RE: [gmx-users] Invalid enum fatal error
Hi Shima, Your question is not clear but from the error message what I can see is that you made a typo (spelling error). You type 'Brendsen' instead of 'Berendsen'. You miss the first 'e'. And, your mdp says pcoupl = Parrinello-Rahman???but you wanted to run 'Berendsen' Read the error messages carefully before you post your question as this one is really easy to solve just only by reading the error message :) Cheers, -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Shima Arasteh Sent: Monday, 4 February 2013 4:17 PM To: Discussion list for GROMACS users Subject: [gmx-users] Invalid enum fatal error Hi all, I want to try Brendsen p-couplingon my system. The setting of npt.mdp is as : ; Temperature coupling is on tcoupl = Nose-Hoover ; modified Berendsen thermostat tc-grps = Protein POPC SOL_CL ; two coupling groups - more accurate tau_t = 0.5 0.5 0.5 ; time constant, in ps ref_t = 310 310 310 ; reference temperature, one for each group, in K pcoupl = Parrinello-Rahman ; no pressure coupling in NVT pcoupltype = semiisotropic tau_p = 4 ref_p = 1.01325 1.01325 compressibility = 4.5e-5 4.5e-5 But I get a fatal error: invalid enum 'Brendsen' for variable Pcoupl, using 'No'* Next time use one of: 'No' 'Berendsen' 'Parrinello-Rahman' 'Isotropic' 'MTTK' Does this message says that I need to change semiisotropicd to the isotropic? How may I solve this problem? Would you help me with your suggestions? Thanks in advance. Sincerely, -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
RE: [gmx-users] How to analysis 10 ns from 20 ns simulation
Use trajconv http://manual.gromacs.org/online/trjconv.html -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Naga Sundar Sent: Monday, 4 February 2013 4:45 PM To: Discussion list for GROMACS users Subject: [gmx-users] How to analysis 10 ns from 20 ns simulation Dear users I performed 20 ns simulation for protein complex. After 10 ns only my system obtained equilibration state . I would like to analyze last 10 ns from the trajectory file.I got problem to generate last 10 ns xtc file from the 20 ns trr file. so, plz help me to sort out this problem -- Regards N.NagaSundaram -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] How to analysis 10 ns from 20 ns simulation
Dear users I performed 20 ns simulation for protein complex. After 10 ns only my system obtained equilibration state . I would like to analyze last 10 ns from the trajectory file.I got problem to generate last 10 ns xtc file from the 20 ns trr file. so, plz help me to sort out this problem -- Regards N.NagaSundaram -- 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] Invalid enum fatal error
Hi all, I want to try Brendsen p-couplingon my system. The setting of npt.mdp is as : ; Temperature coupling is on tcoupl = Nose-Hoover ; modified Berendsen thermostat tc-grps = Protein POPC SOL_CL ; two coupling groups - more accurate tau_t = 0.5 0.5 0.5 ; time constant, in ps ref_t = 310 310 310 ; reference temperature, one for each group, in K pcoupl = Parrinello-Rahman ; no pressure coupling in NVT pcoupltype = semiisotropic tau_p = 4 ref_p = 1.01325 1.01325 compressibility = 4.5e-5 4.5e-5 But I get a fatal error: invalid enum 'Brendsen' for variable Pcoupl, using 'No'* Next time use one of: 'No' 'Berendsen' 'Parrinello-Rahman' 'Isotropic' 'MTTK' Does this message says that I need to change semiisotropicd to the isotropic? How may I solve this problem? Would you help me with your suggestions? Thanks in advance. Sincerely, -- 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] Selectively choose the upper and lower leaflets of a DPPC bilayer.
On 2/3/13 9:57 PM, Rajat Desikan wrote: Hi All, Is there a convenient method to selectively make an index file containing the upper leaflet and the lower leaflet of a DPPC bilayer? g_select can make selections based on geometric criteria. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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] Selectively choose the upper and lower leaflets of a DPPC bilayer.
