[gmx-users] updating amberff.03 files
Hello Gromacs Users, I am trying to update the contents of the top folder. I have parameters for a HEME residue that worked in gromacs 4.0.7, and we're now trying to update to gromacs 4.6.1 (long overdue), and need to migrate the parameters over to the new version. I have done the following: 1. added the HEME atomtypes to the atomtypes.atp file 2. added the hydrogens to the aminoacids.hdb file 3. added the [ HEME ] block to the aminoacids.rtp file I am running into problems in adding the dihedrals. in the old version we had used #define statements in the ffamber03bon.itp file (ffbonded.itp in the 4.6 version) , for example: #define heme_1 0.0 0.0 0.0 0.0 0.0 0.0 #define heme_2 0.62760 1.88280 0.0-2.51040 0.0 0.0 #define heme_3 0.65270 1.95811 0.0-2.61082 0.0 0.0 #define heme_4 16.52680 0.0 -16.52680 0.0 0.0 0.0 #define heme_5 62.76000 0.0 -62.76000 0.0 0.0 0.0 the heme_X term was defined in the ffamber03.rtp file (aminoacids.rtp file in ver 4.6)- for example: [ dihedrals ] HP42 CBD CGD O1D heme_1 HP42 CBD CGD O2D heme_1 HP41 CBD CGD O1D heme_1 HP41 CBD CGD O2D heme_1 HP52 CAD CBD HP41heme_2 HP52 CAD CBD HP42heme_2 HP52 CAD CBD CGD heme_3 I updated all define heme_X lines in the ffbonded.itp file by going back and putting in the actual atomtypes and the corresponding dihedral function and parameters. For example: I replaced #define heme_8 11.92440 0.0 -11.92440 0.0 0.0 0.0 with : FE NO CC CD311.92440 0.0 -11.92440 0.0 0.0 0.0 However, I'm getting errors from the grompp command about the dihedrals. it gives: ERROR 1 [file prot_Other_chain_B2.itp, line 520]: No default Proper Dih. types ERROR 2 [file prot_Other_chain_B2.itp, line 521]: No default Proper Dih. types . . . I'm thinking that it can't find the Dihedral types that I added t the ffbonded.itp file, but I'm not sure why. One thing I've noticed is that in the .itp file generated by pdb2gmx the dihedral type for the heme is given as a 9, but in the ffbonded.itp file, I specify it as a 3. I'm not sure where its reading this from. I'm hoping that this is just a simple thing that I'm missing and someone can help point me in the right direction. Thanks, - Laura -- Laura Kingsley Graduate Student Medicinal Chemistry and Molecular Pharmacology Purdue University Office: RHPH 504A 575 Stadium Mall Dr. West Lafayette, IN 47907 Office Phone: (765) 496-6643 -- 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] updating amberff.03 files
Hi Mark, We'd like to use the Ryckaert-Bellemans dihedral types. Does 3 not work in the new version? Also, I took out the #define lines and replaced them with the actual atomtypes, because that didn't seem to work when I initially tried to add just the #define lines to the ffbonded.itp file. On 04/11/2013 04:51 PM, Mark Abraham wrote: Type 9 was added at some point to GROMACS to make coping with AMBER and CHARMM easier. So you should just change your #defines from 3 to 9. See table in chapter 5. Or you could just leave your solution in the same form as you did for the 4.0.x GROMACS. Mark On Thu, Apr 11, 2013 at 10:36 PM, Laura Kingsleylking...@purdue.eduwrote: Hello Gromacs Users, I am trying to update the contents of the top folder. I have parameters for a HEME residue that worked in gromacs 4.0.7, and we're now trying to update to gromacs 4.6.1 (long overdue), and need to migrate the parameters over to the new version. I have done the following: 1. added the HEME atomtypes to the atomtypes.atp file 2. added the hydrogens to the aminoacids.hdb file 3. added the [ HEME ] block to the aminoacids.rtp file I am running into problems in adding the dihedrals. in the old version we had used #define statements in the ffamber03bon.itp file (ffbonded.itp in the 4.6 version) , for example: #define heme_1 0.0 0.0 0.0 0.0 0.0 0.0 #define heme_2 0.62760 1.88280 