[gmx-users] Hi
Dear all, my self ashish and i am trying to dynamics using gromacs. i am new in these field. in the time of running Pdb2gmx to create .gro file. i am geting these error. Fatal error: Atom HA in residue MET 1 not found in rtp entry with 9 atoms please help me sortout these problem. -- Ashish Pandey NIPER India -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Hi
try the option -ignh, it will ignore the the hydrogen atoms in your pdb file and generate the ones necessary to the force field you choose. On Dec 15, 2009, at 9:52 AM, ashish pandey wrote: Dear all, my self ashish and i am trying to dynamics using gromacs. i am new in these field. in the time of running Pdb2gmx to create .gro file. i am geting these error. Fatal error: Atom HA in residue MET 1 not found in rtp entry with 9 atoms please help me sortout these problem. -- Ashish Pandey NIPER India -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] g_sdf and visualizing using gOpenMol
Hi, I have a mesoporous silica with attached organic surface groups (alkyl chains). I am trying to quantify to what extent these surface groups interact with the mesoporous silica surface they are attached to (as opposed to projecting straight into the pore space). I thought about using the g_sdf tool (on one surface group at a time initially) but am not completely sure what I am doing is correct so I am hoping someone can guide me. My index file looks like this [MCM] 1 [MCM] 2 [MCM] 3 [SI] 4 5 6 7 8 9 10 11 12 13 Where groups 1, 2 and 3 are carbons of the alkyl chain. SI atoms are taken to represent the surface of the mesoporous silica. I run g_sdf in gromacs and get a refmol.gro file (which looks very different to my structure) and a gom_plt.dat file. I've installed gOpenMol but I am having trouble loading the gom_plt.dat file. It is necessary to load coordinates in first so I load in refmol.gro. As soon as I try to load the .dat file (using plot contourimport) the gui window closes and I get the following Will apply a physical translation (x,y,z): 12.236523 18.866343 9.419045 Will apply a MT translation (x,y,z): 0.07 0.04 0.02 Minimum value 0.00 maximum value 134.129913 Signal was caught = : Success Signal code is: 11, errno I am not sure whether this is because I have unreasonable data in my .dat file (or because my refmol.gro file looks strange) or because I haven't got the hang of using gOpenMol. I don't have any idea what the contour plot should like. Could someone e-mail me a working gom_plt.dat file so I can at least check that I can correctly load it and see what a plot looks like? Any further advice is appreciated, Thanks Jenny -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: Regarding g_rmsf
Hi, I simulated one crystallize protein (from pdb) having amino acid entry from 24 to 740. 1 to 23 residues was missing. When i am plotting RMSF for each residues by following command g_rmsf -f md.tpr -s md.trr (with the help of Grace) I am getting plot from 1 to 717 residues. I Think in prior step of simulation, gromacs changed the residues number of original pdb file and allotted the new number, that why residue 24 now become residue 1. I want to analyze RMSF at the spacific residue 340 from pdb entry but after simulation it become 317. Their is no problem in analysing RMSF value at 317 but actual problem in potting it is comming 340. My question is that How i can plot RMSF from residue number 24 to 740, Which is actually in PDB file. Regards Rituraj On Tue, Dec 15, 2009 at 4:30 PM, gmx-users-requ...@gromacs.org wrote: Send gmx-users mailing list submissions to gmx-users@gromacs.org To subscribe or unsubscribe via the World Wide Web, visit http://lists.gromacs.org/mailman/listinfo/gmx-users or, via email, send a message with subject or body 'help' to gmx-users-requ...@gromacs.org You can reach the person managing the list at gmx-users-ow...@gromacs.org When replying, please edit your Subject line so it is more specific than Re: Contents of gmx-users digest... Today's Topics: 1. freeze backbone Pressure scaling error ( ??? ) 2. typo in ffoplsaanb.itp for opls_179 (OS) and opls_180 (OS) (Pradip Biswas) 3. Re: typo in ffoplsaanb.itp for opls_179 (OS) and opls_180 (OS) (Mark Abraham) 4. Re: Freeze backbone Pressure scaling more than 1% (Mark Abraham) 5. Hi (ashish pandey) 6. Re: Hi (XAvier Periole) -- Message: 1 Date: Tue, 15 Dec 2009 13:56:44 +0900 (KST) From: ??? chemg...@hanmail.net Subject: [gmx-users] freeze backbone Pressure scaling error To: gmx-users@gromacs.org gmx-users@gromacs.org Message-ID: 20091215135644.hm.e0fw...@chemgirl.wwl1109.hanmail.net Content-Type: text/plain; charset=us-ascii An HTML attachment was scrubbed... URL: http://lists.gromacs.org/pipermail/gmx-users/attachments/20091215/0867d6a5/attachment-0001.html -- Message: 2 Date: Mon, 14 Dec 2009 23:00:30 -0600 From: Pradip Biswas biswas...@gmail.com Subject: [gmx-users] typo in ffoplsaanb.itp for opls_179 (OS) and opls_180(OS) To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 2301c61d0912142100g675259cfxd374d9adaacff...