[gmx-users] how to deduce charges for gromos forcefield?
Dear gmx-users, I want to develop an itp file for an organic molecule which has 87 atoms. I deduced the charge using the common Resp procedure with RED-III tool.However , I am not quite sure if the Resp charge or Esp charge can be used in Gromos forcefield, if not, how does Gromos forcefied deduce its charge distribution? Any suggestion will be appreciated, thanks in advance.___ 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] how to write the correct top file for membraneprotein system?
Hi Liang, Do you have to define ffoplsaa.itp in your top file? isn't it enough to generate your protein topology with the OPLS forcefield using pdb2gmx and include the protein's generated itp files? I don't use OPLS, but my own definition of the .top file goes like this: ; generic + lipid topology #include ffgmx.itp #include lipid.itp #include dmpc.itp #include ions.itp ; protein #include chain_A.itp #include chain_B.itp #include chain_C.itp #include chain_D.itp ; water #include spc.itp Rest of my molecule definitions are similar (protein first, then lipid, then water, and finally ions to neutralize the system). Hope it helps, Hadas. - Original Message - From: liang [EMAIL PROTECTED] To: Justin A. Lemkul [EMAIL PROTECTED] Cc: gmx-users@gromacs.org Sent: Sunday, November 25, 2007 7:41 AM Subject: Re: [gmx-users] how to write the correct top file for membraneprotein system? Dear Justin, Thanks for you quickly reply. I have tried before to comment out the section of [ defaults ] in the next itp file, but still too many warnings and final crashed. And i think it would not be the best method to solve this problem, because i have to use ffgmx.itp to deal with DPPC. Is there any other method i can try? Thanks Liang - Original Message - From: Justin A. Lemkul [EMAIL PROTECTED] To: liang [EMAIL PROTECTED]; Discussion list for GROMACS users gmx-users@gromacs.org Sent: Sunday, November 25, 2007 12:23 PM Subject: Re: [gmx-users] how to write the correct top file for membrane protein system? Quoting liang [EMAIL PROTECTED]: Dear User, i try to perform simulation on membrane protein ( proterin + DPPC ). And i use OPLS for protein, Berger force field for DPPC. But after i construct this system, i cannot obtain tpr file by using grompp. Here is my topol.top : ; protein #include ffoplsaa.itp #include protein-opls.itp ; membrane #include ffgmx.itp #include lipid.itp #include dppc.itp ; Include water topology #include spc.itp [ system ] ; name Membrane in water [ molecules ] ; name number Protein1 DPPC 123 SOL 14189 here is the result: Fatal error: Invalid order for directive defaults, file /home/gmx331/share/gromacs/top/ffgmx.itp, line 4 I suspect it is a result of using two different force fields. The [ defaults ] will be defined in the first force field (in your case, ffoplsaa.itp), but then grompp is finding a second [ defaults ] in ffgmx.itp. See here: http://wiki.gromacs.org/index.php/Errors#Found_a_second_defaults_directive_file -Justin Could you please give me some suggestion? i appreciate your help. Thanks so much! Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA [EMAIL PROTECTED] | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ ___ 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 -- No virus found in this incoming message. Checked by AVG Free Edition. Version: 7.5.503 / Virus Database: 269.16.5/1148 - Release Date: 11/23/2007 7:39 PM ___ 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] how to deduce charges for gromos forcefield?
