Re: [gmx-users] Cholesterol parameters (Charrm36) in GMX
On 2012-10-31 16:31, Yorquant Wang wrote: Hi GMX-users, Klauda et al (J. Phys. Chem. B, 2012, 116 (1), pp 203–210) recently provided Cholesterol parameters for Charmm FF. Does anyone have the corresponding .itp file for cholesterol in GMX style? Thanks for replying, Yukun there's a script charmm2gromacs-pvm.py on the gromacs website that you can download. Use with care. -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- 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] Cholesterol parameters (Charrm36) in GMX
Hi David: I have tested the script. The input are 1 charmm topology file, 2 corresponding charmm parameter file and 3 foldername. But there are a lots of top_all***.rtf files and par_all***.prm files in toppar_c36_aug12/toppar folder, I don't know which pair is the correct pair. Could you give me a clue? The new parameter for cholesterol is stored in chol_new.str. If it is OK that I just put chol_new.str into the toppar_c36_aug12/toppar/ folder and transfer it directly. Thank you for replying! yorquant 2012/11/1 David van der Spoel sp...@xray.bmc.uu.se On 2012-10-31 16:31, Yorquant Wang wrote: Hi GMX-users, Klauda et al (J. Phys. Chem. B, 2012, 116 (1), pp 203–210) recently provided Cholesterol parameters for Charmm FF. Does anyone have the corresponding .itp file for cholesterol in GMX style? Thanks for replying, Yukun there's a script charmm2gromacs-pvm.py on the gromacs website that you can download. Use with care. -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://www.gromacs.org/Support/Mailing_Lists -- Yukun Wang PhD candidate Institute of Natural Sciences College of Life Science, Shanghai Jiao Tong University Cell phone: 13621806236. China Shanghai -- 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] Cholesterol parameters (Charrm36) in GMX
On 2012-11-01 09:47, Yorquant Wang wrote: Hi David: I have tested the script. The input are 1 charmm topology file, 2 corresponding charmm parameter file and 3 foldername. But there are a lots of top_all***.rtf files and par_all***.prm files in toppar_c36_aug12/toppar folder, I don't know which pair is the correct pair. Could you give me a clue? The new parameter for cholesterol is stored in chol_new.str. If it is OK that I just put chol_new.str into the toppar_c36_aug12/toppar/ folder and transfer it directly. Don't know. I think you need everything gromacs related that comes out. Do it in an empty directory. Thank you for replying! yorquant 2012/11/1 David van der Spoel sp...@xray.bmc.uu.se On 2012-10-31 16:31, Yorquant Wang wrote: Hi GMX-users, Klauda et al (J. Phys. Chem. B, 2012, 116 (1), pp 203–210) recently provided Cholesterol parameters for Charmm FF. Does anyone have the corresponding .itp file for cholesterol in GMX style? Thanks for replying, Yukun there's a script charmm2gromacs-pvm.py on the gromacs website that you can download. Use with care. -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://www.gromacs.org/Support/Mailing_Lists -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- 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] cholesterol
On 4/21/2011 8:05 PM, Preeti Gupta wrote: Hi All, I am new user of gromacs and i want to simulate cholesterol + DOPC as my final year project. firstly i tried gromacs with cholesterol, for which i have downloaded cholesterol pdb and itp file from gromacs site by Monika Hoeltje. i m getting the following error- Residue 'CHOL' not found in residue topology database. ... which you need if only if you want to use pdb2gmx on a structure file. I tried PRODRG for generating cholesterol topology file and coordinate file, but still i got the error- invalid directive of atomtype. So you've got some file format wrong... can someone give me charmm residue topology file for cholesterol or with some solution. I think you will profit from doing some tutorial material and looking at the examples in chapter 5 of the manual. 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
Re: [gmx-users] cholesterol
#ZHAO LINA# wrote: Hi, Are there some tutorials handling the cholesterol stuff. I read several literature but choked in some places. I said this to someone just the other day: if it's not linked at http://www.gromacs.org/Documentation/Tutorials or you can't find it with Google, it probably doesn't exist. What's more, handling the cholesterol stuff doesn't really lend itself to getting useful help. What are you trying to do? Derive parameters? Build a membrane? A micelle? An LDL complex? -Justin Thanks with best regards, lina -- 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] cholesterol
Hi, It will be so bad for me if it really does not exist. I wish probably except asking Dr. google, someone else will be able to provide me some links. I once just wanted to see some examples how they handled its topology even I got one from PRODRG server, but it has problems later. Not so much in those specific simulations yet, just beginning stage. lina From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Justin A. Lemkul [jalem...@vt.edu] Sent: Friday, October 01, 2010 8:35 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] cholesterol #ZHAO LINA# wrote: Hi, Are there some tutorials handling the cholesterol stuff. I read several literature but choked in some places. I said this to someone just the other day: if it's not linked at http://www.gromacs.org/Documentation/Tutorials or you can't find it with Google, it probably doesn't exist. What's more, handling the cholesterol stuff doesn't really lend itself to getting useful help. What are you trying to do? Derive parameters? Build a membrane? A micelle? An LDL complex? -Justin Thanks with best regards, lina -- 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 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] cholesterol