@mail.gmail.com Content-Type: text/plain; charset=iso-8859-1 Hi, The atomic numbers of the atom types opls_179 (OS) and opls_180 (OS) are typed in as 7 in ffoplsaanb.itp instead of 8. Accordingly, while doing QMMM, these oxygen atoms are being recognized as Nitrogen atoms. Biswas. -- next part -- An HTML attachment was scrubbed... URL: http://lists.gromacs.org/pipermail/gmx-users/attachments/20091214/d8f2920f/attachment-0001.html -- Message: 3 Date: Tue, 15 Dec 2009 16:33:28 +1100 From: Mark Abraham mark.abra...@anu.edu.au Subject: Re: [gmx-users] typo in ffoplsaanb.itp for opls_179 (OS) and opls_180(OS) To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 4b271fa8.2030...@anu.edu.au Content-Type: text/plain; charset=ISO-8859-1; format=flowed Pradip Biswas wrote: Hi, The atomic numbers of the atom types opls_179 (OS) and opls_180 (OS) are typed in as 7 in ffoplsaanb.itp instead of 8. Accordingly, while doing QMMM, these oxygen atoms are being recognized as Nitrogen atoms. DvdS fixed this in the git source earlier this week. Mark -- Message: 4 Date: Tue, 15 Dec 2009 16:36:10 +1100 From: Mark Abraham mark.abra...@anu.edu.au Subject: Re: [gmx-users] Freeze backbone Pressure scaling more than 1% To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 4b27204a.3030...@anu.edu.au Content-Type: text/plain; charset=EUC-KR 이진희 wrote: Dear all When I run produnction run using freeze backbone in GROMACS 4.0.5, the error was shown. But I didn't use freeze backboone, the error wasn't shown. Step 1 Warning: Pressure scaling more than 1%. I changed tau_p value from 0.5 to 5 in md.mdp file, but the above error was shown. I don't know how to solve it. Any one give some advice. Provide a full description. What's the system, how big is it, how did you equilibrate it, why/how are you freezing the backbone, does the run finish, does the trajectory look ok? Mark -- Message: 5 Date: Tue, 15 Dec 2009 14:22:39 +0530 From: ashish pandey ashishpande...@gmail.com Subject: [gmx-users] Hi To: gmx
Re: [gmx-users] Re: Regarding g_rmsf
rituraj purohit wrote: Hi, I simulated one crystallize protein (from pdb) having amino acid entry from 24 to 740. 1 to 23 residues was missing. When i am plotting RMSF for each residues by following command g_rmsf -f md.tpr -s md.trr (with the help of Grace) I am getting plot from 1 to 717 residues. I Think in prior step of simulation, gromacs changed the residues number of original pdb file and allotted the new number, that why residue 24 now become residue 1. This is true. I want to analyze RMSF at the spacific residue 340 from pdb entry but after simulation it become 317. Their is no problem in analysing RMSF value at 317 but actual problem in potting it is comming 340. I don't understand your problem. If you know what the re-numbered residue actually is, why is there a problem at all? My question is that How i can plot RMSF from residue number 24 to 740, Which is actually in PDB file. Write a script that re-numbers your .xvg file, which you may even be able to do within Grace, as well. -Justin Regards Rituraj On Tue, Dec 15, 2009 at 4:30 PM, gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org wrote: Send gmx-users mailing list submissions to gmx-users@gromacs.org mailto:gmx-users@gromacs.org To subscribe or unsubscribe via the World Wide Web, visit http://lists.gromacs.org/mailman/listinfo/gmx-users or, via email, send a message with subject or body 'help' to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org You can reach the person managing the list at gmx-users-ow...@gromacs.org mailto:gmx-users-ow...@gromacs.org When replying, please edit your Subject line so it is more specific than Re: Contents of gmx-users digest... Today's Topics: 1. freeze backbone Pressure scaling error ( ??? ) 2. typo in ffoplsaanb.itp for opls_179 (OS) and opls_180 (OS) (Pradip Biswas) 3. Re: typo in ffoplsaanb.itp for opls_179 (OS) and opls_180 (OS) (Mark Abraham) 4. Re: Freeze backbone Pressure scaling more than 1% (Mark Abraham) 5. Hi (ashish pandey) 6. Re: Hi (XAvier Periole) -- Message: 1 Date: Tue, 15 Dec 2009 13:56:44 +0900 (KST) From: ??? chemg...@hanmail.net mailto:chemg...@hanmail.net Subject: [gmx-users] freeze backbone Pressure scaling error To: gmx-users@gromacs.org mailto:gmx-users@gromacs.org gmx-users@gromacs.org mailto:gmx-users@gromacs.org Message-ID: 20091215135644.hm.e0fw...@chemgirl.wwl1109.hanmail.net mailto:20091215135644.hm.e0fw...@chemgirl.wwl1109.hanmail.net Content-Type: text/plain; charset=us-ascii An HTML attachment was scrubbed... URL: http://lists.gromacs.org/pipermail/gmx-users/attachments/20091215/0867d6a5/attachment-0001.html -- Message: 2 Date: Mon, 14 Dec 2009 23:00:30 -0600 From: Pradip Biswas biswas.pk http://biswas.pk@gmail.com http://gmail.com Subject: [gmx-users] typo in ffoplsaanb.itp for opls_179 (OS) and opls_180(OS) To: Discussion list for GROMACS users gmx-users@gromacs.org mailto:gmx-users@gromacs.org Message-ID: 2301c61d0912142100g675259cfxd374d9adaacff...@mail.gmail.com mailto:2301c61d0912142100g675259cfxd374d9adaacff...