Re: [gmx-users] Re: Chain separation problem
> Dear Periole, > Thank you so much for your kind reply, as you suggested I will keep the > discussion on the users list. Please note that I AM GETTING PROBLEM ONLY > WHEN I AM NOT USING ANY BOX. Please also refrain from using all-capitals. It is regarded as the email equivalent of shouting. It will get your email ignored, rather than treated with more urgency. If your proteins-are-moving apart problem is not a PBC artifact, and does not occur when you use PBC, then you have a perplexing problem. First, check your inputs again, so that you really are doing what you think you're doing. Even repeat the whole setup from scratch. The simplest explanation is user error. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: Chain separation problem
Dear Periole, Thank you so much for your kind reply, as you suggested I will keep the discussion on the users list. Please note that I AM GETTING PROBLEM ONLY WHEN I AM NOT USING ANY BOX. When I am keeping the protein in the box with or with out solution chains are not separating. What I understood from your suggestion is solution for the chain separation in the box. Regards Chandu > On Mon, 26 Nov 2007 15:33:36 +0530 (IST) > [EMAIL PROTECTED] wrote: >> Dear Periole, >> Thank you so much for your suggestion. I was not sure weather to reply >> all >> or individually. > > It is always better to keep the discussion on the users list. The info > given might serve other users. > >> I am sorry I am not clear about your answer. I am >> getting the problem only when I am not using the box, but you said to >> center the protein in the box? Could you please explain this. > > When you use a box the program will deal with the position of the > system relative to the box faces. If a molecule (first atom) moves > and crosses the dimension of the box on one axis (x,y,z) -it > physically gets out of the box- it will be replaced inside the box > on the opposite box-side (same axis). Have a look at the manual or > any text book on simulations, this will be more clearly explained. > > When you build your system, it might be that one part of it is > inside the box and the other part is outside. This is more likely > to happen when multimeric structures are simulated. Then the program > will automatically replace the parts of the system that are outside > the box to the inside. Note that the system does not feel it. > > If you want to avoid this you have to center your system before > doing any minimization. Note that the box has to be large enough > to accommodate your system plus solvent. > > XAvier > >> Thanks in advance >> Chandu >> On Mon, 26 Nov 2007 13:45:01 +0530 (IST) >> [EMAIL PROTECTED] wrote: >>> Hi All, >>> I have been trying run energy minimization for a homoTRIMER protein, I >>> have puzzled by the following results! >>> >>> 1) energy minimization in vacuum 1 chain is separated from the >>> remaining 2 >>> chains. I tried for 5 models in 4 models chains are separated and one >>> is >>> normal. >>> >>> 2)energy minimization in box with or with out solvent, no chain >>> separation >>> for all the 5 models. >>> please note that EM method is steepest decent, I have tried size on the >>> box up to 20nm. >> >> you are probably experiencing the effect of PBC. In the cases you >> see "separation", centering the protein in the box should solve the >> problem. >> >> >> -- >> C.Chandra Sekhar Reddy (Research Scholar) >> Laboratoire de Biochimie et Génétique Moléculaire >> Université de La Réunion >> 15, avenue René Cassin >> 97715 Saint Denis Messag Cedex 09 >> La Réunion, France >> Tel : +262 262 93 8641 MOB +262 (0)692 44 49 42 >>Fax : +262 262 93 8237 >> -- >> > > - > XAvier Periole - PhD > > NMR & Molecular Dynamics Group > University of Groningen > The Netherlands > http://md.chem.rug.nl/~periole > - > -- C.Chandra Sekhar Reddy (Research Scholar) Laboratoire de Biochimie et Génétique Moléculaire Université de La Réunion 15, avenue René Cassin 97715 Saint Denis Messag Cedex 09 La Réunion, France Tel : +262 262 93 8641 MOB +262 (0)692 44 49 42 Fax : +262 262 93 8237 -- ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Re: Chain separation problem
