the ligand. I tried -center in trjconv and selected the group that I need to center. Any other suggestions? Use trjconv -fit rot+trans with a custom index group of whatever you'd like to keep (somewhat) fixed. ... and then load two copies of your simulation in your viewer. Show only a single frame of this group in one of them, and show only the group whose motion is of interest with the other. I doubt this general idea will prove very useful, however. Mark You cannot fix any group's position with trjconv; you can only remove periodicity and to least-squares fitting to get a smooth trajectory. -Justin -- gmx-users mailing listgmx-users@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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: Antw: Re: Re: Antw: Re: Re: [gmx-users] constant PH simulations
Dear Emanuel, Here are a few comments that may help your way through the literature already pointed out by others. Most of your questions concern temporal/kinetic aspects (interchange times, etc) and the answer to them is quite simple: constant-pH MD methods are intended to produce a collection of microstates that is representative of equilibrium, regardless of their temporal relation -- that is, they are *sampling* methods. The rationale is that you ignore the real physical process responsible for the (de)protonation changes and, instead, devise a mathematical strategy to produce a good sample of their distribution. If you think about it, the same holds for all other methods to run simulations in non-microcanonical ensembles. For example, when you use a Nose-Hoover bath for constant temperature, you do not try to explicitly account for the transfer of momentum from external environment through the vibrational modes of the material of the container walls -- rather, you simulate a totally unphysical "extended" system in the microcanonical ensemble, which produces a distribution of microstates whose projection on the subspace of your real system happens to be the canonical distribution of the latter. Luckily, the transfer of momentum is so fast that, as long as the MD moves preserve some kinetic contiguity of the microstates, it is easy to get realistic temporal properties by tuning the values of the bath coupling parameters (or piston masses, etc). Unfortunately, the same cannot be done for proton exchanges in constant-pH MD, for two main reasons. First, exchanges with the solvent depend on slow bimolecular collisions (on the microsecond or slower timescale) and thus cannot be sampled in a temporally realistic way with current computer power. Second, the times of intramolecular exchanges depend on the groups involved and would require computing the corresponding free energy barriers. Therefore, even in the case of "discrete" constant-pH MD methods (where sites are empty or occupied with "full" protons), you cannot easily adjust a parameter to get realistic exchange rates. In the case of "continuum" constant-pH MD methods (where sites are occupied by "fractional" protons), asking for realistic exchange rates is bit like asking for temporal realism in free energy calculations using thermodynamic integration or perturbation methods -- the very question becomes meaningless. In short, the studies published so far show that constant-pH MD seems to work pretty well in accounting for (de)protonation-induced structural reorganization (there are actually plenty of comparisons with experimental data; check the literature), but it is obviously not the way to go if you want to investigate rates and energy barriers (in which case you can use MM-based free energy methods or, instead, quantum or semiclassical methods that explicitly model proton association/dissociation). Once you understand that time is not really there in the constant-pH MD "simulations", the usual absence of H+ in the box should become clear -- you just do what you would normally do in a traditional constant-protonation run. So, in most cases you would not add any H+/H3O+/OH- ions, although you may want to at extreme pH values (assuming you have reasonable MM models for that, which is arguable). That's why I stated in one of the papers that you should probably read: "As usual in binding formalisms [refs], we restrict the location of transient protons to the protonatable sites; non-binding protons can be considered as part of the solvent if necessary." [J. Chem. Phys. 107:4184] Essentially, this follows from the statistical thermodynamic fact that sampling and Hamiltonian are independent things, so you should use the same type of model in the constant-protonation and constant-pH cases, because the former is a conditional case of the latter. I hope this helps your reading of the literature. Some statistical thermodynamics background is also the best way to clarify the more conceptual issues. Note also that there are considerable differences between some of the constant-pH MD methods currently in use (Gerrit was mostly commenting on one particular type of "continuous" method). Best, Antonio -- Antonio M. Baptista Instituto de Tecnologia Quimica e Biologica, Universidade Nova de Lisboa Av. da Republica - EAN, 2780-157 Oeiras, Portugal phone: +351-214469619 email: bapti...@itqb.unl.pt fax: +351-214411277 WWW: http://www.itqb.unl.pt/~baptista -- On Wed, 07 Sep 2011 13:41:33 +0200, Emanuel Peter wrote: SMA. João Henriques 07.09.11 13.09 Uhr >>> Why don't you read the papers associated with the link everyone keeps sending you!!! Stop it with the autistic behavior. http://www.gromacs.org/Documentation/How-tos/Constant_pH_Simulation Here is the main paper regarding the CpH-MD method I'm curre
