[gmx-users] implicit solvent system set up
Dear all, This may sound stupid, but just to make sure that I am right track about implicit solvent simulations, the set up involves pdb2gmx editconf grompp I mean, we still need to define the box dimensions by editconf and apply periodicity, right? Besides, what type of ensemble would be a good choice (NPT, NVT, etc)? Best, -- Elif Nihal Korkmaz Research Assistant University of Wisconsin - Biophysics Member of Qiang Cui Thomas Record Labs 1101 University Ave, Rm. 8359 Madison, WI 53706 Phone: 608-265-3644 Email: kork...@wisc.edu -- 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] Re: Error during executing the protein ligand tutorial
I fixed it ... but now after using the command : grompp -f em.mdp -c solv.gro -p topol.top -o ions.tpr I am getting a charge of -9.71e-01 Since the charge has to be in whole number, what shall I do in this case. (The ligand that I am using is phosphotyrosine) On Tue, Jun 21, 2011 at 2:13 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 21/06/2011 3:03 PM, bharat gupta wrote: Now I changed the .top file in this way and I am getting this error now :- change :- ; Include forcefield parameters #include charmm27.ff/forcefield.itp ;Include ligand topology #include PTR.itp [ moleculetype ] ; Namenrexcl Protein_chain_A 3 = error:- Ignoring obsolete mdp entry 'title' Back Off! I just backed up mdout.mdp to ./#mdout.mdp.8# Generated 23220 of the 23220 non-bonded parameter combinations Generating 1-4 interactions: fudge = 1 Generated 20092 of the 23220 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'Protein_chain_A' --**- Program grompp, VERSION 4.5.4 Source code file: toppush.c, line: 1987 Fatal error: No such moleculetype LIG For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/**Documentation/Errorshttp://www.gromacs.org/Documentation/Errors --**- You have to make an attempt to solve your own problems :-) We have better things to do than oversee every move you make. Follow that link and read about this issue. Mark -- 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 -- Bharat Ph.D. Candidate Room No. : 7202A, 2nd Floor Biomolecular Engineering Laboratory Division of Chemical Engineering and Polymer Science Pusan National University Busan -609735 South Korea Lab phone no. - +82-51-510-3680, +82-51-583-8343 Mobile no. - 010-5818-3680 E-mail : monu46...@yahoo.com -- 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] minimum image violation
On 21/06/2011 3:43 PM, Kavyashree M wrote: Sir, I am extremely sorry for this question again :( but I wanted to know this violation exists only in first 50ns but after that even though there appears to be a point of violation its only 1.39nm which is o0.01nm less than the cut off which I hope does not cause serious trouble (as the minimum bond length is of the order of 1 Angs) So can I make use of this part of trajectory? The purpose of the minimum image convention is to help model the real conditions under which your protein exists. The usual case is one of (effectively) infinite dilution. However, if you have a protein atom that is influenced by an atom of a periodic image of the protein, then you are not close to modeling infinite dilution. Arguably, a water atom that can see two different periodic images is also unrealistic, but probably this will be a lower-order effect, and vary from case to case. So as soon as you get a violation, further data about your system is tainted from the previous existence of unrealistic conditions. Even just looking at the first part of the simulation before the violation (assuming it has equilibrated properly so far) is questionable, because you have imposed on its ensemble the restriction that it cannot grow larger than a given diameter for a given orientation. It's up to you to judge whether the effect is small enough to ignore, and that depends on lots of things we can't know. There exist a large number of areas of biomolecular simulations where our inability to exhaustively sample ensembles has limited our ability to quantify the size of various effects. The effect of violations of minimum-image conventions on proteins is one of those areas. The important lesson here is that doing a simulation blindly runs a large risk of wasting resources. Ongoing attention to lots of details is important. As in many fields of human endeavour, there are lots of lessons that have been written in the blood of unfortunate people before you. In research, there will be lessons written in your blood. The trick is to learn from the former in order to minimize the latter :-) Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: Error during executing the protein ligand tutorial
So, after adding 1 NA ion, I started with energy mimization, but I am getting the following error after md run command :- Step=1, Dmax= 1.0e-02 nm, Epot= 1.36889e+09 Fmax= 1.97591e+11, atom= 1248 Step=2, Dmax= 1.2e-02 nm, Epot= 5.46814e+07 Fmax= 3.57239e+09, atom= 972 Step=3, Dmax= 1.4e-02 nm, Epot= 8.68244e+06 Fmax= 5.80655e+08, atom= 1253 Step=4, Dmax= 1.7e-02 nm, Epot= 3.33619e+06 Fmax= 9.98000e+07, atom= 1248 Step=5, Dmax= 2.1e-02 nm, Epot= 2.30163e+06 Fmax= 1.19057e+07, atom= 1253 Step=6, Dmax= 2.5e-02 nm, Epot= 2.07254e+06 Fmax= 3.20568e+06, atom= 1304 Step=7, Dmax= 3.0e-02 nm, Epot= 1.97667e+06 Fmax= 1.59513e+06, atom= 1045 Step=8, Dmax= 3.6e-02 nm, Epot= 1.85877e+06 Fmax= 8.25518e+05, atom= 3616 Step=9, Dmax= 4.3e-02 nm, Epot= 1.66148e+06 Fmax= 7.69483e+05, atom= 3616 Step= 10, Dmax= 5.2e-02 nm, Epot= 1.43976e+06 Fmax= 6.47087e+05, atom= 3616 Step= 11, Dmax= 6.2e-02 nm, Epot= 1.16869e+06 Fmax= 6.39015e+05, atom= 3616 Step= 12, Dmax= 7.4e-02 nm, Epot= 8.84664e+05 Fmax= 5.75494e+05, atom= 3616 Step= 13, Dmax= 8.9e-02 nm, Epot= 6.62825e+05 Fmax= 1.01984e+07, atom= 47956 step 14: Water molecule starting at atom 47956 can not be settled. Check for bad contacts and/or reduce the timestep if appropriate. Wrote pdb files with previous and current coordinates Step= 15, Dmax= 5.3e-02 nm, Epot= 5.67330e+05 Fmax= 5.36987e+05, atom= 36166 Step= 16, Dmax= 6.4e-02 nm, Epot= 3.51341e+05 Fmax= 4.19647e+05, atom= 3619 Step= 17, Dmax= 7.7e-02 nm, Epot= 6.34731e+04 Fmax= 1.56555e+06, atom= 3616 Step= 18, Dmax= 9.2e-02 nm, Epot= -2.03364e+04 Fmax= 4.60916e+05, atom= 3616 Step= 