0.0-2.51040 0.0 0.0 #define heme_3 0.65270 1.95811 0.0-2.61082 0.0 0.0 #define heme_4 16.52680 0.0 -16.52680 0.0 0.0 0.0 #define heme_5 62.76000 0.0 -62.76000 0.0 0.0 0.0 the heme_X term was defined in the ffamber03.rtp file (aminoacids.rtp file in ver 4.6)- for example: [ dihedrals ] HP42 CBD CGD O1D heme_1 HP42 CBD CGD O2D heme_1 HP41 CBD CGD O1D heme_1 HP41 CBD CGD O2D heme_1 HP52 CAD CBD HP41heme_2 HP52 CAD CBD HP42heme_2 HP52 CAD CBD CGD heme_3 I updated all define heme_X lines in the ffbonded.itp file by going back and putting in the actual atomtypes and the corresponding dihedral function and parameters. For example: I replaced #define heme_8 11.92440 0.0 -11.92440 0.0 0.0 0.0 with : FE NO CC CD311.92440 0.0 -11.92440 0.0 0.0 0.0 However, I'm getting errors from the grompp command about the dihedrals. it gives: ERROR 1 [file prot_Other_chain_B2.itp, line 520]: No default Proper Dih. types ERROR 2 [file prot_Other_chain_B2.itp, line 521]: No default Proper Dih. types . . . I'm thinking that it can't find the Dihedral types that I added t the ffbonded.itp file, but I'm not sure why. One thing I've noticed is that in the .itp file generated by pdb2gmx the dihedral type for the heme is given as a 9, but in the ffbonded.itp file, I specify it as a 3. I'm not sure where its reading this from. I'm hoping that this is just a simple thing that I'm missing and someone can help point me in the right direction. Thanks, - Laura -- Laura Kingsley Graduate Student Medicinal Chemistry and Molecular Pharmacology Purdue University Office: RHPH 504A 575 Stadium Mall Dr. West Lafayette, IN 47907 Office Phone: (765) 496-6643 -- 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 -- Laura Kingsley Graduate Student Medicinal Chemistry and Molecular Pharmacology Purdue University Office: RHPH 504A 575 Stadium Mall Dr. West Lafayette, IN 47907 Office Phone: (765) 496-6643 -- 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] updating amberff.03 files
So if I'm understanding you correctly in the .rtp file under [ HEME ] [ dihedrals ] I should change: HP42 CBD CGD O1D HP42 CBD CGD O2D ... to HP42 CBD CGD O1D30.65270 1.95811 0.0 -2.61082 0.0 0.0 HP42 CBD CGD O2D30.65270 1.95811 0.0 -2.61082 0.0 0.0 Do I need to remove these definitions from the ffbonded.itp files then? - Laura On 04/11/2013 05:43 PM, Mark Abraham wrote: On Thu, Apr 11, 2013 at 11:14 PM, Laura Kingsleylking...@purdue.eduwrote: Hi Mark, We'd like to use the Ryckaert-Bellemans dihedral types. Does 3 not work in the new version? Sorry, I was thinking of 4 and 9, which are basically interchangeable. The default for AMBER did change to 9 at some point (see top of aminoacids.rtp). You can use the old approach if you change the types of just the heme dihedrals to 3 in the .itp files produced by pdb2gmx. Or you can probably edit the heme .rtp entry to specify type 3 (plus parameters, perhaps via the #defines). Also, I took out the #define lines and replaced them with the actual atomtypes, because that didn't seem to work when I initially tried to add just the #define lines to the ffbonded.itp file. The parameters need to go either on the lines in the .rtp that define the interactions, or on the lines that define the dihedraltypes. Only the latter needs the atom types (because that's how the lookup works). The old-style #defines cannot work in ffbonded.itp, because they assume the context of the .rtp, where the atoms are already identified. Mark On 04/11/2013 04:51 PM, Mark Abraham wrote: Type 9 was added at some point to GROMACS to make coping with AMBER and CHARMM easier. So you should just change your #defines from 3 to 9. See table in chapter 5. Or you could just leave your solution in the same form as you did for the 4.0.x GROMACS. Mark On Thu, Apr 11, 2013 at 10:36 PM, Laura Kingsleylking...