#ZHAO LINA# wrote: Hi, It will be so bad for me if it really does not exist. I wish probably except asking Dr. google, someone else will be able to provide me some links. I once just wanted to see some examples how they handled its topology even I got one from PRODRG server, but it has problems later. Not so much in those specific simulations yet, just beginning stage. If your problem is with deriving parameters, then do a thorough literature search. Simulations with cholesterol have been done with numerous force fields, so parameterization methodology and/or suitable parameters should be available. -Justin lina From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Justin A. Lemkul [jalem...@vt.edu] Sent: Friday, October 01, 2010 8:35 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] cholesterol #ZHAO LINA# wrote: Hi, Are there some tutorials handling the cholesterol stuff. I read several literature but choked in some places. I said this to someone just the other day: if it's not linked at http://www.gromacs.org/Documentation/Tutorials or you can't find it with Google, it probably doesn't exist. What's more, handling the cholesterol stuff doesn't really lend itself to getting useful help. What are you trying to do? Derive parameters? Build a membrane? A micelle? An LDL complex? -Justin Thanks with best regards, lina -- 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 -- 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] cholesterol
Hi, Thanks for your answer, I will spend some time to figure it out. By the way, any links or literature or something relevant to it warmly welcome to introduce them to me. Best regards, lina From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Justin A. Lemkul [jalem...@vt.edu] Sent: Friday, October 01, 2010 9:06 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] cholesterol #ZHAO LINA# wrote: Hi, It will be so bad for me if it really does not exist. I wish probably except asking Dr. google, someone else will be able to provide me some links. I once just wanted to see some examples how they handled its topology even I got one from PRODRG server, but it has problems later. Not so much in those specific simulations yet, just beginning stage. If your problem is with deriving parameters, then do a thorough literature search. Simulations with cholesterol have been done with numerous force fields, so parameterization methodology and/or suitable parameters should be available. -Justin lina From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Justin A. Lemkul [jalem...@vt.edu] Sent: Friday, October 01, 2010 8:35 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] cholesterol #ZHAO LINA# wrote: Hi, Are there some tutorials handling the cholesterol stuff. I read several literature but choked in some places. I said this to someone just the other day: if it's not linked at http://www.gromacs.org/Documentation/Tutorials or you can't find it with Google, it probably doesn't exist. What's more, handling the cholesterol stuff doesn't really lend itself to getting useful help. What are you trying to do? Derive parameters? Build a membrane? A micelle? An LDL complex? -Justin Thanks with best regards, lina -- 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 -- 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 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] cholesterol
I can think of a few cholesterol topologies just off the top of my head: GROMOS43A1-S3 forcefield has an entry for cholesterol There is a stream file for cholesterol available for use with the CHARMM forcefields. There are other available too, you should use google to find them. I have never used any of them so would not like to comment on which to use, this is up to you to decide after a thorough read of the literature. Cheers Tom #ZHAO LINA# wrote: Hi, Thanks for your answer, I will spend some time to figure it out. By the way, any links or literature or something relevant to it warmly welcome to introduce them to me. Best regards, lina From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Justin A. Lemkul [jalem...@vt.edu] Sent: Friday, October 01, 2010 9:06 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] cholesterol #ZHAO LINA# wrote: Hi, It will be so bad for me if it really does not exist. I wish probably except asking Dr. google, someone else will be able to provide me some links. I once just wanted to see some examples how they handled its topology even I got one from PRODRG server, but it has problems later. Not so much in those specific simulations yet, just beginning stage. If your problem is with deriving parameters, then do a thorough literature search. Simulations with cholesterol have been done with numerous force fields, so parameterization methodology and/or suitable parameters should be available. -Justin lina From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Justin A. Lemkul [jalem...@vt.edu] Sent: Friday, October 01, 2010 8:35 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] cholesterol #ZHAO LINA# wrote: Hi, Are there some tutorials handling the cholesterol stuff. I read several literature but choked in some places. I said this to someone just the other day: if it's not linked at http://www.gromacs.org/Documentation/Tutorials or you can't find it with Google, it probably doesn't exist. What's more, handling the cholesterol stuff doesn't really lend itself to getting useful help. What are you trying to do? Derive parameters? Build a membrane? A micelle? An LDL complex? -Justin Thanks with best regards, lina -- 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 -- 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 -- Dr Thomas Piggot University of Southampton, UK. -- 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] cholesterol