@mail.gmail.com Content-Type: text/plain; charset=iso-8859-1 Hi, The atomic numbers of the atom types opls_179 (OS) and opls_180 (OS) are typed in as 7 in ffoplsaanb.itp instead of 8. Accordingly, while doing QMMM, these oxygen atoms are being recognized as Nitrogen atoms. Biswas. -- next part -- An HTML attachment was scrubbed... URL: http://lists.gromacs.org/pipermail/gmx-users/attachments/20091214/d8f2920f/attachment-0001.html -- Message: 3 Date: Tue, 15 Dec 2009 16:33:28 +1100 From: Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au Subject: Re: [gmx-users] typo in ffoplsaanb.itp for opls_179 (OS) and opls_180(OS) To: Discussion list for GROMACS users gmx-users@gromacs.org mailto:gmx-users@gromacs.org Message-ID: 4b271fa8.2030...@anu.edu.au mailto:4b271fa8.2030...@anu.edu.au Content-Type: text/plain; charset=ISO-8859-1; format=flowed Pradip Biswas wrote: Hi, The atomic numbers of the atom types opls_179 (OS) and opls_180 (OS) are typed in as 7 in ffoplsaanb.itp instead of 8. Accordingly, while doing QMMM, these oxygen atoms are being recognized as Nitrogen atoms. DvdS fixed this in the git source earlier this week. Mark -- Message: 4 Date: Tue, 15 Dec 2009 16:36:10 +1100 From: Mark Abraham mark.abra
Re: [gmx-users] Check for bad contacts and/or reduce the timestep
You can try a normal md-simulation after the energy minimisation, with a very low timestep (around two orders of magnitude lower, for 5ps). For this use no T-couple, or if with, then with a very low temperature. I had a case where i had a box of well ordered benzene molecules and only energyminimization didn't helpt much (In normal md simulation i got many lincs warning form the beginning). After the short NVE-md-simulation the benzene molecules weren't ordered and after a second energy minimization it was possible to do a normal md simulation at 300 K without any lincs warnings. Could be possible that the same protocol works also in your case, else follow Justin's advice. Greetings Thomas Message: 3 Date: Mon, 14 Dec 2009 14:09:47 -0500 From: Justin A. Lemkul jalem...@vt.edu Subject: Re: [gmx-users] Check for bad contacts and/or reduce the timestep To: Gromacs Users' List gmx-users@gromacs.org Message-ID: 4b268d7b.1060...@vt.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed nishap.pa...@utoronto.ca wrote: snip Steepest Descents converged to machine precision in 34 steps, but did not reach the requested Fmax 10. Potential Energy = -3.7206969e+04 Maximum force = 2.0111207e+04 on atom 1217 Norm of force = 6.9283209e+02 I don't understand constraints I need to turn off, since I haven't mentioned any in my grompp file. This is just generic advice that mdrun provides. The fact is your starting structure contains atomic overlap or clashes that cannot be resolved by energy minimization. Have a look at the trajectory and see if you can get some insight into where things are going wrong (since problematic atom numbers are being printed, and perhaps re-consider how you built your system. -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/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/mailing_lists/users.php
[gmx-users] DPPC to CG DPPC
Dear All, I have downloaded the 128 DPPC lipid molecules from Dr. Tielmen's Website and I am trying to convert the Atomistic structure to CG structure. For that I am using atom2cg script provided by the martini folks but it doesn't convert the Atomistic structure to CG structure. atom2cg script works well for converting the atomistic structure of PROTEIN to CG structure of protein but for LIPIDS it doesn't work. Does anyone know how can I convert the 128 DPPC atomistic structure of lipids to CG structure. Best Regards, Sunny -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] DPPC to CG DPPC
sunny mishra wrote: Dear All, I have downloaded the 128 DPPC lipid molecules from Dr. Tielmen's Website and I am trying to convert the Atomistic structure to CG structure. For that I am using atom2cg script provided by the martini folks but it doesn't convert the Atomistic structure to CG structure. atom2cg script works well for converting the atomistic structure of PROTEIN to CG structure of protein but for LIPIDS it doesn't work. Does Right, because it's designed specifically for proteins. anyone know how can I convert the 128 DPPC atomistic structure of lipids to CG structure. There is no need. On the MARTINI site, they offer several pre-equilibrated CG lipid membranes, suitable topologies, etc. -Justin Best Regards, Sunny -- 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/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/mailing_lists/users.php
Re: [gmx-users] DPPC to CG DPPC
I have downloaded the 128 DPPC lipid molecules from Dr. Tielmen's Website and I am trying to convert the Atomistic structure to CG structure. For that I am using atom2cg script provided by the martini folks but it doesn't convert the Atomistic structure to CG structure. atom2cg script works well for converting the atomistic structure of PROTEIN to CG structure of protein but for LIPIDS it doesn't work. Does anyone know how can I convert the 128 DPPC atomistic structure of lipids to CG structure. This is correct. atom2cg is only working for proteins ... I would suggest you take dppc structure file from the martini web site! Best Regards, Sunny -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] DPPC to CG DPPC