@purdue.edu** wrote: Hello Gromacs Users, I am trying to update the contents of the top folder. I have parameters for a HEME residue that worked in gromacs 4.0.7, and we're now trying to update to gromacs 4.6.1 (long overdue), and need to migrate the parameters over to the new version. I have done the following: 1. added the HEME atomtypes to the atomtypes.atp file 2. added the hydrogens to the aminoacids.hdb file 3. added the [ HEME ] block to the aminoacids.rtp file I am running into problems in adding the dihedrals. in the old version we had used #define statements in the ffamber03bon.itp file (ffbonded.itp in the 4.6 version) , for example: #define heme_1 0.0 0.0 0.0 0.0 0.0 0.0 #define heme_2 0.62760 1.88280 0.0-2.51040 0.0 0.0 #define heme_3 0.65270 1.95811 0.0-2.61082 0.0 0.0 #define heme_4 16.52680 0.0 -16.52680 0.0 0.0 0.0 #define heme_5 62.76000 0.0 -62.76000 0.0 0.0 0.0 the heme_X term was defined in the ffamber03.rtp file (aminoacids.rtp file in ver 4.6)- for example: [ dihedrals ] HP42 CBD CGD O1D heme_1 HP42 CBD CGD O2D heme_1 HP41 CBD CGD O1D heme_1 HP41 CBD CGD O2D heme_1 HP52 CAD CBD HP41heme_2 HP52 CAD CBD HP42heme_2 HP52 CAD CBD CGD heme_3 I updated all define heme_X lines in the ffbonded.itp file by going back and putting in the actual atomtypes and the corresponding dihedral function and parameters. For example: I replaced #define heme_8 11.92440 0.0 -11.92440 0.0 0.0 0.0 with : FE NO CC CD311.92440 0.0 -11.92440 0.0 0.0 0.0 However, I'm getting errors from the grompp command about the dihedrals. it gives: ERROR 1 [file prot_Other_chain_B2.itp, line 520]: No default Proper Dih. types ERROR 2 [file prot_Other_chain_B2.itp, line 521]: No default Proper Dih. types . . . I'm thinking that it can't find the Dihedral types that I added t the ffbonded.itp file, but I'm not sure why. One thing I've noticed is that in the .itp file generated by pdb2gmx the dihedral type for the heme is given as a 9, but in the ffbonded.itp file, I specify it as a 3. I'm not sure where its reading this from. I'm hoping that this is just a simple thing that I'm missing and someone can help point me in the right direction. Thanks, - Laura -- Laura Kingsley Graduate Student Medicinal Chemistry and Molecular Pharmacology Purdue University Office: RHPH 504A 575 Stadium Mall Dr. West Lafayette, IN 47907 Office Phone: (765) 496-6643 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-usershttp://lists.gromacs.org/**mailman/listinfo/gmx-users htt**p://lists.gromacs.org/mailman/**listinfo/gmx-usershttp
[gmx-users] make_ndx: duplicates groups appearing in index.ndx file
Hello, I've just switched from using Gromacs version 4.0.5 to 4.5.5, and I'm having an issue with make_ndx. Using the old version I have a single group showing up for each odd residue, eg JJJ shows up once as group 16 for example. When I use the new version on the same file I get 2 groups appearing for residue JJJ and others. Here is the output of that I get from make_ndx. Is there some way I can prevent this? 0 System : 126928 atoms 1 Other : 137 atoms 2 NGL : 9 atoms 3 CY1 :10 atoms 4 CAR :25 atoms 5 HEM :73 atoms 6 JJJ : 1 atoms 7 CPZ :19 atoms 8 Cl : 6 atoms 9 Protein : 7475 atoms 10 Protein-H : 3733 atoms 11 C-alpha : 461 atoms 12 Backbone: 1383 atoms 13 MainChain : 1844 atoms 14 MainChain+Cb: 2275 atoms 15 MainChain+H : 2275 atoms 16 SideChain : 5200 atoms 17 SideChain-H : 1889 atoms 18 Prot-Masses : 7475 atoms 19 non-Protein : 119453 atoms 20 Water : 119310 atoms 21 SOL : 119310 atoms 22 non-Water : 7618 atoms 23 Ion : 6 atoms 24 NGL : 9 atoms 25 CY1 :10 atoms 26 CAR :25 atoms 27 HEM :73 atoms 28 JJJ : 1 atoms 29 CPZ :19 atoms 30 Cl : 6 atoms 31 Water_and_ions : 119316 atoms Thanks, - Laura -- Laura Kingsley Graduate Student Medicinal Chemistry and Molecular Pharmacology Purdue University Office: RHPH 504A 575 Stadium Mall Dr. West Lafayette, IN 47907 Office Phone: (765) 496-6643 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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] PMF trails off to infinity.