19, Dmax= 1.1e-01 nm, Epot= -3.50504e+05 Fmax= 1.53090e+06, atom= 213514 step 20: Water molecule starting at atom 213514 can not be settled. Check for bad contacts and/or reduce the timestep if appropriate. Wrote pdb files with previous and current coordinates Step= 20, Dmax= 1.3e-01 nm, Epot= -4.11692e+05 Fmax= 4.49357e+05, atom= 3619 Step= 21, Dmax= 1.6e-01 nm, Epot= -4.87207e+05 Fmax= 3.39700e+07, atom= 3629 Step= 22, Dmax= 1.9e-01 nm, Epot= -7.85503e+05 Fmax= 3.56083e+05, atom= 3619 step 23: Water molecule starting at atom 206593 can not be settled. Check for bad contacts and/or reduce the timestep if appropriate. step 23: Water molecule starting at atom 212776 can not be settled. Check for bad contacts and/or reduce the timestep if appropriate. Wrote pdb files with previous and current coordinates Wrote pdb files with previous and current coordinates Step= 23, Dmax= 2.3e-01 nm, Epot= 1.95863e+09 Fmax= 6.76309e+11, atom= 3633 step 24: Water molecule starting at atom 212776 can not be settled. Check for bad contacts and/or reduce the timestep if appropriate. Wrote pdb files with previous and current coordinates Step= 25, Dmax= 5.8e-02 nm, Epot= -9.28980e+05 Fmax= 2.81692e+05, atom= 362976 step 26: Water molecule starting at atom 42463 can not be settled. Check for bad contacts and/or reduce the timestep if appropriate. Wrote pdb files with previous and current coordinates Step= 27, Dmax= 3.5e-02 nm, Epot= -1.03111e+06 Fmax= 2.76677e+05, atom= 36293 Step= 28, Dmax= 4.1e-02 nm, Epot= -1.14733e+06 Fmax= 2.66398e+05, atom= 3629 Step= 29, Dmax= 5.0e-02 nm, Epot= -1.26821e+06 Fmax= 2.51779e+05, atom= 3629 Step= 30, Dmax= 6.0e-02 nm, Epot= -1.42873e+06 Fmax= 2.31393e+05, atom= 3629 Step= 31, Dmax= 7.2e-02 nm, Epot= -1.59623e+06 Fmax= 3.53379e+06, atom= 3633 step 32: Water molecule starting at atom 292885 can not be settled. Check for bad contacts and/or reduce the timestep if appropriate. Wrote pdb files with previous and current coordinates Step= 33, Dmax= 4.3e-02 nm, Epot= -1.62300e+06 Fmax= 2.45780e+05, atom= 361985 Step= 34, Dmax= 5.2e-02 nm, Epot= -1.75124e+06 Fmax= 2.87155e+05, atom= 213958 Step= 35, Dmax= 6.2e-02 nm, Epot= -1.86014e+06 Fmax= 6.76483e+05, atom= 3634 step 36: Water molecule starting at atom 256024 can not be settled. Check for bad contacts and/or reduce the timestep if appropriate. Wrote pdb files with previous and current coordinates Step= 36, Dmax= 7.4e-02 nm, Epot= -1.91639e+06 Fmax= 2.49523e+05, atom= 3619 Step= 37, Dmax= 8.9e-02 nm, Epot= -2.11154e+06 Fmax= 4.87466e+05, atom= 3636 Step= 38, Dmax= 1.1e-01 nm, Epot= -2.20858e+06 Fmax= 1.92308e+05, atom= 3629 Step= 40, Dmax= 6.4e-02 nm, Epot= -2.34036e+06 Fmax= 3.07614e+06, atom= 3634 Step= 41, Dmax= 7.7e-02 nm, Epot= -2.36181e+06 Fmax= 1.95100e+05, atom= 3634 Step= 42, Dmax= 9.2e-02 nm, Epot= -2.55367e+06 Fmax= 1.66837e+05, atom= 3629 Step= 43, Dmax= 1.1e-01 nm, Epot= -2.67052e+06 Fmax= 1.01067e+07, atom= 3618 Step= 44, Dmax= 1.3e-01 nm, Epot= -2.76975e+06 Fmax= 2.25183e+05, atom= 3618 Step= 45, Dmax= 1.6e-01 nm, Epot= -2.95070e+06 Fmax= 5.66364e+05, atom= 3614 step 46: Water molecule starting at atom 249877 can not be settled. Check for bad contacts and/or reduce the timestep if appropriate. step 46: Water molecule starting at atom 85966 can not be
[gmx-users] cosine content
Dear users, When are checking the cosine content of a PC, (Pls. Correct me if I am wrong) This is the command we use - g_analyze -f input-principle-component.xvg -cc outputcosine content.xvg and for first PC output says - Cosine content of set 1 with 0.5 periods: --- for nth PC also it says - Cosine content of set 1 with 0.5 periods: --- Where does this get the information that the cosine wave that it has to fit is half the eigenvector rank? is it y axis label ? Thank you With regards M. Kavyashree -- 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] Re: Error during executing the protein ligand tutorial
On 21/06/2011 4:15 PM, bharat gupta wrote: I fixed it ... but now after using the command : grompp -f em.mdp -c solv.gro -p topol.top -o ions.tpr I am getting a charge of -9.71e-01 Since the charge has to be in whole number, what shall I do in this case. (The ligand that I am using is phosphotyrosine) OK, that's what I expected you were doing - truncating the output and not rounding appropriately. See http://www.gromacs.org/Documentation/Floating_Point_Arithmetic again - I've updated it to deal with this issue more explicitly. Mark On Tue, Jun 21, 2011 at 2:13 PM, Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au wrote: On 21/06/2011 3:03 PM, bharat gupta wrote: Now I changed the .top file in this way and I am getting this error now :- change :- ; Include forcefield parameters #include charmm27.ff/forcefield.itp ;Include ligand topology #include PTR.itp [ moleculetype ] ; Namenrexcl Protein_chain_A 3 = error:- Ignoring obsolete mdp entry 'title' Back Off! I just backed up mdout.mdp to ./#mdout.mdp.8# Generated 23220 of the 23220 non-bonded parameter combinations Generating 1-4 interactions: fudge = 1 Generated 20092 of the 23220 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'Protein_chain_A' --- Program grompp, VERSION 4.5.4 Source code file: toppush.c, line: 1987 Fatal error: No such moleculetype LIG For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- You have to make an attempt to solve your own problems :-) We have better things to do than oversee every move you make. Follow that link and read about this issue. Mark -- gmx-users mailing list gmx-users@gromacs.org mailto:gmx-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 mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Bharat Ph.D. Candidate Room No. : 7202A, 2nd Floor Biomolecular Engineering Laboratory Division of Chemical Engineering and Polymer Science Pusan National University Busan -609735 South Korea Lab phone no. - +82-51-510-3680, +82-51-583-8343 Mobile no. - 010-5818-3680 E-mail : monu46...@yahoo.com mailto:monu46...@yahoo.com -- 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] Re: Error during executing the protein ligand tutorial