Thanks for the reply. I have another quick question that If I have to do the Position Restrained EM Simulation of CG DPPC lipid then is it done the same way we do for atomistic structure of proteins like by defining the LIPPOSRES in the lipid.mdp file or while using MARTINI forcefield is there any other way of doing the Position Restrained EM simulation of CG DPPC lipids? On Tue, Dec 15, 2009 at 10:55 AM, XAvier Periole x.peri...@rug.nl wrote: I have downloaded the 128 DPPC lipid molecules from Dr. Tielmen's Website and I am trying to convert the Atomistic structure to CG structure. For that I am using atom2cg script provided by the martini folks but it doesn't convert the Atomistic structure to CG structure. atom2cg script works well for converting the atomistic structure of PROTEIN to CG structure of protein but for LIPIDS it doesn't work. Does anyone know how can I convert the 128 DPPC atomistic structure of lipids to CG structure. This is correct. atom2cg is only working for proteins ... I would suggest you take dppc structure file from the martini web site! Best Regards, Sunny -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 thewww interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] DPPC to CG DPPC
No need of position restrained simulation with the CG lipids. CG is very forgiving :)) For proteins it is more delicate. On Dec 15, 2009, at 6:02 PM, sunny mishra wrote: Thanks for the reply. I have another quick question that If I have to do the Position Restrained EM Simulation of CG DPPC lipid then is it done the same way we do for atomistic structure of proteins like by defining the LIPPOSRES in the lipid.mdp file or while using MARTINI forcefield is there any other way of doing the Position Restrained EM simulation of CG DPPC lipids? On Tue, Dec 15, 2009 at 10:55 AM, XAvier Periole x.peri...@rug.nl wrote: I have downloaded the 128 DPPC lipid molecules from Dr. Tielmen's Website and I am trying to convert the Atomistic structure to CG structure. For that I am using atom2cg script provided by the martini folks but it doesn't convert the Atomistic structure to CG structure. atom2cg script works well for converting the atomistic structure of PROTEIN to CG structure of protein but for LIPIDS it doesn't work. Does anyone know how can I convert the 128 DPPC atomistic structure of lipids to CG structure. This is correct. atom2cg is only working for proteins ... I would suggest you take dppc structure file from the martini web site! Best Regards, Sunny -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 thewww interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] DPPC to CG DPPC
Alright thanks. So should I do it for proteins? On Tue, Dec 15, 2009 at 12:12 PM, XAvier Periole x.peri...@rug.nl wrote: No need of position restrained simulation with the CG lipids. CG is very forgiving :)) For proteins it is more delicate. On Dec 15, 2009, at 6:02 PM, sunny mishra wrote: Thanks for the reply. I have another quick question that If I have to do the Position Restrained EM Simulation of CG DPPC lipid then is it done the same way we do for atomistic structure of proteins like by defining the LIPPOSRES in the lipid.mdp file or while using MARTINI forcefield is there any other way of doing the Position Restrained EM simulation of CG DPPC lipids? On Tue, Dec 15, 2009 at 10:55 AM, XAvier Periole x.peri...@rug.nl wrote: I have downloaded the 128 DPPC lipid molecules from Dr. Tielmen's Website and I am trying to convert the Atomistic structure to CG structure. For that I am using atom2cg script provided by the martini folks but it doesn't convert the Atomistic structure to CG structure. atom2cg script works well for converting the atomistic structure of PROTEIN to CG structure of protein but for LIPIDS it doesn't work. Does anyone know how can I convert the 128 DPPC atomistic structure of lipids to CG structure. This is correct. atom2cg is only working for proteins ... I would suggest you take dppc structure file from the martini web site! Best Regards, Sunny -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 thewww interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] DPPC to CG DPPC
Well if you put a protein CG into your DPPC bilayer you'll have to be soft on the start. PR is one way to do it and you can do similar to when doing on a atomistic simulation. On Dec 15, 2009, at 6:13 PM, sunny mishra wrote: Alright thanks. So should I do it for proteins? On Tue, Dec 15, 2009 at 12:12 PM, XAvier Periole x.peri...@rug.nl wrote: No need of position restrained simulation with the CG lipids. CG is very forgiving :)) For proteins it is more delicate. On Dec 15, 2009, at 6:02 PM, sunny mishra wrote: Thanks for the reply. I have another quick question that If I have to do the Position Restrained EM Simulation of CG DPPC lipid then is it done the same way we do for atomistic structure of proteins like by defining the LIPPOSRES in the lipid.mdp file or while using MARTINI forcefield is there any other way of doing the Position Restrained EM simulation of CG DPPC lipids? On Tue, Dec 15, 2009 at 10:55 AM, XAvier Periole x.peri...@rug.nl wrote: I have downloaded the 128 DPPC lipid molecules from Dr. Tielmen's Website and I am trying to convert the Atomistic structure to CG structure. For that I am using atom2cg script provided by the martini folks but it doesn't convert the Atomistic structure to CG structure. atom2cg script works well for converting the atomistic structure of PROTEIN to CG structure of protein but for LIPIDS it doesn't work. Does anyone know how can I convert the 128 DPPC atomistic structure of lipids to CG structure. This is correct. atom2cg is only working for proteins ... I would suggest you take dppc structure file from the martini web site! Best Regards, Sunny -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 thewww interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] DPPC to CG DPPC
