[gmx-users] Convert to Sammon map
Dear All I'd like to convert a gromacs RSMD matrix (xmp) to a Sammon map. Could you give me any suggestion? Thanks-- 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] Cluster analysis
Dear all Could you give me any suggestion about how I can interpretate output result of g_cluster? Is there a detailed tutorial? Thanks-- 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] grompp error for CNT simulation
niaz poorgholami wrote: Dear gmx users, I am using gromacs 4.5.3 to simulate CNT in water. up to now I have done these things: 1. I used packmol to create my PDB file and the used editconf to change PDB to gro file. 2. I copied oplsaa.ff folder in my working directory 3. I added following lines to atomname2type.n2t Copls_9950 12.011 2C 0.142 C 0.142 Copls_9960 12.011 3C 0.142 C 0.142 C 0.142 Copls_9970 12.011 4C 0.142 C 0.142 C 0.142 C 0.142 Copls_9980 12.011 5C 0.142 C 0.142 C 0.142 C 0.142 C 0.142 4. I added these to atomtypes.atp opls_995 12.01100 opls_996 12.01100 opls_997 12.01100 opls_998 12.01100 5. I added these to ffbonded.itp [ bondtypes ] C C 1 0.14210 478900 [ angletypes ] C C C 1 120.000 397.480 [ dihedraltypes ] C C 1 0.000 167.360 1 6. I used g_x2top to create topology for CNT. Command line was: g_x2top -f CNT.gro -o CNT.top -pbc -nopairs -name CNT -nexcl 5 7. I wrote a .top file given below, ; Include forcefield parameters #include "./oplsaa.ff/forcefield.itp" ; Include topology for water #include "oplsaa.ff/spc.itp" ; Include topology for CNT #include "oplsaa.ff/CNT.itp" [ system ] ; Name SDS and CNT in water [ molecules ] ; Compound#mols water 9000 CNT 1 8. when I run grompp for EM with this command line :grompp -f md.mdp -c cnt_alone.gro -p topol.top -o em.tpr it gave me the following error:Atomtype opls_995 not found. atomtypes.atp is only read by pdb2gmx. You need to introduce the proper nonbonded parameters for your new atom types in ffnonbonded.itp. -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] Half double pair list method in GROMACS [update]
Hi Sai I am also agree with Christ, your approach seems also correct to me. But don't to forget to test your change to be sure, by doing a single point energy test as it is said in the Christ's message. Good luck Stephane -- Message: 1 Date: Fri, 02 Dec 2011 16:07:19 -0500 From: Chris Neale Subject: [gmx-users] Half double pair list method in GROMACS [update] To: gmx-users@gromacs.org Message-ID: <4ed93e07.5070...@utoronto.ca> Content-Type: text/plain; charset=ISO-8859-1; format=flowed What you have done seems alright. I didn't look closely enough to be sure though. One of the good things about this method is that you can easily test it yourself. To do this, create two different .gro files, one containing the atoms from one ff and the other containing the other atoms. For each, do separate zero-step mdrun evaluations of their energies under (a) their original ff, and (b) the combined HEDP ff that you have constructed. The energy evaluations should be the same once you account for rounding errors. Then all that is left is for you to be certain that you didn't cause any problems for nonbonded interactions. Note that you'll need to return to the original atomtypes for the first half of this test. Note that the only thing that the HEDP method is intended to perturb is the 1-4 interactions (and by perturb I mean that they will now be correct). Chris. -- original message -- Hi Stephane & Chris, I followed all the threads posted by you two. I have a protein using ff99SB and GLYCAM for sugars. I have a disaccharide bound to protein. In xleap of AMBERTOOLS, I use the GLYCAM and ff99SB to generate the topology and coordinate files. I did the tests as Chris' original posts and by Stephane. The 1-4 interaction terms match for sugar alone and protein alone with HEDP method. When I generate topology and coordinate files with xleap of AMBER, there are three atom types that are common to protein and sugar. The atom types for my case are H1, OH and HO. Since for protein pairtypes using ff99SB, the epsilon has to be divided by 10 and pairs section be replicated five times and for sugar the epsilon in the pairtypes be divided by six and replicated six times, I am a little concerned about the three atomtypes that are common. So what I did was to change the atomtypes of sugar as H1S, OHS HOS for sugar and H1, OH and HO for protein and I made the changes accordingly in the pairtypes section for protein and sugar. Is this a valid approach? Any suggestion will be helpful. To make things little more clear: H1H10. 