On 21/06/2011 4:33 PM, bharat gupta wrote: So, after adding 1 NA ion, I started with energy mimization, but I am getting the following error after md run command :- Please search for help first. http://www.gromacs.org/Documentation/Errors#LINCS.2fSETTLE.2fSHAKE_warnings Mark Step=1, Dmax= 1.0e-02 nm, Epot= 1.36889e+09 Fmax= 1.97591e+11, atom= 1248 Step=2, Dmax= 1.2e-02 nm, Epot= 5.46814e+07 Fmax= 3.57239e+09, atom= 972 Step=3, Dmax= 1.4e-02 nm, Epot= 8.68244e+06 Fmax= 5.80655e+08, atom= 1253 Step=4, Dmax= 1.7e-02 nm, Epot= 3.33619e+06 Fmax= 9.98000e+07, atom= 1248 Step=5, Dmax= 2.1e-02 nm, Epot= 2.30163e+06 Fmax= 1.19057e+07, atom= 1253 Step=6, Dmax= 2.5e-02 nm, Epot= 2.07254e+06 Fmax= 3.20568e+06, atom= 1304 Step=7, Dmax= 3.0e-02 nm, Epot= 1.97667e+06 Fmax= 1.59513e+06, atom= 1045 Step=8, Dmax= 3.6e-02 nm, Epot= 1.85877e+06 Fmax= 8.25518e+05, atom= 3616 Step=9, Dmax= 4.3e-02 nm, Epot= 1.66148e+06 Fmax= 7.69483e+05, atom= 3616 Step= 10, Dmax= 5.2e-02 nm, Epot= 1.43976e+06 Fmax= 6.47087e+05, atom= 3616 Step= 11, Dmax= 6.2e-02 nm, Epot= 1.16869e+06 Fmax= 6.39015e+05, atom= 3616 Step= 12, Dmax= 7.4e-02 nm, Epot= 8.84664e+05 Fmax= 5.75494e+05, atom= 3616 Step= 13, Dmax= 8.9e-02 nm, Epot= 6.62825e+05 Fmax= 1.01984e+07, atom= 47956 step 14: Water molecule starting at atom 47956 can not be settled. Check for bad contacts and/or reduce the timestep if appropriate. Wrote pdb files with previous and current coordinates Step= 15, Dmax= 5.3e-02 nm, Epot= 5.67330e+05 Fmax= 5.36987e+05, atom= 36166 Step= 16, Dmax= 6.4e-02 nm, Epot= 3.51341e+05 Fmax= 4.19647e+05, atom= 3619 Step= 17, Dmax= 7.7e-02 nm, Epot= 6.34731e+04 Fmax= 1.56555e+06, atom= 3616 Step= 18, Dmax= 9.2e-02 nm, Epot= -2.03364e+04 Fmax= 4.60916e+05, atom= 3616 Step= 19, Dmax= 1.1e-01 nm, Epot= -3.50504e+05 Fmax= 1.53090e+06, atom= 213514 step 20: Water molecule starting at atom 213514 can not be settled. Check for bad contacts and/or reduce the timestep if appropriate. Wrote pdb files with previous and current coordinates Step= 20, Dmax= 1.3e-01 nm, Epot= -4.11692e+05 Fmax= 4.49357e+05, atom= 3619 Step= 21, Dmax= 1.6e-01 nm, Epot= -4.87207e+05 Fmax= 3.39700e+07, atom= 3629 Step= 22, Dmax= 1.9e-01 nm, Epot= -7.85503e+05 Fmax= 3.56083e+05, atom= 3619 step 23: Water molecule starting at atom 206593 can not be settled. Check for bad contacts and/or reduce the timestep if appropriate. step 23: Water molecule starting at atom 212776 can not be settled. Check for bad contacts and/or reduce the timestep if appropriate. Wrote pdb files with previous and current coordinates Wrote pdb files with previous and current coordinates Step= 23, Dmax= 2.3e-01 nm, Epot= 1.95863e+09 Fmax= 6.76309e+11, atom= 3633 step 24: Water molecule starting at atom 212776 can not be settled. Check for bad contacts and/or reduce the timestep if appropriate. Wrote pdb files with previous and current coordinates Step= 25, Dmax= 5.8e-02 nm, Epot= -9.28980e+05 Fmax= 2.81692e+05, atom= 362976 step 26: Water molecule starting at atom 42463 can not be settled. Check for bad contacts and/or reduce the timestep if appropriate. Wrote pdb files with previous and current coordinates Step= 27, Dmax= 3.5e-02 nm, Epot= -1.03111e+06 Fmax= 2.76677e+05, atom= 36293 Step= 28, Dmax= 4.1e-02 nm, Epot= -1.14733e+06 Fmax= 2.66398e+05, atom= 3629 Step= 29, Dmax= 5.0e-02 nm, Epot= -1.26821e+06 Fmax= 2.51779e+05, atom= 3629 Step= 30, Dmax= 6.0e-02 nm, Epot= -1.42873e+06 Fmax= 2.31393e+05, atom= 3629 Step= 31, Dmax= 7.2e-02 nm, Epot= -1.59623e+06 Fmax= 3.53379e+06, atom= 3633 step 32: Water molecule starting at atom 292885 can not be settled. Check for bad contacts and/or reduce the timestep if appropriate. Wrote pdb files with previous and current coordinates Step= 33, Dmax= 4.3e-02 nm, Epot= -1.62300e+06 Fmax= 2.45780e+05, atom= 361985 Step= 34, Dmax= 5.2e-02 nm, Epot= -1.75124e+06 Fmax= 2.87155e+05, atom= 213958 Step= 35, Dmax= 6.2e-02 nm, Epot= -1.86014e+06 Fmax= 6.76483e+05, atom= 3634 step 36: Water molecule starting at atom 256024 can not be settled. Check for bad contacts and/or reduce the timestep if appropriate. Wrote pdb files with previous and current coordinates Step= 36, Dmax= 7.4e-02 nm, Epot= -1.91639e+06 Fmax= 2.49523e+05, atom= 3619 Step= 37, Dmax= 8.9e-02 nm, Epot= -2.11154e+06 Fmax= 4.87466e+05, atom= 3636 Step= 38, Dmax= 1.1e-01 nm, Epot= -2.20858e+06 Fmax= 1.92308e+05, atom= 3629 Step= 40, Dmax= 6.4e-02 nm, Epot= -2.34036e+06 Fmax= 3.07614e+06, atom= 3634 Step= 41, Dmax= 7.7e-02 nm, Epot= -2.36181e+06 Fmax= 1.95100e+05, atom= 3634 Step= 42, Dmax= 9.2e-02 nm, Epot= -2.55367e+06 Fmax= 1.66837e+05, atom= 3629 Step= 43, Dmax= 1.1e-01 nm, Epot= -2.67052e+06 Fmax= 1.01067e+07, atom= 3618 Step= 44, Dmax= 1.3e-01 nm, Epot= -2.76975e+06 Fmax= 2.25183e+05, atom= 3618 Step= 45, Dmax= 1.6e-01 nm, Epot= -2.95070e+06 Fmax= 5.66364e+05,
[gmx-users] How to calculate RMSD per residue with Gromacs ?
Hi How to calculate RMSD per residue with Gromacs ? Thank you Lin -- 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] radius of gyration - compactness - accessible surface area
Hi Shahab, When comparing two variables, they have to share an axis. Time for instance... Cheers, Tsjerk On Tue, Jun 21, 2011 at 6:36 AM, shahab shariati shahab.shari...@gmail.com wrote: Dear Tsjerk thanks for your attention. larger radius of gyration, more surface. and smaller radius of gyration, less surface. I want to obtain solvent accessible surface area using g_sas. g_sas -f *.xtc -s *.tpr -n *.ndx -o -or -oa. I will obtain three output files containing: area.xvg, resarea.xvg and atomarea.xvg If I want to obtain average of ASA to compare with Rg (I want to know in my system, with increase of Rg, how do ASA change?), which of above output files are suitable for this aim? -- gmx-users mailing list gmx-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 -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- 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] implicit solvent system set up
E. Nihal Korkmaz wrote: Dear all, This may sound stupid, but just to make sure that I am right track about implicit solvent simulations, the set up involves pdb2gmx editconf grompp I mean, we still need to define the box dimensions by editconf and apply periodicity, right? Not usually. Proper settings usually include pbc = no and long cutoffs. This has been discussed at length in the list archive. Besides, what type of ensemble would be a good choice (NPT, NVT, etc)? Typically NVT. There is nothing compressible for NPT to act upon - you have, e.g., a protein in an imaginary bath of solvent. If you apply NPT conditions, the box will just collapse in on itself. -Justin Best, -- Elif Nihal Korkmaz Research Assistant University of Wisconsin - Biophysics Member of Qiang Cui Thomas Record Labs 1101 University Ave, Rm. 8359 Madison, WI 53706 Phone: 608-265-3644 Email: kork...@wisc.edu mailto:kork...@wisc.edu -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] How to calculate RMSD per residue with Gromacs ?