Q733 wrote: Dear gmx-users, I want to develop an itp file for an organic molecule which has 87 atoms. I deduced the charge using the common Resp procedure with RED-III tool.However , I am not quite sure if the Resp charge or Esp charge can be used in Gromos forcefield, if not, how does Gromos forcefied deduce its charge distribution? empirically. Any suggestion will be appreciated, thanks in advance. ___ 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 -- 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 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ 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] grompp
Hi Jestin, Read chapter 5 thoroughly :) It seems that in your topology file (minding the #includes) the directive [ system ] is given too early, e.g. before the definition of the [ moleculetypes ]. Tsjerk On 25 Nov 2007 05:51:50 -, JMandumpal [EMAIL PROTECTED] wrote: Dear Gromacs users, When I tried to build up .tpr file for running energy minimisation, I encountered some problems: This is the command I used: grompp -f em.mdp -p topol.top -c out.gro -o pr.tpr and I received the following error message: Fatal error: Invalid order for directive system, file topol.top, line 4 --- How can I solve this? regards, Jestin Mandumpal ___ 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 -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 ___ 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] area by lipid
Well I know that the x/y directions are scaled isotropically and the z direction is scaled independiently, and i must give just 2 compresibility valors, but people don't give this valor in the most of the papers about membrane simulations. For example i use on DPPC membrane compressibility =4.5e-5 4.5e-5 ref-p= 1.0 1.0 the area change from 0.64 to 0.62. When i use the same parameter on POPG or POPC bilayer the system is exploding. If i change to on POPC and POPG compressibility =1.0e-5 4.5e-5 ref-p= 1.0 1.0 it gives areas about 0.639 (POPC) and 0.53 (POPG). The POPG area is according to Atomic-scale structure and electrostatics of anionic POPG lipid bilayers with Na+ counterions, W. Zhao, T. Rog, A.A. Gurtovenko, I. Vattulainen, and M. Karttunen, Biophys J. 92, 1114-1124 (2007), and I'm using the same temperature. But the POPC area isn't good. My questions are: Can i use compressibility =0 4.5e-5 and ref-p = 0 1.0 on peptide-membrane systems? (at first the peptide is about 10 A to the bilayer interface and after it's inserting in the membrane) What are the correct valors for the compressibility on membrane systems? Thanks a lot, Maité On Nov 24, 2007 10:27 PM, Mark Abraham [EMAIL PROTECTED] wrote: Hi: I am working on membrane simulation under lipid (DPPC, from Peter Tieleman group site). I equilibrated dppc membrane for 10 ns and when i got the area by lipid (x*y/ # lipids) using g_energy, i obtained that the area is constant (0.64), there isn't any fluctuaction during 10 ns..althougth the volumen isn't constant. What's wrong in this simulation? Did you notice that your box dimensions are not changing in X and Y directions? Do you understand what semiisotropic pressure coupling does? 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 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] how to write the correct top file for membraneprotein system?
Hi Hadas, i have tried to use gromos87 for protein, everything is ok. (just with ffgmx.itp) but if i use opls for protein, i have to add ffoplsaa.itp in top file, otherwise it cannot provide some parameters for protein. Did you use gromos87 to generate your protein itp files (chain_A .itp ...) ? Thanks Liang - Original Message - From: Hadas Leonov [EMAIL PROTECTED] To: liang [EMAIL PROTECTED]; Discussion list for GROMACS users gmx-users@gromacs.org Sent: Sunday, November 25, 2007 5:26 PM Subject: Re: [gmx-users] how to write the correct top file for membraneprotein system? Hi Liang, Do you have to define ffoplsaa.itp in your top file? isn't it enough to generate your protein topology with the OPLS forcefield using pdb2gmx and include the protein's generated itp files? I don't use OPLS, but my own definition of the .top file goes like this: ; generic + lipid topology #include ffgmx.itp #include lipid.itp #include dmpc.itp #include ions.itp ; protein #include chain_A.itp #include chain_B.itp #include chain_C.itp #include chain_D.itp ; water #include spc.itp Rest of my molecule definitions are similar (protein first, then lipid, then water, and finally ions to neutralize the system). Hope it helps, Hadas. - Original Message - From: liang [EMAIL PROTECTED] To: Justin A. Lemkul [EMAIL PROTECTED] Cc: gmx-users@gromacs.org Sent: Sunday, November 25, 2007 7:41 AM Subject: Re: [gmx-users] how to write the correct top file for membraneprotein system? Dear Justin, Thanks for you quickly reply. I have tried before to comment out the section of [ defaults ] in the next itp file, but still too many warnings and final crashed. And i think it would not be the best method to solve this problem, because i have to use ffgmx.itp to deal with DPPC. Is there any other method i can try? Thanks Liang - Original Message - From: Justin A. Lemkul [EMAIL PROTECTED] To: liang [EMAIL PROTECTED]; Discussion list for GROMACS users gmx-users@gromacs.org Sent: Sunday, November 25, 2007 12:23 PM Subject: Re: [gmx-users] how to write the correct top file for membrane protein system? Quoting liang [EMAIL PROTECTED]: Dear User, i try to perform simulation on membrane protein ( proterin + DPPC ). And i use OPLS for protein, Berger force field for DPPC. But after i construct this system, i cannot obtain tpr file by using grompp. Here is my topol.top : ; protein #include ffoplsaa.itp #include protein-opls.itp ; membrane #include ffgmx.itp #include lipid.itp #include dppc.itp ; Include water topology #include spc.itp [ system ] ; name Membrane in water [ molecules ] ; name number Protein1 DPPC 123 SOL 14189 here is the result: Fatal error: Invalid order for directive defaults, file /home/gmx331/share/gromacs/top/ffgmx.itp, line 4 I suspect it is a result of using two different force fields. The [ defaults ] will be defined in the first force field (in your case, ffoplsaa.itp), but then grompp is finding a second [ defaults ] in ffgmx.itp. See here: http://wiki.gromacs.org/index.php/Errors#Found_a_second_defaults_directive_file -Justin Could you please give me some suggestion? i appreciate your help. Thanks so much! Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA [EMAIL PROTECTED] | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ ___ 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 -- No virus found in this incoming message. Checked by AVG Free Edition. Version: 7.5.503 / Virus Database: 269.16.5/1148 - Release Date: 11/23/2007 7:39 PM ___ 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] grompp
Dear Gromacs users, When I tried to build up .tpr file for running energy minimisation, I encountered some problems: This is the command I used: grompp -f em.mdp -p topol.top -c out.gro -o pr.tpr and I received the following error message: Fatal error: Invalid order for directive system, file topol.top, line 4 --- How can I solve this? http://wiki.gromacs.org/index.php/Errors#Invalid_order_for_directive_defaults Read chapter 5 of the manual. 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
Re: [gmx-users] how to write the correct top file for membrane protein system?