ok. Thats the step where I am really confused that how to apply the PR on my system file (system file is a combination of CG protein and CG lipid). On Tue, Dec 15, 2009 at 12:16 PM, XAvier Periole x.peri...@rug.nl wrote: Well if you put a protein CG into your DPPC bilayer you'll have to be soft on the start. PR is one way to do it and you can do similar to when doing on a atomistic simulation. On Dec 15, 2009, at 6:13 PM, sunny mishra wrote: Alright thanks. So should I do it for proteins? On Tue, Dec 15, 2009 at 12:12 PM, XAvier Periole x.peri...@rug.nl wrote: No need of position restrained simulation with the CG lipids. CG is very forgiving :)) For proteins it is more delicate. On Dec 15, 2009, at 6:02 PM, sunny mishra wrote: Thanks for the reply. I have another quick question that If I have to do the Position Restrained EM Simulation of CG DPPC lipid then is it done the same way we do for atomistic structure of proteins like by defining the LIPPOSRES in the lipid.mdp file or while using MARTINI forcefield is there any other way of doing the Position Restrained EM simulation of CG DPPC lipids? On Tue, Dec 15, 2009 at 10:55 AM, XAvier Periole x.peri...@rug.nlwrote: I have downloaded the 128 DPPC lipid molecules from Dr. Tielmen's Website and I am trying to convert the Atomistic structure to CG structure. For that I am using atom2cg script provided by the martini folks but it doesn't convert the Atomistic structure to CG structure. atom2cg script works well for converting the atomistic structure of PROTEIN to CG structure of protein but for LIPIDS it doesn't work. Does anyone know how can I convert the 128 DPPC atomistic structure of lipids to CG structure. This is correct. atom2cg is only working for proteins ... I would suggest you take dppc structure file from the martini web site! Best Regards, Sunny -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 thewww interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] DPPC to CG DPPC
For the steps to go through to have an embedded protein in membrane bilayer Justin has made a nice tutorial ... look in the mail list archive On Dec 15, 2009, at 6:21 PM, sunny mishra wrote: ok. Thats the step where I am really confused that how to apply the PR on my system file (system file is a combination of CG protein and CG lipid). On Tue, Dec 15, 2009 at 12:16 PM, XAvier Periole x.peri...@rug.nl wrote: Well if you put a protein CG into your DPPC bilayer you'll have to be soft on the start. PR is one way to do it and you can do similar to when doing on a atomistic simulation. On Dec 15, 2009, at 6:13 PM, sunny mishra wrote: Alright thanks. So should I do it for proteins? On Tue, Dec 15, 2009 at 12:12 PM, XAvier Periole x.peri...@rug.nl wrote: No need of position restrained simulation with the CG lipids. CG is very forgiving :)) For proteins it is more delicate. On Dec 15, 2009, at 6:02 PM, sunny mishra wrote: Thanks for the reply. I have another quick question that If I have to do the Position Restrained EM Simulation of CG DPPC lipid then is it done the same way we do for atomistic structure of proteins like by defining the LIPPOSRES in the lipid.mdp file or while using MARTINI forcefield is there any other way of doing the Position Restrained EM simulation of CG DPPC lipids? On Tue, Dec 15, 2009 at 10:55 AM, XAvier Periole x.peri...@rug.nl wrote: I have downloaded the 128 DPPC lipid molecules from Dr. Tielmen's Website and I am trying to convert the Atomistic structure to CG structure. For that I am using atom2cg script provided by the martini folks but it doesn't convert the Atomistic structure to CG structure. atom2cg script works well for converting the atomistic structure of PROTEIN to CG structure of protein but for LIPIDS it doesn't work. Does anyone know how can I convert the 128 DPPC atomistic structure of lipids to CG structure. This is correct. atom2cg is only working for proteins ... I would suggest you take dppc structure file from the martini web site! Best Regards, Sunny -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 thewww interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read
[gmx-users] New ion parameters and OPLS-AA