Chih-Ying Lin wrote: Hi How to calculate RMSD per residue with Gromacs ? g_rmsf -od -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/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] radius of gyration - compactness - accessible surface area
Dear Tsjerk very thanks for your useful guidance. I now know that I should compare output of g_gyrate (containing Rg vs time) by area.xvg output file of g_sas (containing area vs time). In area.xvg output file, there are several columns: Hydrophobic, Hydrophilic and Total. for example in time, 100 ps: 10035.9501 60.9389 96.8891 area is in nm2. from above number I understand that 35.9501 nm2 of area of protein that is accessible to solvent belongs to hydrophobic part of protein. and 60.9389 nm2 of area of protein that is accessible to solvent belongs to hydrophilic part of protein. is my understanding true? any help will highly appreciated. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] xvg plotting
Hi, I am a new user in gromacs and i would like to create a plot from several .xvg files. Can anyone guide me through the process? Thank you in advance N.V. -- 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] xvg plotting
On 21/06/2011 7:40 PM, Nicole Varvarigou wrote: Hi, I am a new user in gromacs and i would like to create a plot from several .xvg files. Can anyone guide me through the process? That's not really the purpose of this list, which is for GROMACS-related questions. I can suggest that you look for tutorial material on your plotting tool of choice (e.g. grace, gnuplot), which should take you most of the way towards such a solution. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] radius of gyration - compactness - accessible surface area
You understand correctly. On Tue, Jun 21, 2011 at 11:35 AM, shahab shariati shahab.shari...@gmail.com wrote: Dear Tsjerk very thanks for your useful guidance. I now know that I should compare output of g_gyrate (containing Rg vs time) by area.xvg output file of g_sas (containing area vs time). In area.xvg output file, there are several columns: Hydrophobic, Hydrophilic and Total. for example in time, 100 ps: 100 35.9501 60.9389 96.8891 area is in nm2. from above number I understand that 35.9501 nm2 of area of protein that is accessible to solvent belongs to hydrophobic part of protein. and 60.9389 nm2 of area of protein that is accessible to solvent belongs to hydrophilic part of protein. is my understanding true? any help will highly appreciated. -- gmx-users mailing list gmx-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 -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] xvg plotting
Hi Nicole In linux/unix, there are a program named xmgr aor xmgrace by default. Just you type in command line : xmgr 1.xvg 2.xvg 3.xvg .. -- Leila Karami Ph.D. student of Physical Chemistry K.N. Toosi University of Technology Theoretical Physical Chemistry Group -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] PMF analysis and pull_dim (Step 6 of Justin's tutorial)
Dear Gromacs Users, I've done Justin's tutorial regarding PMF/umbrella sampling and now, when approaching my own system I have a couple of questions. (Link to the tutorial here: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/06_umbrella.html) My system is comprise of a transport protein (embedded in membrane) and a ligand. The system is positions so that Z axis is the axis on which I've made PMF windows. The next step on this is to run these windows separately and I didn't quite understand why in step-6 of the tutorial it specifies to still use pull_dim = N N Y and pull_rate1 = 0.0. As far as I understood, during the production run we want to sample the Z position. Shouldn't then it use pull_dim = Y Y N ? And what does it mean to the system when we set pull_rate1 = 0.0 ? Does it mean that when pull_dim = N N Y and pull_rate1 = 0.0 it restrains pull_group0 on the Z-axis? This came a bit longish, Thanks in advance, -Shay P.S. Using Gromacs 4.0.7 -- 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] PMF analysis and pull_dim (Step 6 of Justin's tutorial)
Shay Teaching wrote: Dear Gromacs Users, I've done Justin's tutorial regarding PMF/umbrella sampling and now, when approaching my own system I have a couple of questions. (Link to the tutorial here: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/06_umbrella.html ) My system is comprise of a transport protein (embedded in membrane) and a ligand. The system is positions so that Z axis is the axis on which I've made PMF windows. The next step on this is to run these windows separately and I didn't quite understand why in step-6 of the tutorial it specifies to still use pull_dim = N N Y and pull_rate1 = 0.0. As far as I understood, during the production run we want to sample the Z position. Shouldn't then it use pull_dim = Y Y N ? No, that would confine the pulled group to the x-y plane, but allow it to move freely in z. And what does it mean to the system when we set pull_rate1 = 0.0 ? The harmonic restraint is applied to pull_group1 such that there is no net change in position. Does it mean that when pull_dim = N N Y and pull_rate1 = 0.0 it restrains pull_group0 on the Z-axis? Not pull_group0 (which is the reference group), but pull_group1. Otherwise, yes. -Justin This came a bit longish, Thanks in advance, -Shay P.S. Using Gromacs 4.0.7 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] PMF analysis and pull_dim (Step 6 of Justin's tutorial)