Thanks for your clue. I found the very interesting paper about that force field. Thanks again, lina From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Thomas Piggot [t.pig...@soton.ac.uk] Sent: Friday, October 01, 2010 9:22 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] cholesterol I can think of a few cholesterol topologies just off the top of my head: GROMOS43A1-S3 forcefield has an entry for cholesterol There is a stream file for cholesterol available for use with the CHARMM forcefields. There are other available too, you should use google to find them. I have never used any of them so would not like to comment on which to use, this is up to you to decide after a thorough read of the literature. Cheers Tom #ZHAO LINA# wrote: Hi, Thanks for your answer, I will spend some time to figure it out. By the way, any links or literature or something relevant to it warmly welcome to introduce them to me. Best regards, lina From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Justin A. Lemkul [jalem...@vt.edu] Sent: Friday, October 01, 2010 9:06 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] cholesterol #ZHAO LINA# wrote: Hi, It will be so bad for me if it really does not exist. I wish probably except asking Dr. google, someone else will be able to provide me some links. I once just wanted to see some examples how they handled its topology even I got one from PRODRG server, but it has problems later. Not so much in those specific simulations yet, just beginning stage. If your problem is with deriving parameters, then do a thorough literature search. Simulations with cholesterol have been done with numerous force fields, so parameterization methodology and/or suitable parameters should be available. -Justin lina From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Justin A. Lemkul [jalem...@vt.edu] Sent: Friday, October 01, 2010 8:35 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] cholesterol #ZHAO LINA# wrote: Hi, Are there some tutorials handling the cholesterol stuff. I read several literature but choked in some places. I said this to someone just the other day: if it's not linked at http://www.gromacs.org/Documentation/Tutorials or you can't find it with Google, it probably doesn't exist. What's more, handling the cholesterol stuff doesn't really lend itself to getting useful help. What are you trying to do? Derive parameters? Build a membrane? A micelle? An LDL complex? -Justin Thanks with best regards, lina -- 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 -- 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 -- Dr Thomas Piggot University of Southampton, UK. -- 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
Re: [gmx-users] cholesterol distortion
Hi Jian, seems like there's something seriously wrong with the topology of the cholesterols - check if the angles impropers are set and reasonable. Cheers Steffen Hi, all: I got the initial structure of a DPPC bilayer from Dr. Karttunen's website, use the parameters (hopefully) from their paper: Patra, Karttunen, Hyvönen, Falck, Lindqvist, Vattulainen, Biophys. J. *84*, 3636-3645 (2003) to run for 100ns then replace some DPPC molecules with cholesterols, do the energy minimization, run for 20ns and the cholesterols are distorted as shown in the attached file. Here are parameters for the pure DPPC run which I deem important: nstcomm = 1 comm_grps= DPPC SOL nstlist = 10 ns_type = grid pbc = xyz rlist= 1.0 coulombtype = PME rcoulomb = 1.0 vdwtype = Cutoff rvdw = 1.0 ewald_rtol = 1e-5 optimize_fft = yes tcoupl = Berendsen tau_t= 0.1 0.1 tc_grps = DPPC SOL ref_t= 323 323 pcoupl = Berendsen pcoupltype = semiisotropic tau_p= 1 1 compressibility = 4.5e-5 4.5e-5 ref_p= 1.01.0 gen_vel = yes gen_temp = 325 gen_seed = 173529 constraints = all-bonds constraint_algorithm = LINCS lincs_order = 4 For the DPPC-CHOL combined system I only changed corresponding sections to: comm_grps= DPPC CHOL SOL tau_t= 0.1 0.1 0.1 tc_grps = DPPC CHOL SOL ref_t= 323 323 323 Any suggestion is appreciated. Thank you. Jian ___ 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 -- Dipl.-Chem. Steffen Wolf Fellow of the Ruhr-University Research School Department of Biophysics University of Bochum ND 04/67 44780 Bochum Germany Tel: +49 (0)234 32 28363 Fax: +49 (0)234 32 14626 E-Mail: [EMAIL PROTECTED] Web: http://www.bph.rub.de ___ 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] cholesterol distortion
Jian Dai wrote: For the DPPC-CHOL combined system I only changed corresponding sections to: comm_grps= DPPC CHOL SOL tau_t= 0.1 0.1 0.1 tc_grps = DPPC CHOL SOL ref_t= 323 323 323 Any suggestion is appreciated. Thank you. The points made here http://wiki.gromacs.org/index.php/Thermostats#What_Not_To_Do apply to these cholesterols. You should expect the thermal properties of cholesterol to resemble that of DPPC, and so coupling them together is far more sensible. Otherwise, it's hard to see from a still image without hydrogens whether the behaviour is actually bad. 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