Hi All, Is there a convenient method to selectively make an index file containing the upper leaflet and the lower leaflet of a DPPC bilayer? Thanks. -- View this message in context: http://gromacs.5086.n6.nabble.com/Selectively-choose-the-upper-and-lower-leaflets-of-a-DPPC-bilayer-tp5005134.html Sent from the GROMACS Users Forum mailing list archive at Nabble.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] protein-SWCNT md simulation
On 2/3/13 2:17 PM, Atila Petrosian wrote: Dear Justin Thanks for your reply You're specifying two force fields and hoping they will work together. You need one, unified force field that adequately describes all elements of your system. I used only one force field (amber 03) for both of protein and cnt. #include "./cnt.ff/forcefield.itp" I used cnt.ff folder for cnt in g_x2top. This folder contains 6 files: ffcnt.atp ffcnt.rtp ffcnt.n2t ffcntbon.itp ffcntnonbon.itp forcefield.itp In these files, all parameters for carbon atoms of the cnt were taken from type CA for aromatic carbon atoms in the amber 03 force field. Thus, I used a single force field. Then you should be able to properly construct everything you need within Amber03 rather than having multiple force field #include statements that are potentially conflicting or otherwise syntactically ill-formed. If my manner is incorrect, please give me more information about correct manner. How to do md simulation of the protein-cnt system by gromacs? The exact details depend upon what you want to do, but the construction of any heterogeneous protein-containing system can be done in the same way: 1. Generate protein topology (.top) with pdb2gmx 2. Create topology for other elements using g_x2top or other external software and convert them to .itp 3. Include any new topologies from step 2 into system .top (from step 1) using #include mechanism 4. Proceed with construction and equilibration -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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] Dynamics of the salt-bridges
On 2/3/13 12:36 PM, James Starlight wrote: Justin, 1 )for example I want to select in index file only all asp, glu and his residues ( I could find selection by residue type only). What you would do is create a complement to that group - keep all the Asp, Glu, and His charged and use -zeroq to remove charges on all other atoms. 2) Than I'd like that gromacs compute dynamics of the distance between that charge groups (providing only truncated .tpr file as the input) Don't use a truncated .tpr file - you'll have problems. but only. Could other than g_saltbr gromacs tools be used for that (E,g g_dist ) ? Yes, iterative calls to g_dist can easily be scripted. In that case, though, we're talking about something different - you would need each residue (or representative atoms thereof) in its own separate group to measure distances between them. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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] Dynamics of the salt-bridges
Justin, 1 )for example I want to select in index file only all asp, glu and his residues ( I could find selection by residue type only). 2) Than I'd like that gromacs compute dynamics of the distance between that charge groups (providing only truncated .tpr file as the input) but only. Could other than g_saltbr gromacs tools be used for that (E,g g_dist ) ? James 2013/2/3 Justin Lemkul : > > > On 2/3/13 1:01 AM, James Starlight wrote: >> >> Justin, >> >> thanks again for suggestions. >> >> I'm not quite sure how I can use tpbconv -zeroq. For example I want to >> reduce charges of all amino acids except Asp Glu and His ( to monitor >> s.b dynamics between that groups only). >> >> As I understood -zeroq working with the groups defined in the index >> file so I should just select all residues that I need in that file, >> shouldnt it ? Also doest it possible to select pairs of residues > > > Yes. > > >> placed in the sequence on the distant sites ? (e.g by selecting only >> pairs within some range of n1 and n2+k where k>n1+10) >> > > I don't understand what you mean. tpbconv will only take one index group > for zeroing charges, so I don't understand how such a relative scheme would > work for all cases. > > > -Justin > > -- > > > Justin A. Lemkul, Ph.D. > Research Scientist > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the www > interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] protein-SWCNT md simulation