Thanks for you prompt reply! Clear and to the point. -Shay On Tue, Jun 21, 2011 at 2:03 PM, Justin A. Lemkul jalem...@vt.edu wrote: Shay Teaching wrote: Dear Gromacs Users, I've done Justin's tutorial regarding PMF/umbrella sampling and now, when approaching my own system I have a couple of questions. (Link to the tutorial here: http://www.bevanlab.biochem.** vt.edu/Pages/Personal/justin/**gmx-tutorials/umbrella/06_**umbrella.htmlhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/06_umbrella.html) My system is comprise of a transport protein (embedded in membrane) and a ligand. The system is positions so that Z axis is the axis on which I've made PMF windows. The next step on this is to run these windows separately and I didn't quite understand why in step-6 of the tutorial it specifies to still use pull_dim = N N Y and pull_rate1 = 0.0. As far as I understood, during the production run we want to sample the Z position. Shouldn't then it use pull_dim = Y Y N ? No, that would confine the pulled group to the x-y plane, but allow it to move freely in z. And what does it mean to the system when we set pull_rate1 = 0.0 ? The harmonic restraint is applied to pull_group1 such that there is no net change in position. Does it mean that when pull_dim = N N Y and pull_rate1 = 0.0 it restrains pull_group0 on the Z-axis? Not pull_group0 (which is the reference group), but pull_group1. Otherwise, yes. -Justin This came a bit longish, Thanks in advance, -Shay P.S. Using Gromacs 4.0.7 -- ==**== 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/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- 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 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] query regarding g_ras command
I want to obtain solvent accessible surface area using g_sas command: g_sas -f *.xtc -s *.tpr -n *.ndx -o -or -oa.plz tell me the full command as i am getting error while running this command.thanx in advance!! how I will obtain three output files containing: area.xvg, resarea.xvg and atomarea.xvg -- [image: images[12]] “Many Smiles Begin Because Of Another Smile . . . . Regards, Rashi image004.jpg-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] g_msd uncertainty
Dear Gromacs community I would like to better understand how the uncertainty on the diffusion coefficient is calculated in GROMACS. I am calculating water diffusivity for different water models at different temperatures. I am using Gomacs 4.5.4 Reading the manual, I am a bit confused on how g_msd calculate the uncertainty on the average. Indeed, the manual told me (pag 285-286) 1) g_msd computes the mean square displacement (MSD) of atoms from a set of initial positions. This provides an easy way to compute the diffusion constant using the Einstein relation. The time between the reference points for the MSD calculation is set with -trestart. The diffusion constant is calculated by least squares fitting a straight line (D*t + c) through the MSD(t) from -beginfit to -endfit (note that t is time from the reference positions, not simulation time). An error estimate given, which is the difference of the diffusion coefficients obtained from fits over the two halves of the fit interval. 2) By the way, few lines below The diffusion coefficient is determined by linear regression of the MSD, where, unlike for the normal output of D, the times are weighted according to the number of reference points, i.e. short times have a higher weight. Also when -beginfit=-1,fitting starts at 10% and when -endfit=-1, fitting goes to 90%.Using this option one also gets an accurate error estimate based on the statistics between individual molecules. Note that this diffusion coefficient and error estimate are only accurate when the MSD is completely linear between -beginfit and -endfit. Based on this last paragraph, I suppose that g_msd calculates for each molecule the diffusion coefficient and then it calculates the average and standard deviation from the daset of the diffusion coefficients of each molecules. So, if I compute g_msd -f traj.xtc -s topol.tpr -n index.ndx.ndx -o msd.xvg -b 0 -e 10 -beginfit 15000 -endfit 25000 -trestart 10 -type z at the top of my output file msd.xvg I can read # MSD gathered over 10 ps with 10001 restarts # Diffusion constants fitted from time 1500 to 25000 ps # D[all_10] = 0.1230 (+/- 0.0060) (1e-5 cm^2/s) So, 0.0060 is one standard deviation based on the statistic between different molecules (second method) or is calculated using the difference of the diffusion coefficient on the two halves of the fitting region (first method)? I was searching in the mail list without success...thanks for any help Ivan -- -- Ivan Gladich, Ph.D. Postdoctoral Fellow Academy of Sciences of the Czech Republic Institute of Organic Chemistry and Biochemistry AS CR, v.v.i. Flemingovo nám. 2. 166 10 Praha 6 Czech Republic Tel: +420775504164 e-mail: ivan.glad...@uochb.cas.cz web page:http://www.molecular.cz/~gladich/ - -- 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] query regarding g_ras command
rashi parihar wrote: I want to obtain solvent accessible surface area using g_sas command: g_sas -f *.xtc -s *.tpr -n *.ndx -o -or -oa.plz tell me the full command as i am getting error while running this command.thanx in advance!! To get an answer you need to provide an actual command and the actual error message. There's nothing informative here. -Justin how I will obtain three output files containing: area.xvg, resarea.xvg and atomarea.xvg -- images[12] “Many Smiles Begin Because Of Another Smile . . . . Regards, Rashi -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] query regarding g_ras command
thanx justin..my problem is that i do not know exactly the syntax of command.i get to know about this command through this community only.i.e why i want the full command? On Tue, Jun 21, 2011 at 6:53 PM, Justin A. Lemkul jalem...@vt.edu wrote: rashi parihar wrote: I want to obtain solvent accessible surface area using g_sas command: g_sas -f *.xtc -s *.tpr -n *.ndx -o -or -oa.plz tell me the full command as i am getting error while running this command.thanx in advance!! To get an answer you need to provide an actual command and the actual error message. There's nothing informative here. -Justin how I will obtain three output files containing: area.xvg, resarea.xvg and atomarea.xvg -- images[12] “Many Smiles Begin Because Of Another Smile . . . . Regards, Rashi -- ==**== 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/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- 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 -- [image: images[12]] “Many Smiles Begin Because Of Another Smile . . . . Regards, Rashi image004.jpg-- 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] query regarding g_ras command