Hello, I am using steered MD and umbrella sampling to generate a PMF profile for pulling a small ligand 3 nm. As I pull the ligand from 3A toward 0 A, the PMF starts a dramatic uphill climb. This does not agree with the force profile which seems to level out. Any ideas about what might be going wrong here? I am thinking this probably isn't correct, but I don't know where I've messed up. Thanks! I can attach the graphs if necessary. - Laura -- Laura Kingsley Graduate Student Medicinal Chemistry and Molecular Pharmacology Purdue University Office: RHPH 504A 575 Stadium Mall Dr. West Lafayette, IN 47907 Office Phone: (765) 496-6643 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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] PMF trails off to infinity.
Basically what I'm doing is pulling a ligand toward a dummy atom. I pull the ligand until its COM is very close (a few angstroms) from the dummy atom. Could this be causing this behavior? What information would help? I'm having a tough time getting the figures attached but may be I could email them directly to you? Let me know. Thanks, - Laura On 07/02/2012 03:42 PM, Justin A. Lemkul wrote: On 7/2/12 9:54 AM, Laura Kingsley wrote: Hello, I am using steered MD and umbrella sampling to generate a PMF profile for pulling a small ligand 3 nm. As I pull the ligand from 3A toward 0 A, the PMF starts a dramatic uphill climb. This does not agree with the force profile which seems to level out. Any ideas about what might be going wrong here? I am thinking this probably isn't correct, but I don't know where I've messed up. Thanks! I can attach the graphs if necessary. We'll probably need a better description of what you're doing, along with any applicable figures. It sounds to me like your ligand is crashing into something in your system, but that's just a guess based on incomplete information. -Justin -- Laura Kingsley Graduate Student Medicinal Chemistry and Molecular Pharmacology Purdue University Office: RHPH 504A 575 Stadium Mall Dr. West Lafayette, IN 47907 Office Phone: (765) 496-6643 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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] PMF trails off to infinity.
Just for clarification, the PMF is read from right to left and the force profile is read from left to right. On 07/02/2012 04:27 PM, Kingsley, Laura J wrote: Here is a link to both the PMF profile and the force profile: http://s1064.photobucket.com/albums/u370/laurakingsley/?action=viewcurrent=pull_fig.jpg -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul Sent: Monday, July 02, 2012 3:56 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] PMF trails off to infinity. On 7/2/12 3:53 PM, Laura Kingsley wrote: Basically what I'm doing is pulling a ligand toward a dummy atom. I pull the ligand until its COM is very close (a few angstroms) from the dummy atom. Could this be causing this behavior? What information would help? I'm having a tough Collisions between any elements of your system would explain the problem, if it looks like what I'm picturing in my head :) time getting the figures attached but may be I could email them directly to you? Let me know. Bullet point #4 here provides a suggestion: http://www.gromacs.org/Support/Mailing_Lists#Mailing_List_Etiquette -Justin -- Laura Kingsley Graduate Student Medicinal Chemistry and Molecular Pharmacology Purdue University Office: RHPH 504A 575 Stadium Mall Dr. West Lafayette, IN 47907 Office Phone: (765) 496-6643 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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] PMF trails off to infinity.