Dear Justin, Thanks for you quickly reply. I have tried before to comment out the section of [ defaults ] in the next itp file, but still too many warnings and final crashed. And i think it would not be the best method to solve this problem, because i have to use ffgmx.itp to deal with DPPC. Is there any other method i can try? Don't mix forcefields unless you already have hard evidence that this combination works - and I'm not aware of any. The link Justin provided warns you about that. You need to find a force field that has parameters optimized that suit your system. Mixing anything else is about 99% likely to make an expensive (and poor) random number generator. 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
Re: [gmx-users] how to write the correct top file for membraneprotein system?
Hi Liang, Do you have to define ffoplsaa.itp in your top file? isn't it enough to generate your protein topology with the OPLS forcefield using pdb2gmx and include the protein's generated itp files? No, because the .itp file is not self-contained. It is a topology for use with a particular forcefield, and requires the ability to look up values like atom types that are defined for that force field. This is a *good thing* because it inhibits people from mixing and matching forcefields for different parts of their system. 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
Re: [gmx-users] how to write the correct top file for membraneprotein system?
Yes, I used GROMOS87. Although it's deprecated now and I'm not sure which ff to switch to. Hadas. On Sun, 2007-11-25 at 19:03 +0800, liang wrote: Hi Hadas, i have tried to use gromos87 for protein, everything is ok. (just with ffgmx.itp) but if i use opls for protein, i have to add ffoplsaa.itp in top file, otherwise it cannot provide some parameters for protein. Did you use gromos87 to generate your protein itp files (chain_A .itp ...) ? Thanks Liang - Original Message - From: Hadas Leonov [EMAIL PROTECTED] To: liang [EMAIL PROTECTED]; Discussion list for GROMACS users gmx-users@gromacs.org Sent: Sunday, November 25, 2007 5:26 PM Subject: Re: [gmx-users] how to write the correct top file for membraneprotein system? Hi Liang, Do you have to define ffoplsaa.itp in your top file? isn't it enough to generate your protein topology with the OPLS forcefield using pdb2gmx and include the protein's generated itp files? I don't use OPLS, but my own definition of the .top file goes like this: ; generic + lipid topology #include ffgmx.itp #include lipid.itp #include dmpc.itp #include ions.itp ; protein #include chain_A.itp #include chain_B.itp #include chain_C.itp #include chain_D.itp ; water #include spc.itp Rest of my molecule definitions are similar (protein first, then lipid, then water, and finally ions to neutralize the system). Hope it helps, Hadas. - Original Message - From: liang [EMAIL PROTECTED] To: Justin A. Lemkul [EMAIL PROTECTED] Cc: gmx-users@gromacs.org Sent: Sunday, November 25, 2007 7:41 AM Subject: Re: [gmx-users] how to write the correct top file for membraneprotein system? Dear Justin, Thanks for you quickly reply. I have tried before to comment out the section of [ defaults ] in the next itp file, but still too many warnings and final crashed. And i think it would not be the best method to solve this problem, because i have to use ffgmx.itp to deal with DPPC. Is there any other method i can try? Thanks Liang - Original Message - From: Justin A. Lemkul [EMAIL PROTECTED] To: liang [EMAIL PROTECTED]; Discussion list for GROMACS users gmx-users@gromacs.org Sent: Sunday, November 25, 2007 12:23 PM Subject: Re: [gmx-users] how to write the correct top file for membrane protein system? Quoting liang [EMAIL PROTECTED]: Dear User, i try to perform simulation on membrane protein ( proterin + DPPC ). And i use OPLS for protein, Berger force field for DPPC. But after i construct this system, i cannot obtain tpr file by using grompp. Here is my topol.top : ; protein #include ffoplsaa.itp #include protein-opls.itp ; membrane #include ffgmx.itp #include lipid.itp #include dppc.itp ; Include water topology #include spc.itp [ system ] ; name Membrane in water [ molecules ] ; name number Protein1 DPPC 123 SOL 14189 here is the result: Fatal error: Invalid order for directive defaults, file /home/gmx331/share/gromacs/top/ffgmx.itp, line 4 I suspect it is a result of using two different force fields. The [ defaults ] will be defined in the first force field (in your case, ffoplsaa.itp), but then grompp is finding a second [ defaults ] in ffgmx.itp. See here: http://wiki.gromacs.org/index.php/Errors#Found_a_second_defaults_directive_file -Justin Could you please give me some suggestion? i appreciate your help. Thanks so much! Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA [EMAIL PROTECTED] | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ ___ 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 -- No virus found in this incoming message. Checked by AVG Free Edition. Version: 7.5.503 / Virus Database: 269.16.5/1148 - Release Date: 11/23/2007 7:39 PM ___ 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
