Dear Justin, Based on your questions to my simulation, I posted here yesterday hopefully it was the correct way to reply in this forum.
In this morning I got a list of new windows of umbrella sampling, the overlap is sufficient enough, but I saw another problem: In the histogram figure, the base of peak covers the distance of 2 nm instead of 0.2 nm., that's horrible! However, when I checked back to the simulation results of each window, the fluctuation of my pulled protein is only 0.4nm in maximum. So the base of peak shouldn't cover such long distance, right? Thank you very much, Jiangfeng. Jiangfeng Du, PhD Student Cardiovascular Research Institute Maastricht Department of Biochemistry P.O. Box 616 Mobile: +31-681741859 FAX: +31-43-3884159 6200 MD Maastricht The Netherlands ________________________________________ From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf Of gmx-users-requ...@gromacs.org [gmx-users-requ...@gromacs.org] Sent: Wednesday, May 16, 2012 2:59 PM To: gmx-users@gromacs.org Subject: gmx-users Digest, Vol 97, Issue 120 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. Re: grompp Unkown bond_atomtype C2 (Justin A. Lemkul) 2. Re: grompp Unkown bond_atomtype C2 (Lara Bunte) 3. Re: grompp Unkown bond_atomtype C2 (Justin A. Lemkul) 4. Re: Wierd results from Umbrella sampling (Justin A. Lemkul) 5. (no subject) (rama david) 6. Re: (no subject) (Justin A. Lemkul) 7. forcefields for lipids (Shima Arasteh) ---------------------------------------------------------------------- Message: 1 Date: Wed, 16 May 2012 07:22:31 -0400 From: "Justin A. Lemkul" <jalem...@vt.edu> Subject: Re: [gmx-users] grompp Unkown bond_atomtype C2 To: Lara Bunte <lara.bu...@yahoo.de>, Discussion list for GROMACS users <gmx-users@gromacs.org> Message-ID: <4fb38df7.2060...@vt.edu> Content-Type: text/plain; charset=ISO-8859-1; format=flowed On 5/16/12 3:56 AM, Lara Bunte wrote: > Hi > > After: > > pdb2gmx -f mymol.pdb -water tip3p > editconf -f conf.gro -bt dodecahedron -d 1.3 -o box.gro > > genbox -cp box.gro -cs spc216.gro -p topol.top -o solvated.gro > > > I typed: > > > grompp -f em.mdp -p topol.top -c solvated.gro -o em.tpr > > > where em.mdp is my energy minimization file and I got: > > Fatal error: > Unknown bond_atomtype C2 > > > What is here the problem? All atom types should be declared by me, I guess. > You're making use of an atom type called "C2" in some bonded interaction, but such an atom type doesn't exist. You need to define it. -Justin -- ======================================== Justin A. Lemkul, Ph.D. Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ======================================== ------------------------------ Message: 2 Date: Wed, 16 May 2012 13:05:24 +0100 (BST) From: Lara Bunte <lara.bu...@yahoo.de> Subject: Re: [gmx-users] grompp Unkown bond_atomtype C2 To: "jalem...@vt.edu" <jalem...@vt.edu> Cc: "gmx-users@gromacs.org" <gmx-users@gromacs.org> Message-ID: <1337169924.86371.yahoomail...@web29405.mail.ird.yahoo.com> Content-Type: text/plain; charset=iso-8859-1 Hi in my .rtp file I wrote in the [ atoms ] block C2?? CN1A??? 0.7481?? 1 but in the atomtypes.atp file I wrote CN1A??? 12.01100 So I declared it. So what do you mean with "such an atom type doesn't exist"? Greetings Lara ----- Urspr?ngliche Message ----- Von: Justin A. Lemkul <jalem...@vt.edu> An: Lara Bunte <lara.bu...@yahoo.de>; Discussion list for GROMACS users <gmx-users@gromacs.org> CC: Gesendet: 13:22 Mittwoch, 16.Mai 2012 Betreff: Re: [gmx-users] grompp Unkown bond_atomtype C2 On 5/16/12 3:56 AM, Lara Bunte wrote: > Hi > > After: > > pdb2gmx -f mymol.pdb -water tip3p > editconf -f conf.gro -bt dodecahedron -d 1.3 -o box.gro > > genbox -cp box.gro -cs spc216.gro -p topol.top -o solvated.gro > > > I typed: > > > grompp -f em.mdp -p topol.top -c solvated.gro -o em.tpr > > > where em.mdp is my energy minimization file and I got: > > Fatal error: > Unknown bond_atomtype C2 > > > What is here the problem? All atom types should be declared by me, I guess. > You're making use of an atom type called "C2" in some bonded interaction, but such an atom type doesn't exist.? You need to define it. -Justin -- ======================================== Justin A. Lemkul, Ph.D. Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ======================================== ------------------------------ Message: 3 Date: Wed, 16 May 2012 08:08:29 -0400 From: "Justin A. Lemkul" <jalem...@vt.edu> Subject: Re: [gmx-users] grompp Unkown bond_atomtype C2 To: Discussion list for GROMACS users <gmx-users@gromacs.org> Message-ID: <4fb398bd.6010...@vt.edu> Content-Type: text/plain; charset=ISO-8859-1; format=flowed On 5/16/12 8:05 AM, Lara Bunte wrote: > Hi > > > in my .rtp file I wrote in the [ atoms ] block > > C2 CN1A 0.7481 1 > > > but in the atomtypes.atp file I wrote > > CN1A 12.01100 > > > So I declared it. So what do you mean with "such an atom type doesn't exist"? > Neither of those actions constitutes what you need. Your atom name is C2, while its type is CN1A. Apparently somewhere in the bonded parameters you've assigned C2 as a type, which is wrong. You need to be using CN1A if adding a new bonded parameter. The CN1A atom type already exists in the force field so you don't need to do anything special. Note for the future that in order to add a new atom type (if necessary), it needs to have its parameters listed in ffbonded.itp. Mentioning it in the .rtp and .atp files does not do much for you; it simply makes that atom type accessible in the topology, but if it doesn't have parameters assigned, it is useless. -Justin -- ======================================== Justin A. Lemkul, Ph.D. Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ======================================== ------------------------------ Message: 4 Date: Wed, 16 May 2012 08:11:49 -0400 From: "Justin A. Lemkul" <jalem...@vt.edu> Subject: Re: [gmx-users] Wierd results from Umbrella sampling To: Discussion list for GROMACS users <gmx-users@gromacs.org> Message-ID: <4fb39985.9000...@vt.edu> Content-Type: text/plain; charset=ISO-8859-1; format=flowed On 5/16/12 4:08 AM, Du Jiangfeng (BIOCH) wrote: > Dear Sir/Madam, > > I have performed umbrella pulling and umbrella sampling my protein from a > DOPC/DOPS membrane. Unfortunately, the results are really bad (Energy curve > suddenly turns to zero at the last 1 nm) and the histograph does not show any > overlap. Actually, I did it strictly based on Justin's tutorial, with the > sample spacing of 0.2 nm. > Please note that the exact protocol in the tutorial may or may not be applicable to all systems. The overall workflow is the same, but details regarding use of groups, .mdp files, etc may vary. > Here are some lines from the end of the energy file (The energy should not > decrease since it was in summation): > > Distance(nm) Energy (Kcal/mol) 5.288348 5.705318e+01 5.316250 > 4.881724e+01 > 5.344152 4.022505e+01 5.372054 3.101854e+01 5.399956 2.208200e+01 > 5.427858 > 1.343340e+01 5.455761 4.267619e+00 5.483663 -5.084078e+00 ? minus 5.511565 > -1.486168e+01 ? minus 5.539467 -2.393515e+01 ? minus 5.567369 > -3.343453e+01 > ? minus > What energetic term is this? A summation can decrease if the values being added are all negative. > > Followings are some lines from the end of histograph file: > > Distance(nm) 5.455761 0 0 0 0 0 0 0 > 0 0 0 0 0 0 0 0 0 0 > 0 8 5.483663 0 0 0 0 > 0 0 0 0 0 0 0 0 0 0 > 0 0 0 0 8 5.511565 0 0 0 0 > 0 0 0 0 0 0 0 0 0 0 > 0 0 0 0 12 > 5.539467 0 0 0 0 0 0 0 0 > 0 0 0 0 0 0 0 0 0 0 > 4 5.567369 0 0 0 0 0 0 0 0 > 0 0 > 0 0 0 0 0 0 0 0 2 > > > I am really depressed because it took me quiet a long time to sampling but it > seems in vain... I really no idea to find out what went wrong. > Nor do we. What is in your .mdp file? How many windows are you using? What is the total desired length of the reaction coordinate, and what are the initial and final COM distances that you are restraining? What are your box dimensions? -Justin -- ======================================== Justin A. Lemkul, Ph.D. Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ======================================== ------------------------------ Message: 5 Date: Wed, 16 May 2012 18:19:59 +0530 From: rama david <ramadavidgr...@gmail.com> Subject: [gmx-users] (no subject) To: Discussion list for GROMACS users <gmx-users@gromacs.org> Message-ID: <CAD=-syfb_2xts+wmvduqbpngee_v2h4b9yznkdxxe1sdlyd...@mail.gmail.com> Content-Type: text/plain; charset="iso-8859-1" Hi Gromacs Friends, I plan to simulate protein In Trifluoro Ethanol solvent using G96 53a6 FF Please help to define parameters in md.mdp For water I am using following mdp file .... lincs_order = 4 ; also related to accuracy ; Neighborsearching ns_type = grid ; search neighboring grid cells nstlist = 5 ; 10 fs rlist = 0.9 ; short-range neighborlist cutoff (in nm) rcoulomb = 0.9 ; short-range electrostatic cutoff (in nm) vdw-type = Cut-off rvdw = 1.4 ; short-range van der Waals cutoff (in nm) ; Electrostatics coulombtype = PME For TFE and water mix of different conc , What should be the mdp file parameter ??? I am using following ones.. Twin range cutt-off for nnonbonded interactions.. Short range cut-off 0.8 and long range 1.4 for both coulombic and lennard-jones Short range updates for every 5 step togather with pair list.. Please give me valuable suggestion .. Thank you in advance .. With Best Wishes, Rama David -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.gromacs.org/pipermail/gmx-users/attachments/20120516/0c02f568/attachment-0001.html ------------------------------ Message: 6 Date: Wed, 16 May 2012 08:55:00 -0400 From: "Justin A. Lemkul" <jalem...@vt.edu> Subject: Re: [gmx-users] (no subject) To: Discussion list for GROMACS users <gmx-users@gromacs.org> Message-ID: <4fb3a3a4.4060...@vt.edu> Content-Type: text/plain; charset=ISO-8859-1; format=flowed On 5/16/12 8:49 AM, rama david wrote: > Hi Gromacs Friends, > > I plan to simulate protein In Trifluoro Ethanol solvent > using G96 53a6 FF > > Please help to define parameters in md.mdp > > For water I am using following mdp file .... > > lincs_order = 4 ; also related to accuracy > ; Neighborsearching > ns_type = grid ; search neighboring grid cells > nstlist = 5 ; 10 fs > rlist = 0.9 ; short-range neighborlist cutoff (in nm) > rcoulomb = 0.9 ; short-range electrostatic cutoff (in nm) > vdw-type = Cut-off > rvdw = 1.4 ; short-range van der Waals cutoff (in nm) > ; Electrostatics > coulombtype = PME > > > > For TFE and water mix of different conc , What should be the mdp file > parameter ??? > > I am using following ones.. > > Twin range cutt-off for nnonbonded interactions.. > Short range cut-off 0.8 and long range 1.4 for both > coulombic and lennard-jones > Short range updates for every 5 step togather with pair > list.. > > > Please give me valuable suggestion .. > The settings given in an .mdp file are dependent upon the force field, not the molecules in the system. So if you have water or water/TFE, the requirements of the force field are still the same. -Justin -- ======================================== Justin A. Lemkul, Ph.D. Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ======================================== ------------------------------ Message: 7 Date: Wed, 16 May 2012 05:59:22 -0700 (PDT) From: Shima Arasteh <shima_arasteh2...@yahoo.com> Subject: [gmx-users] forcefields for lipids To: Discussion list for GROMACS users <gmx-users@gromacs.org> Message-ID: <1337173162.97860.yahoomail...@web36403.mail.mud.yahoo.com> Content-Type: text/plain; charset="iso-8859-1" Dear gmx users, Which force fields are suggested for lipids? Except CHARMM, any other forcefields? Anybody may suggest me articles in this about? Thanks in advance ? Sincerely, Shima -------------- next part -------------- An HTML attachment was scrubbed... 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