Basically what I'm doing is pulling a ligand out of a protein towards a dummy atom, which has a mass of 1 and no charge. I've attached the a portion .mdp files for both the smd portion and the umbrella sampling. I know that the ligand gets very close possibly crashing into the dummy atom. So from what you're saying, I'm thinking this might be the source of the problem. - Laura ## smd.mdp## ; Generate velocites is on at 300 K. gen_vel = yes gen_temp= 300.0 gen_seed= 123456 ;COM PULLING ; Pull type: no, umbrella, constraint or constant_force pull= umbrella ; Pull geometry: distance, direction, cylinder or position pull_geometry = distance ; Select components for the pull vector. default: Y Y Y pull_dim= Y Y Y ; Cylinder radius for dynamic reaction force groups (nm) pull_r1 = 1 ; Switch from r1 to r0 in case of dynamic reaction force pull_r0 = 1.5 pull_constr_tol = 1e-06 pull_start = yes pull_nstxout= 10 pull_nstfout= 1 ; Number of pull groups pull_ngroups= 1 ; Group name, weight (default all 1), vector, init, rate (nm/ps), kJ/(mol*nm^2) pull_group0 =JJJ pull_weights0 = pull_pbcatom0 = 0 pull_group1 = CPZ pull_weights1 = pull_pbcatom1 = 0 pull_vec1 = pull_init1 = pull_rate1 = -0.0006 pull_k1 = 800 pull_kB1= ### um.mdp ## ;COM PULLING ; Pull type: no, umbrella, constraint or constant_force pull= umbrella ; Pull geometry: distance, direction, cylinder or position pull_geometry = distance ; Select components for the pull vector. default: Y Y Y pull_dim= Y Y Y ; Cylinder radius for dynamic reaction force groups (nm) pull_r1 = 1 ; Switch from r1 to r0 in case of dynamic reaction force pull_r0 = 1.5 pull_constr_tol = 1e-06 pull_start = yes pull_nstxout= 100 pull_nstfout= 100 ; Number of pull groups pull_ngroups= 1 ; Group name, weight (default all 1), vector, init, rate (nm/ps), kJ/(mol*nm^2) pull_group0 =JJJ pull_weights0 = pull_pbcatom0 = 0 pull_group1 = CPZ pull_weights1 = pull_pbcatom1 = 0 pull_vec1 = pull_init1 = 0 pull_rate1 = 0 pull_k1 = 1000 pull_kB1= On 07/02/2012 04:38 PM, Justin A. Lemkul wrote: On 7/2/12 4:30 PM, Laura Kingsley wrote: Just for clarification, the PMF is read from right to left and the force profile is read from left to right. The dramatic change in the magnitude and sign of the force, coupled with the steady increase in PMF, indicates to me that some elements of your system are crashing into one another. In the absence of an accompanying explanation of what you're doing (description of system, procedure with .mdp parameters, etc) that's the best I can offer. -Justin On 07/02/2012 04:27 PM, Kingsley, Laura J wrote: Here is a link to both the PMF profile and the force profile: http://s1064.photobucket.com/albums/u370/laurakingsley/?action=viewcurrent=pull_fig.jpg -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul Sent: Monday, July 02, 2012 3:56 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] PMF trails off to infinity. On 7/2/12 3:53 PM, Laura Kingsley wrote: Basically what I'm doing is pulling a ligand toward a dummy atom. I pull the ligand until its COM is very close (a few angstroms) from the dummy atom. Could this be causing this behavior? What information would help? I'm having a tough Collisions between any elements of your system would explain the problem, if it looks like what I'm picturing in my head :) time getting the figures attached but may be I could email them directly to you? Let me know. Bullet point #4 here provides a suggestion: http://www.gromacs.org/Support/Mailing_Lists#Mailing_List_Etiquette -Justin -- Laura Kingsley Graduate Student Medicinal Chemistry and Molecular Pharmacology Purdue University Office: RHPH 504A 575 Stadium Mall Dr. West Lafayette, IN 47907 Office Phone: (765) 496-6643 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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] Jarzinsky's inequality from SMD simulation