Hi All, Recently there has been a new set of ion parameters published by Joung and Chetham and I am interested in running some test runs using these parameters. These set of parameters are based on using LB rule (arithmetic mean) for sigmas. However I am using OPLS-AA ff so I am using the combination rule 3 (geometric mean of corresponding A and B values). My question is that can I use the exact sigma values from Cheatham for my simulations? I'm almost positive that I have to change these sigma values to be consistent with the combination rule that I am using. In fact there is a paper by Horinek et al that has a nice table of different ionic sigma and epsilon values from different parameter sets (Aqvist, Jensen, Cheatham,..). The article is here: http://scitation.aip.org/getabs/servlet/GetabsServlet?prog=normalid=JCPSA60001301212450701idtype=cvipsgifs=Yes In that table, they have mentioned two sigmas; a usual sigma (which is used with rule 2) and a sigma prime (which can be used with rule 3). However it seems sort of unclear to me how they got these value since in some references that they've mentioned I could find either sigma or sigma prime, not both. So I am guessing there must be some way to convert these two sigmas to each other. So does anyone know if there is such way? Does GROMACS internally treats sigmas as sigma prime for OPLS-AA? I looked at the manual and also searched the mailing list to find an explanation but without luck. I really appreciate any help on clarifying this. Regards, Reza Salari -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] g_sdf and visualizing using gOpenMol
Rename it to .plt might be a good start, since that is the file extension it is meant to have (as noted in the help information for g_sdf). Also, there is an issue with the reference structure built was the script, it is not correct. Has been noted by a couple of people. Been meaning to check if there is a bug submitted for it. Catch ya, Dr Dallas Warren Pharmacy and Pharmaceutical Sciences Monash University A polar bear is a Cartesian bear that has undergone a polar transformation -Original Message- From: gmx-users-boun...@gromacs.org on behalf of Jennifer Williams Sent: Tue 12/15/2009 11:41 PM To: gmx-users@gromacs.org Subject: [gmx-users] g_sdf and visualizing using gOpenMol Hi, I have a mesoporous silica with attached organic surface groups (alkyl chains). I am trying to quantify to what extent these surface groups interact with the mesoporous silica surface they are attached to (as opposed to projecting straight into the pore space). I thought about using the g_sdf tool (on one surface group at a time initially) but am not completely sure what I am doing is correct so I am hoping someone can guide me. My index file looks like this [MCM] 1 [MCM] 2 [MCM] 3 [SI] 4 5 6 7 8 9 10 11 12 13 Where groups 1, 2 and 3 are carbons of the alkyl chain. SI atoms are taken to represent the surface of the mesoporous silica. I run g_sdf in gromacs and get a refmol.gro file (which looks very different to my structure) and a gom_plt.dat file. I've installed gOpenMol but I am having trouble loading the gom_plt.dat file. It is necessary to load coordinates in first so I load in refmol.gro. As soon as I try to load the .dat file (using plot contourimport) the gui window closes and I get the following Will apply a physical translation (x,y,z): 12.236523 18.866343 9.419045 Will apply a MT translation (x,y,z): 0.07 0.04 0.02 Minimum value 0.00 maximum value 134.129913 Signal was caught = : Success Signal code is: 11, errno I am not sure whether this is because I have unreasonable data in my .dat file (or because my refmol.gro file looks strange) or because I haven't got the hang of using gOpenMol. I don't have any idea what the contour plot should like. Could someone e-mail me a working gom_plt.dat file so I can at least check that I can correctly load it and see what a plot looks like? Any further advice is appreciated, Thanks Jenny -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php winmail.dat-- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] g_sdf and visualizing using gOpenMol
Also, forgot to mention, if you use VMD, it will load it as well. With VMD you don't need any structure file to load the .plt file, just load it as a new molecule. Catch ya, Dr Dallas Warren Pharmacy and Pharmaceutical Sciences Monash University A polar bear is a Cartesian bear that has undergone a polar transformation -Original Message- From: gmx-users-boun...@gromacs.org on behalf of Dallas B. Warren Sent: Wed 12/16/2009 8:25 AM To: Discussion list for GROMACS users Subject: RE: [gmx-users] g_sdf and visualizing using gOpenMol Rename it to .plt might be a good start, since that is the file extension it is meant to have (as noted in the help information for g_sdf). Also, there is an issue with the reference structure built was the script, it is not correct. Has been noted by a couple of people. Been meaning to check if there is a bug submitted for it. Catch ya, Dr Dallas Warren Pharmacy and Pharmaceutical Sciences Monash University A polar bear is a Cartesian bear that has undergone a polar transformation -Original Message- From: gmx-users-boun...