rashi parihar wrote: thanx justin..my problem is that i do not know exactly the syntax of command.i get to know about this command through this community only.i.e why i want the full command? Please read the contents of the manual about g_sas and/or g_sas -h for a full list of options (like you can do for all Gromacs programs). You said you were getting an error - is that true? If you have an error message, post it and likely someone will know how to fix it. If you simply don't know how to run a command, then say so, but the solution is always going to be the -h option. -Justin On Tue, Jun 21, 2011 at 6:53 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: rashi parihar wrote: I want to obtain solvent accessible surface area using g_sas command: g_sas -f *.xtc -s *.tpr -n *.ndx -o -or -oa.plz tell me the full command as i am getting error while running this command.thanx in advance!! To get an answer you need to provide an actual command and the actual error message. There's nothing informative here. -Justin how I will obtain three output files containing: area.xvg, resarea.xvg and atomarea.xvg -- images[12] “Many Smiles Begin Because Of Another Smile . . . . Regards, Rashi -- ==__== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==__== -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/__mailman/listinfo/gmx-users http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/__Support/Mailing_Lists/Search 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 mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/__Support/Mailing_Lists http://www.gromacs.org/Support/Mailing_Lists -- images[12] “Many Smiles Begin Because Of Another Smile . . . . Regards, Rashi -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Questions about GB parameters
Can anyone comment further on either of these issues? -Justin Mark Abraham wrote: On 15/06/2011 4:24 AM, Justin A. Lemkul wrote: Hi All, I wanted to dig up an old discussion that hit the list a long time ago because I'm now encountering some problems understanding the GB settings myself. The discussion in question is here: http://lists.gromacs.org/pipermail/gmx-users/2010-August/053373.html I wanted to post a couple of questions based on Per's response. 1. Based on that post, it seems to me that the value in the gbr column should have a dielectric offset added to it during the GB calculations. In the code, though (genborn.c, around line 484 in the latest release-4-5-patches), it looks like the dielectric offset is subtracted, not added. I guess the code is reversing the process, going from GB radius back to vdW radius by subtracting the dielectric offset? It seems, then, that the parameters in gbsa.itp should specify GB radii, not vdW radii, though the manual says the gbr column is atomic van der Waals radii, which are used in computing the Born radii. Is the opposite actually true? It does look to me as though something is mis-sense here. The quantity given in gb_dielectric_offset is always subtracted from a value that I think is found in the gbr column of [implicit_genborn_parameters]. Mark 2. I am still unclear on the source of the HCT scaling factors. From the reference cited in the manual, it would seem that scaling factors are interaction-dependent, at least when H atoms are concerned. I also cannot find any indication of where these values came from. None of the values of Table 2 in the HCT reference match the contents of the hct column. Again I wonder if I'm missing something obvious :) Thanks for any insight! -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/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] Re: Fw: properdihedrals
Dear Prema: 1. Do you think my e-mail is an alias for gromacs mailing list, please? I am not sure. 2. What about downloading the manual and referring yourself to the section where topology files are described? Enjoy gromaxing... Dr. Vitaly V. Chaban, 430 Hutchison Hall, Chem. Dept. Univ. Rochester, Rochester, New York 14627-0216 THE UNITED STATES OF AMERICA On Tue, Jun 21, 2011 at 2:05 PM, Prema Awati prem...@iiserpune.ac.inwrote: *-- Original Message --* From: prem...@iiserpune.ac.in To: gmxus...@gromacs.org Date: Tue, 21 Jun 2011 23:25:51 +0530 (GMT+05:30) Subject: properdihedrals Sir, I am looking forward for your help to calculate Ryckaert-Belleman's (RB) coefficients using proper dihedrals.Is there any way to get Fourier coefficients value from the equation; Vd (φijkl ) = kφ (1 + cos(nφ - φs )) ; so that I can use it in following way to get RB coefficients; C0 = F2 + 1 (F1 + F3 ) C1 = 1 (-F1 + 3 F3 ) C2 = -F2 + 4 F4 C3 = -2 F3 C4 = -4 F4 C5 = 0 I am referring Gromacs-4.5.3 manual for the above conversion. Looking for your quick response Thankyou. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Fw: properdihedrals
-- Original Message -- From: prem...@iiserpune.ac.in To: gmxus...@gromacs.org Date: Tue, 21 Jun 2011 23:25:51 +0530 (GMT+05:30) Subject: properdihedrals Sir, I am looking forward for your help to calculate Ryckaert-Belleman's (RB) coefficients using proper dihedrals.Is there any way to get Fourier coefficients value from the equation; Vd (?ijkl ) = k? (1 + cos(n? ? ?s )) ; so that I can use it in following way to get RB coefficients; C0 = F2 + 1 (F1 + F3 ) C1 = 1 (?F1 + 3 F3 ) C2 = ?F2 + 4 F4 C3 = ?2 F3 C4 = ?4 F4 C5 = 0 I am referring Gromacs-4.5.3 manual for the above conversion. Looking for your quick response Thankyou. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] classic Ewald pressure tensor