On 2/3/13 8:20 AM, Atila Petrosian wrote: Dear gromacs users I'd like to study the interaction between carbon nanotube and a protein. I used amber03 parameters for both protein and cnt. I have made cnt.top for the nanotube by g_x2top and pr.top for protein by pdb2gmx. I made adjustments to cnt.top to become cnt.itp file to be #included in pr.top file. My cnt.top file is as follows: ; Include forcefield parameters #include "./cnt.ff/forcefield.itp" [ moleculetype ] ; Namenrexcl cnt 3 [ atoms ] . . . [ bonds ] . . . [ pairs ] . . . [ angles ] . . . [ dihedrals ] . . . [ system ] ; Name cnt [ molecules ] ; Compound#mols cnt 1 For creation the cnt.itp from cnt.top file, I deleted ; Include forcefield parameters #include "./cnt.ff/forcefield.itp" *** and *** [ system ] ; Name cnt [ molecules ] ; Compound#mols cnt 1 --- Then I added ; Include forcefield parameters #include "./cnt.ff/forcefield.itp" to the pr.top file so that first lines of pr.top are as follows: ; Include forcefield parameters #include "amber03.ff/forcefield.itp" #include "./cnt.ff/forcefield.itp" Given the information you posted in your other message, this can't work. You're specifying two force fields and hoping they will work together. You need one, unified force field that adequately describes all elements of your system. Mixing and matching is a recipe for disaster. and the end of pr.top file is as follows: ; Include Position restraint file #ifdef POSRES #include "posre.itp" #endif ; Include cnt topology #include "cnt.itp" ; Include water topology #include "amber03.ff/tip3p.itp" #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 #endif ; Include topology for ions #include "amber03.ff/ions.itp" [ system ] ; Name Protein-cnt complex [ molecules ] ; Compound#mols Protein 1 cnt 1 When I use grompp grompp -f em.mdp -c pr_cnt.gro -p pr.top -o em.tpr, grompp give me the following error message: WARNING 1 [file forcefield.itp, line 1]: Too few gb parameters for type Couldn't find topology match for atomtype Aborted Is my manner true? No, see above. How to resolve this problem? Use a single force field, and if you're running an implicit solvent simulation, be sure that all of the atomtypes have all the necessary parameters for doing so. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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] Dynamics of the salt-bridges
On 2/3/13 1:01 AM, James Starlight wrote: Justin, thanks again for suggestions. I'm not quite sure how I can use tpbconv -zeroq. For example I want to reduce charges of all amino acids except Asp Glu and His ( to monitor s.b dynamics between that groups only). As I understood -zeroq working with the groups defined in the index file so I should just select all residues that I need in that file, shouldnt it ? Also doest it possible to select pairs of residues Yes. placed in the sequence on the distant sites ? (e.g by selecting only pairs within some range of n1 and n2+k where k>n1+10) I don't understand what you mean. tpbconv will only take one index group for zeroing charges, so I don't understand how such a relative scheme would work for all cases. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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] atb topology files
hi, i want to ask which files should be selected when ligand topology is generated by prodrg server? and do they need also modification regards kalsoom -- 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] g_wham missing option
Hi Justin, Thanks for the reply. You were spot on about the version difference. Thanks again. Anthony From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Justin Lemkul [jalem...@vt.edu] Sent: 02 February 2013 18:06 To: Discussion list for GROMACS users Subject: Re: [gmx-users] g_wham missing option On 2/2/13 12:58 PM, Nash, Anthony wrote: > Hi All, > > I am using Gromacs 4.5.5 and running free energy calculations. According to > the article "g_wham - A Free Weighted Histogram.." (J. Chem. Theory. > Comput. 2010, 6, 3713-3720), there is the option -bs-method. However, I am > unable to find this option when running g_wham. I want to use bayesian > bootstraps of complete histograms. > > I have a feeling I am missing something completely obvious. Any help would be > appreciated. > Take a closer look at g_wham -h. The option you're asking about is definitely there. Also be sure you're using the version you think you are; g_wham was overhauled between 4.0.7 and 4.5. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