@gromacs.org on behalf of Jennifer Williams Sent: Tue 12/15/2009 11:41 PM To: gmx-users@gromacs.org Subject: [gmx-users] g_sdf and visualizing using gOpenMol Hi, I have a mesoporous silica with attached organic surface groups (alkyl chains). I am trying to quantify to what extent these surface groups interact with the mesoporous silica surface they are attached to (as opposed to projecting straight into the pore space). I thought about using the g_sdf tool (on one surface group at a time initially) but am not completely sure what I am doing is correct so I am hoping someone can guide me. My index file looks like this [MCM] 1 [MCM] 2 [MCM] 3 [SI] 4 5 6 7 8 9 10 11 12 13 Where groups 1, 2 and 3 are carbons of the alkyl chain. SI atoms are taken to represent the surface of the mesoporous silica. I run g_sdf in gromacs and get a refmol.gro file (which looks very different to my structure) and a gom_plt.dat file. I've installed gOpenMol but I am having trouble loading the gom_plt.dat file. It is necessary to load coordinates in first so I load in refmol.gro. As soon as I try to load the .dat file (using plot contourimport) the gui window closes and I get the following Will apply a physical translation (x,y,z): 12.236523 18.866343 9.419045 Will apply a MT translation (x,y,z): 0.07 0.04 0.02 Minimum value 0.00 maximum value 134.129913 Signal was caught = : Success Signal code is: 11, errno I am not sure whether this is because I have unreasonable data in my .dat file (or because my refmol.gro file looks strange) or because I haven't got the hang of using gOpenMol. I don't have any idea what the contour plot should like. Could someone e-mail me a working gom_plt.dat file so I can at least check that I can correctly load it and see what a plot looks like? Any further advice is appreciated, Thanks Jenny -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php winmail.dat-- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] New ion parameters and OPLS-AA
Read the manual. You can explicitly declare all of your cross terms rather than using the same mixing rule for all terms. You can easily write a script to modify your input files accordingly, Andrew On Tue, Dec 15, 2009 at 4:06 PM, Reza Salari resa...@yahoo.com wrote: Hi All, Recently there has been a new set of ion parameters published by Joung and Chetham and I am interested in running some test runs using these parameters. These set of parameters are based on using LB rule (arithmetic mean) for sigmas. However I am using OPLS-AA ff so I am using the combination rule 3 (geometric mean of corresponding A and B values). My question is that can I use the exact sigma values from Cheatham for my simulations? I'm almost positive that I have to change these sigma values to be consistent with the combination rule that I am using. In fact there is a paper by Horinek et al that has a nice table of different ionic sigma and epsilon values from different parameter sets (Aqvist, Jensen, Cheatham,..). The article is here: http://scitation.aip.org/getabs/servlet/GetabsServlet?prog=normalid=JCPSA60001301212450701idtype=cvipsgifs=Yes In that table, they have mentioned two sigmas; a usual sigma (which is used with rule 2) and a sigma prime (which can be used with rule 3). However it seems sort of unclear to me how they got these value since in some references that they've mentioned I could find either sigma or sigma prime, not both. So I am guessing there must be some way to convert these two sigmas to each other. So does anyone know if there is such way? Does GROMACS internally treats sigmas as sigma prime for OPLS-AA? I looked at the manual and also searched the mailing list to find an explanation but without luck. I really appreciate any help on clarifying this. Regards, Reza Salari -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] g_sdf and visualizing using gOpenMol
FYI, there is a listing in bugzilla http://bugzilla.gromacs.org/show_bug.cgi?id=356 Catch ya, Dr Dallas Warren Pharmacy and Pharmaceutical Sciences Monash University A polar bear is a Cartesian bear that has undergone a polar transformation winmail.dat-- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] New ion parameters and OPLS-AA
Thanks for your response. While I will try that (although it seems it needs quite amount of scripting), I remember in the past some people in the mailing list mentioned problems while using nonbond_params directvie with OPLS-AA and in response it was generally suggested to avoid doing this kind of mixing. Like Dr Abraham suggestion here: http://www.mail-archive.com/gmx-users@gromacs.org/msg23147.html Have you tried this kind of mixing for OPLS successfully, without being overridden by the default rules? The main thing that I am still unsure about is how the previously mentioned paper converted the sigma values for different combination rules. It seems that there must be a relatively direct way to do this without going through the re-parametrization process. Regards, Reza Salari From: Andrew Paluch apal...@nd.edu To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Tue, December 15, 2009 4:34:18 PM Subject: Re: [gmx-users] New ion parameters and OPLS-AA Read the manual. You can explicitly declare all of your cross terms rather than using the same mixing rule for all terms. You can easily write a script to modify your input files accordingly, Andrew On Tue, Dec 15, 2009 at 4:06 PM, Reza Salari resa...