On Mon, 26 Nov 2007 11:44:22 +0100 "Xavier Periole" <[EMAIL PROTECTED]> wrote: On Mon, 26 Nov 2007 15:33:36 +0530 (IST) [EMAIL PROTECTED] wrote: Dear Periole, Thank you so much for your suggestion. I was not sure weather to reply all or individually. It is always better to keep the discussion on the users list. The info given might serve other users. I am sorry I am not clear about your answer. I am getting the problem only when I am not using the box, but you said to center the protein in the box? Could you please explain this. Sorry I thought you had the problem only when using a box! Then I am also confused. Without boundaries this should not happen. Check you input must be something funny there. XAvier When you use a box the program will deal with the position of the system relative to the box faces. If a molecule (first atom) moves and crosses the dimension of the box on one axis (x,y,z) -it physically gets out of the box- it will be replaced inside the box on the opposite box-side (same axis). Have a look at the manual or any text book on simulations, this will be more clearly explained. When you build your system, it might be that one part of it is inside the box and the other part is outside. This is more likely to happen when multimeric structures are simulated. Then the program will automatically replace the parts of the system that are outside the box to the inside. Note that the system does not feel it. If you want to avoid this you have to center your system before doing any minimization. Note that the box has to be large enough to accommodate your system plus solvent. XAvier Thanks in advance Chandu On Mon, 26 Nov 2007 13:45:01 +0530 (IST) [EMAIL PROTECTED] wrote: Hi All, I have been trying run energy minimization for a homoTRIMER protein, I have puzzled by the following results! 1) energy minimization in vacuum 1 chain is separated from the remaining 2 chains. I tried for 5 models in 4 models chains are separated and one is normal. 2)energy minimization in box with or with out solvent, no chain separation for all the 5 models. please note that EM method is steepest decent, I have tried size on the box up to 20nm. you are probably experiencing the effect of PBC. In the cases you see "separation", centering the protein in the box should solve the problem. -- C.Chandra Sekhar Reddy (Research Scholar) Laboratoire de Biochimie et Génétique Moléculaire Université de La Réunion 15, avenue René Cassin 97715 Saint Denis Messag Cedex 09 La Réunion, France Tel : +262 262 93 8641 MOB +262 (0)692 44 49 42 Fax : +262 262 93 8237 -- - XAvier Periole - PhD NMR & Molecular Dynamics Group University of Groningen The Netherlands http://md.chem.rug.nl/~periole - ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php - XAvier Periole - PhD NMR & Molecular Dynamics Group University of Groningen The Netherlands http://md.chem.rug.nl/~periole - ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: Chain separation problem
On Mon, 26 Nov 2007 15:33:36 +0530 (IST) [EMAIL PROTECTED] wrote: Dear Periole, Thank you so much for your suggestion. I was not sure weather to reply all or individually. It is always better to keep the discussion on the users list. The info given might serve other users. I am sorry I am not clear about your answer. I am getting the problem only when I am not using the box, but you said to center the protein in the box? Could you please explain this. When you use a box the program will deal with the position of the system relative to the box faces. If a molecule (first atom) moves and crosses the dimension of the box on one axis (x,y,z) -it physically gets out of the box- it will be replaced inside the box on the opposite box-side (same axis). Have a look at the manual or any text book on simulations, this will be more clearly explained. When you build your system, it might be that one part of it is inside the box and the other part is outside. This is more likely to happen when multimeric structures are simulated. Then the program will automatically replace the parts of the system that are outside the box to the inside. Note that the system does not feel it. If you want to avoid this you have to center your system before doing any minimization. Note that the box has to be large enough to accommodate your system plus solvent. XAvier Thanks in advance Chandu On Mon, 26 Nov 2007 13:45:01 +0530 (IST) [EMAIL PROTECTED] wrote: Hi All, I have been trying run energy minimization for a homoTRIMER protein, I have puzzled by the following results! 1) energy minimization in vacuum 1 chain is separated from the remaining 2 chains. I tried for 5 models in 4 models chains are separated and one is normal. 2)energy minimization in box with or with out solvent, no chain separation for all the 5 models. please note that EM method is steepest decent, I have tried size on the box up to 20nm. you are probably experiencing the effect of PBC. In the cases you see "separation", centering the protein in the box should solve the problem. -- C.Chandra Sekhar Reddy (Research Scholar) Laboratoire de Biochimie et Génétique Moléculaire Université de La Réunion 15, avenue René Cassin 97715 Saint Denis Messag Cedex 09 La Réunion, France Tel : +262 262 93 8641 MOB +262 (0)692 44 49 42 Fax : +262 262 93 8237 -- - XAvier Periole - PhD NMR & Molecular Dynamics Group University of Groningen The Netherlands http://md.chem.rug.nl/~periole - ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