There is a way to extract the PMF from sMD simulations using the weighted histogram analysis method (WHAM) in gromacs- Justin Lemkul's tutorial does a nice job of explaining it: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/index.html - Laura On 10/31/2011 11:05 AM, Sanku M wrote: Hi, I have done some steered MD simulation and I want to construct the potential of mean force from these pull-profile using Jarzinsky's inequality. I wanted to see whether, in updated version of gromacs, there is any implementation of extracting PMF from SMD simulations. If not, can anyone suggest some guidelines how to do it. Sanku -- Laura Kingsley Graduate Student Medicinal Chemistry and Molecular Pharmacology Purdue University Office: RHPH 504A 575 Stadium Mall Dr. West Lafayette, IN 47907 Office Phone: (765) 496-6643 -- 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] Jarzinsky's inequality from SMD simulation
Yes, I believe that is correct. I know that this is one way to get the PMF using Gromacs. I am not sure if there is a way to use the Jarzinsky equation explicitly to extract the PMF from just a sMD run with Gromacs. On 10/31/2011 01:29 PM, Sanku M wrote: using SMD simulation. What is does that it uses SMD to generate the initial configurations for different windows and then perform umbrella sampling separately on each windows to subsequently extract the PMF using WHAM based on the data set on umbrella sampling. -- Laura Kingsley Graduate Student Medicinal Chemistry and Molecular Pharmacology Purdue University Office: RHPH 504A 575 Stadium Mall Dr. West Lafayette, IN 47907 Office Phone: (765) 496-6643 -- 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] AFM pulling simulations
http://www.gromacs.org/Documentation/Tutorials On 03/22/2011 11:02 AM, X Rules wrote: Hello All, I am looking for a very simple (step-by-step) tutorial on AFM pulling simulations (constant force/ constant velocity) with gromacs. Can someone point me to a simple tutorial to perform these simulations with gromacs? Thanks, -- Laura Kingsley Graduate Student Medicinal Chemistry and Molecular Pharmacology Purdue University Office: RHPH 504A 575 Stadium Mall Dr. West Lafayette, IN 47907 Office Phone: (765) 496-6643 -- 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] Umbrella sampling windows
Hello Susana, I agree with Justin, 3000 kj/molnm2 seems pretty high. I've been using about a 1000kj/molnm2 force constant with window separation of about 0.8, that seems to work well for my system. -Laura On 02/15/2011 09:51 AM, Susana Tomasio wrote: Hi all, I'm running umbrella sampling of an ion through a lipid bilayer with gromacs 4.5.1. I used g_wham to create the histograms of the configurations within the umbrella sampling windows (1 Angstrom interval). I did not get a sufficient overlap between the windows, so I was wodering which is the better way of increasing the sampling: to include additional windows in the regions where there is no overlap or to increase the force constant ? If I increase the force constant can I continue the simulation with the new constant or do I have to start again? I used a force contant of 3000 kJ mol^-1 nm^-2. Thank you in advance, Susana -- Laura Kingsley Graduate Student Medicinal Chemistry and Molecular Pharmacology Purdue University Office: RHPH 504A 575 Stadium Mall Dr. West Lafayette, IN 47907 Office Phone: (765) 496-6643 -- 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