[gmx-users] Problem with replica exchange in vacuum
Hi all, I am performing a REMD simulation in vacuum. Although I minimized the energy of each initial replica by using a stringent convergence criterion, after the the third attempt, the system exploided because of a huge deviation in the Lincs algorithm. Although I started to the simulation via low-energy structures, what may be the probable reason for this? Is it because of vacuum? Thank you Ozge ___ 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] Problem with replica exchange in vacuum
Hi all, I am performing a REMD simulation in vacuum. Although I minimized the energy of each initial replica by using a stringent convergence criterion, after the the third attempt, the system exploided because of a huge deviation in the Lincs algorithm. Although I started to the simulation via low-energy structures, what may be the probable reason for this? Is it because of vacuum? Thank you Ozge ___ 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] Problem with replica exchange in vacuum
On Sun, 25 Nov 2007 19:00:47 +0200 OZGE ENGIN [EMAIL PROTECTED] wrote: Hi all, I am performing a REMD simulation in vacuum. Although I minimized the energy of each initial replica by using a stringent convergence criterion, after the the third attempt, the system exploided because of a huge deviation in the Lincs algorithm. What is the range of temperature you use? What time step you use? At high temperature you need do decrease the integration time step to avoid the increase of integration error due to the temperature. Such a simulation, REMD in vacuo, is typically what you do not want to do. You might think that you'll increase your sampling and thus have better statistics. This won't give you any realistic picture of your system. At least put a continuum model! Even though ... XAvier Although I started to the simulation via low-energy structures, what may be the probable reason for this? Is it because of vacuum? Thank you Ozge ___ 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: how to write the correct top file for membrane protein
Dear Mark, Thanks for your advice, but from my understanding, Berger's force field is based on OPLS/Amber. Lipid itp files from Tieleman's website just use the atom type definitions from GROMOS87. And GROMOS87 is out of fashion now. So thats why i think it would be better to use OPLS for protein and ffgmx.itp for lipids. I am not sure whether I misunderstand the usage of Berger's force field, if i am wrong, please give me further instruction. I hope it would not be bothering you. Thanks so much! Liang Dear Justin, Thanks for you quickly reply. I have tried before to comment out the section of [ defaults ] in the next itp file, but still too many warnings and final crashed. And i think it would not be the best method to solve this problem, because i have to use ffgmx.itp to deal with DPPC. Is there any other method i can try? Don't mix forcefields unless you already have hard evidence that this combination works - and I'm not aware of any. The link Justin provided warns you about that. You need to find a force field that has parameters optimized that suit your system. Mixing anything else is about 99% likely to make an expensive (and poor) random number generator. 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
Re: [gmx-users] Re: how to write the correct top file for membrane protein
liang wrote: Dear Mark, Thanks for your advice, but from my understanding, Berger's force field is based on OPLS/Amber. Lipid itp files from Tieleman's website just use the atom type definitions from GROMOS87. And GROMOS87 is out of fashion now. So thats why i think it would be better to use OPLS for protein and ffgmx.itp for lipid. Fine, but you can't use them both at the same time (unless you want to produce indefensible gibberish), and ffgmx is deprecated anyway. I am not sure whether I misunderstand the usage of Berger's force field, if i am wrong, please give me further instruction. See my advice last time. Don't mix forcefields unless you already have hard evidence that this combination works - and I'm not aware of any. The link Justin provided warns you about that. You need to find a force field that has parameters optimized that suit your system. Mixing anything else is about 99% likely to make an expensive (and poor) random number generator. Look in the literature for systems similar to yours and see if their ideas on force fields are suitable for you to use. Making it up based on stuff you found on the web is for high school students doing assignments :-) 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