@yahoo.com wrote: Hi All, Recently there has been a new set of ion parameters published by Joung and Chetham and I am interested in running some test runs using these parameters. These set of parameters are based on using LB rule (arithmetic mean) for sigmas. However I am using OPLS-AA ff so I am using the combination rule 3 (geometric mean of corresponding A and B values). My question is that can I use the exact sigma values from Cheatham for my simulations? I'm almost positive that I have to change these sigma values to be consistent with the combination rule that I am using. In fact there is a paper by Horinek et al that has a nice table of different ionic sigma and epsilon values from different parameter sets (Aqvist, Jensen, Cheatham,..). The article is here: http://scitation.aip.org/getabs/servlet/GetabsServlet?prog=normalid=JCPSA60001301212450701idtype=cvipsgifs=Yes In that table, they have mentioned two sigmas; a usual sigma (which is used with rule 2) and a sigma prime (which can be used with rule 3). However it seems sort of unclear to me how they got these value since in some references that they've mentioned I could find either sigma or sigma prime, not both. So I am guessing there must be some way to convert these two sigmas to each other. So does anyone know if there is such way? Does GROMACS internally treats sigmas as sigma prime for OPLS-AA? I looked at the manual and also searched the mailing list to find an explanation but without luck. I really appreciate any help on clarifying this. Regards, Reza Salari -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] New ion parameters and OPLS-AA
Hi Reza, -- Message: 4 Date: Tue, 15 Dec 2009 14:03:36 -0800 (PST) From: Reza Salari resa...@yahoo.com Subject: Re: [gmx-users] New ion parameters and OPLS-AA To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 858209.12986...@web35303.mail.mud.yahoo.com Content-Type: text/plain; charset=us-ascii Thanks for your response. While I will try that (although it seems it needs quite amount of scripting), I remember in the past some people in the mailing list mentioned problems while using nonbond_params directvie with OPLS-AA and in response it was generally suggested to avoid doing this kind of mixing. Like Dr Abraham suggestion here: http://www.mail-archive.com/gmx-users@gromacs.org/msg23147.html Have you tried this kind of mixing for OPLS successfully, without being overridden by the default rules? I have successfully done so. My topology looks like this: #include ffoplsaa.itp [ nonbond_params ] opls_272 opls_412 1 0.277 1.2857 #include frm.itp ; Include Position restraint file #ifdef POSRES #include posre.itp #endif . . . Of course there should be a line for every possible pair interaction. It is important to put the [ nonbond_params ] after the include to ffoplsaa.itp The main thing that I am still unsure about is how the previously mentioned paper converted the sigma values for different combination rules. It seems that there must be a relatively direct way to do this without going through the re-parametrization process. Regards, Reza Salari From: Andrew Paluch apal...@nd.edu To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Tue, December 15, 2009 4:34:18 PM Subject: Re: [gmx-users] New ion parameters and OPLS-AA Read the manual. You can explicitly declare all of your cross terms rather than using the same mixing rule for all terms. You can easily write a script to modify your input files accordingly, Andrew On Tue, Dec 15, 2009 at 4:06 PM, Reza Salari resa...@yahoo.com wrote: Hi All, Recently there has been a new set of ion parameters published by Joung and Chetham and I am interested in running some test runs using these parameters. These set of parameters are based on using LB rule (arithmetic mean) for sigmas. However I am using OPLS-AA ff so I am using the combination rule 3 (geometric mean of corresponding A and B values). My question is that can I use the exact sigma values from Cheatham for my simulations? I'm almost positive that I have to change these sigma values to be consistent with the combination rule that I am using. In fact there is a paper by Horinek et al that has a nice table of different ionic sigma and epsilon values from different parameter sets (Aqvist, Jensen, Cheatham,..). The article is here: http://scitation.aip.org/getabs/servlet/GetabsServlet?prog=normalid=JCPSA60001301212450701idtype=cvipsgifs=Yes In that table, they have mentioned two sigmas; a usual sigma (which is used with rule 2) and a sigma prime (which can be used with rule 3). However it seems sort of unclear to me how they got these value since in some references that they've mentioned I could find either sigma or sigma prime, not both. So I am guessing there must be some way to convert these two sigmas to each other. So does anyone know if there is such way? Does GROMACS internally treats sigmas as sigma prime for OPLS-AA? I looked at the manual and also searched the mailing list to find an explanation but without luck. I really appreciate any help on clarifying this. Regards, Reza Salari -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