Greetings Gromacs Users, I have run single precision isothermal-isobaric ensemble simulations using particle mesh Ewald (PME) (in Gromacs 4.0.5) and compared the results to those of (what I think should be) equivalent single precision simulations using the classic implementation of Ewald. The systems under study are binary mixtures of methanol + water at 300 K and 1 bar across the full composition range. The classic Ewald simulations have a more negative total potential energy (PE) for each composition, with the difference increasing as the mole fraction of methanol increases. The reduced PE differences, (PME total PE - Ewald total PE)/RT (angled brackets denote time averages), range between 0.29 for pure water and 0.93 for pure methanol. When starting an Ewald simulation from a structure that was equilibrated with PME, convergence to the more negative (incorrect) Ewald potential energy takes place within approximately twenty picoseconds. The box volume also decreases in the classic Ewald simulations e.g., to 81% of its original volume in the equimolar methanol + water composition. A test of the number of lattice vectors used in the simulations shows that the results are converged. All the simulations employ the Nose-Hoover thermostat and the Parrinello-Rahman barostat. Canonical ensemble classic Ewald simulations do however reproduce the canonical and isothermal-isobaric PME average total PE, however the pressure is incorrect, averaging ~-5,000 bar. Below my message, please find the mdp file used in the classic Ewald simulations. The only differences between the mdp file below and that used in the PME simulations are the following lines: coulombtype = PME fourierspacing = 0.12 Is it possible that the pressure tensor is incorrect in the classic Ewald code? Sincerely, Elizabeth Ploetz ; ; File 'mdout.mdp' was generated ; By user: onbekend (0) ; On host: onbekend ; At date: Tue Dec 23 12:23:42 2008 ; ; VARIOUS PREPROCESSING OPTIONS title= ; Preprocessor - specify a full path if necessary. cpp = /lib/cpp include = define = ; RUN CONTROL PARAMETERS integrator = md ; Start time and timestep in ps tinit= 1 dt = 0.002 nsteps = 50 ; For exact run continuation or redoing part of a run init_step= 0 ; mode for center of mass motion removal comm-mode= Linear ; number of steps for center of mass motion removal nstcomm = 500 ; group(s) for center of mass motion removal comm-grps= ; LANGEVIN DYNAMICS OPTIONS ; Friction coefficient (amu/ps) and random seed bd-fric = 0 ld-seed = 1993 ; ENERGY MINIMIZATION OPTIONS ; Force tolerance and initial step-size emtol= 10 emstep = 0.01 ; Max number of iterations in relax_shells niter= 20 ; Step size (ps^2) for minimization of flexible constraints fcstep = 0 ; Frequency of steepest descents steps when doing CG nstcgsteep = 1000 nbfgscorr= 10 ; OUTPUT CONTROL OPTIONS ; Output frequency for coords (x), velocities (v) and forces (f) nstxout = 500 nstvout = 500 nstfout = 0 ; Checkpointing helps you continue after crashes nstcheckpoint= 5000 ; Output frequency for energies to log file and energy file nstlog = 500 nstenergy= 500 ; Output frequency and precision for xtc file nstxtcout= 0 xtc-precision= 1000 ; This selects the subset of atoms for the xtc file. You can ; select multiple groups. By default all atoms will be written. xtc-grps = ; Selection of energy groups energygrps = MOH SOL ; NEIGHBORSEARCHING PARAMETERS ; nblist update frequency nstlist = 10 ; ns algorithm (simple or grid) ns-type = Grid ; Periodic boundary conditions: xyz (default), no (vacuum) ; or full (infinite systems only) pbc = xyz ; nblist cut-off rlist= 1.5 domain-decomposition = no ; OPTIONS FOR ELECTROSTATICS AND VDW ; Method for doing electrostatics coulombtype = Ewald rcoulomb-switch = 0 rcoulomb = 1.5 ; Relative dielectric constant for the medium and the reaction field epsilon-r= 1.0 epsilon_rf = 1.0 ; Method for doing Van der Waals vdw-type = Cut-off ; cut-off lengths rvdw-switch = 0 rvdw = 1.5 ; Apply long range dispersion corrections for Energy and Pressure DispCorr = No ; Extension of the potential lookup tables beyond the cut-off
[gmx-users] Programs to add residues
Hi all, Is there a program that allows the user to add residues to the N and C terminus, without using the electron density? I would like to add a short linker to my protein which doesn't exist in the electron density. Thanks a lot, Sincerely, Zack -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Programs to add residues
Try Loopy. You can get it to build termini in addition to loops. http://wiki.c2b2.columbia.edu/honiglab_public/index.php/Software:Loopy Nevertheless, I'd suggest simply omitting that part of the protein and capping your new terminus to remove the charge. You will have more difficulties converging the conformation of the unstructured terminus than you may expect. CHris. -- original message -- Hi all, Is there a program that allows the user to add residues to the N and C terminus, without using the electron density? I would like to add a short linker to my protein which doesn't exist in the electron density. Thanks a lot, Sincerely, Zack -- 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] error bars g_wham
On 6/20/11 Jun 20,1:01 PM, Gavin Melaugh wrote: Hi all I have read the manual and the recent JCTC paper on g_wham, and I was wondering how to actually get the error bars on the profile.xvg file outputted from g_wham. Many Thanks Gavin Hi Gavin, the error bars are at the moment only in bsResult.xvg (option -bsres), not in profile.xvg. Cheers, Jochen -- --- Dr. Jochen Hub Computational and Systems Biology Dept. of Cell Molecular Biology Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46-18-4715056 Fax: +46-18-511755 http://xray.bmc.uu.se/~jochen/index.html --- -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Autocorrelation of dipole moment
Hi, Is it possible to get negative values for normalized autocorrelation of total dipole moment. Thank you. Regards, Chathurika. -- 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] xvg plotting
Any graphing program will do, the .xvg file is a text data file, so you can import it into Excel, Sigma Plot, xmgrace, gnuplot etc. Catch ya, Dr. Dallas Warren Medicinal Chemistry and Drug Action Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@monash.edu +61 3 9903 9304 - When the only tool you own is a hammer, every problem begins to resemble a nail. From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Nicole Varvarigou Sent: Tuesday, 21 June 2011 7:40 PM To: gmx-users@gromacs.org Subject: [gmx-users] xvg plotting Hi, I am a new user in gromacs and i would like to create a plot from several .xvg files. Can anyone guide me through the process? Thank you in advance N.V. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] How to set proper temperature and pressure coupling parameters, especially when using solvents other than water?
Dear gromacs-ers I am using stochastic dynamics integrator (integrator = sd), so most of the time, I only need to adjust following parameters for temperature and pressure coupling: tau_t pcoupl tau_p (ref_t is room temperature and ref_p is 1 atm, compressibility can be taken from experimental numbers). In the manual, a tau_t between 1 and 2ps is recommended for the sake of simulation stability, but I see someone use a tau_t of 0.1ps with the same integrator (integration was performed with Langevin dynamics,49 with a reference temperature of 300 K and a weak frictional constant of 10 ps-1,) when simulating water solvent. I also see someone use a tau_t of 0.2ps with the same integrator (To obtain a isothermal–isobaric ensemble at 293 K, a leap-frog stochastic dynamics integrator16 was used to integrate the equations of motion. The inverse friction constant was set to 0.2 ps.) when simulating some organic solvent. I check the references mentioned in these gromacs papers so I am pretty sure they are using the same integrator. So I am a bit confusing here, what tau_t should I use, the number between 1 and 2ps as recommended by the manual, or the numbers below 1ps, as reported in these papers? Does this parameter depend on what solvent (water, cyclohexane) I use? Can I just use any number between 0.1ps and 2ps and check if my simulations look fine or there is some ‘best’ number for a particular solvent? When I use berendsen or Parrinello-Rahman, the same questions apply: Is there some ‘best’ number for a particular solvent, or I can just use any number between 0.5ps and 5ps and check if my simulations run well? When I read papers, I find many different pressure coupling constant (tau_p) ranging from 0.5ps to 1ps (water), 1ps to 5ps (organic solvent) with weak coupling scheme in gromacs. I am wondering why they use bigger number for organic solvent? If I use Parrinello-Rahman (it is said to be better than berendsen in the manual), do I need to change tau_p, or I can just use the same tau_p as berendsen? Thank you so much for your kind help, any suggestions or clues are very welcome. Yours xiaodong huang Research School of Chemistry ANU -- 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] How to set proper temperature and pressure coupling parameters, especially when using solvents other than water?
xiaodong huang wrote: Dear gromacs-ers I am using stochastic dynamics integrator (integrator = sd), so most of the time, I only need to adjust following parameters for temperature and pressure coupling: tau_t pcoupl tau_p (ref_t is room temperature and ref_p is 1 atm, compressibility can be taken from experimental numbers). In the manual, a tau_t between 1 and 2ps is recommended for the sake of simulation stability, but I see someone use a tau_t of 0.1ps with the same integrator (integration was performed with Langevin dynamics,49 with a reference temperature of 300 K and a weak frictional constant of 10 ps-1,) when simulating water solvent. I also see someone use a tau_t of 0.2ps with the same integrator (To obtain a isothermal–isobaric ensemble at 293 K, a leap-frog stochastic dynamics integrator16 was used to integrate the equations of motion. The inverse friction constant was set to 0.2 ps.) when simulating some organic solvent. I check the references mentioned in these gromacs papers so I am pretty sure they are using the same integrator. So I am a bit confusing here, what tau_t should I use, the number between 1 and 2ps as recommended by the manual, or the numbers below 1ps, as reported in these papers? Does this parameter depend on what solvent (water, cyclohexane) I use? Can I just use any number between 0.1ps and 2ps and check if my simulations look fine or there is some ‘best’ number for a particular solvent? This was discussed recently: http://lists.gromacs.org/pipermail/gmx-users/2011-June/061992.html When I use berendsen or Parrinello-Rahman, the same questions apply: Is there some ‘best’ number for a particular solvent, or I can just use any number between 0.5ps and 5ps and check if my simulations run well? When I read papers, I find many different pressure coupling constant (tau_p) ranging from 0.5ps to 1ps (water), 1ps to 5ps (organic solvent) with weak coupling scheme in gromacs. I am wondering why they use bigger number for organic solvent? If I use Parrinello-Rahman (it is said to be better than berendsen in the manual), do I need to change tau_p, or I can just use the same tau_p as berendsen? Time constants are a bit empirical. The Berendsen algorithm is more forgiving; it relaxes very quickly and thus low values of tau_t/tau_p are stable. For methods that allow for wider oscillations (N-H for temperature, P-R for pressure), small tau_t/tau_p values are unstable due to the nature of these algorithms. The most important information is whether or not you obtain proper distributions for the desired ensemble. Any algorithm can be made to behave artificially rigorously or artificially relaxed. -Justin Thank you so much for your kind help, any suggestions or clues are very welcome. Yours xiaodong huang Research School of Chemistry ANU -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