0. A 2.47135e-01 6.56888e-02 ;originally obtained using amb2gmx.pl H1S H1S 0. 0. A 2.47135e-01 6.56888e-02 ;Glycam Hydrogen of Sugar ( I changed this so that the common atom types be separated) In the ffnonbonded_complex_mod.itp: ;;using combination rule of 2 [ pairtypes ] ;;for protein H1 H1 1 0.247135000 0.006568880 ;the epsilon is divided by 10 ;;for sugar H1S H1S 1 0.24713500 0.010948133 ;the epsilon is divided by 6 Thanks for your time, Regards Sai On Mon, Sep 5, 2011 at 11:33 AM, ABEL Stephane 175950 wrote: > Dear All, > > Below a little update and results about the application of half double > pair list method to scale properly the Coulombic 1-4 interactions in case > of a system where the AMBER99SB (fudgeLJ=0.5 and fudgeLJ=0.8333) and > GLYCAM06 (fudgeLJ=1.0 and fudgeLJ=1.0) force fields are combined. > > I have followed the 4 steps described in [1] and used the following values > in my forcefield.itp file > > [ defaults ] > ; nbfunccomb-rule gen-pairs fudgeLJ fudgeQQ > 1 2 yes 1.0 0.16 > #include "ffnonbonded_mod.itp" > ;#include "ffnonbonded.itp" > #include "ffbonded.itp" > > I used two different topology files for the glycolipid (bDM) and the > peptide. One with (*_mod.itp) with pair list parameters duplicated 6 times > (bDM) and 5 times (peptide) and with single pair list (*_no_mod.itp) as > decribed in [1]. > > TESTING: > > Three 3 different systems were examined: > > A. A first system containing 1 glycolipid (bDM) in water cubic box > B. A second system with 1 peptide in TIP3P water > C. And a third system with 1 peptide and 1 glycolipid in water cubic box > > To obtain the glycolipid and peptide energy pairs, I did one step of MD in > NVT ensemble with the *.mdp file given in [2] with different energygrps and > tc_grps. > For 1. energygrps and tc_grps = bDM SOL > For 2. energygrps and tc_grps = Protein SOL > For 3. energygrps and = Protein bDM SOL > > bDM/water system > > Test_A1 > > ## Control with GLYCAM force field fudgeLJ fudgeQQ parameters and the > *_no_mod.itp file : > ##; nbfunccomb-rule gen-pairs fudgeLJ fudgeQQ > ## 1 2 yes 1
[gmx-users] output logfile
Hi, It might be a very minor issue but I find in versions of gromacs 4.5.4, the output log file ( in verbose mode) writes the progress of the simulation in a single line ( unlike in previous gromacs 4.0.7 version) where it used to write the progress in a new lines. As a result, in gromacs4.5.4, opening a logfile or issuing unix 'tail' command to see last few lines becomes a bit time-consuming as the progress is written in a single line. An example is shown below for gromacs 4.5.4: ^Mstep 2100, will finish Sat Dec 3 19:55:12 2011vol 0.79 imb F 0% ^Mstep 2200, will finish Sat Dec 3 19:54:59 2011vol 0.80 imb F 1% ^Mstep 2300, will finish Sat Dec 3 19:54:49 2011vol 0.79 imb F 1% ^Mstep 2400, will finish Sat Dec 3 19:54:40 2011vol 0.80 imb F 0% ^Mstep 2500, will finish Sat Dec 3 19:54:31 2011vol 0.80 imb F 1% ^Mstep 2600, will finish Sat Dec 3 19:54:22 2011vol 0.80 imb F 1% ^Mstep 2700, will finish Sat Dec 3 I wonder whether there is an fix for this minor issue. Thanks Sanku -- 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] output logfile
Hi Sanku The ^M ‘s in that sample indicate a line break that was issued by a different text formatting standard. This frequently happens if files are generated in one OS say Windows then viewed in another say unix. Is your version of gromacs compiled for your system or was is compiled for a different machine/OS? Richard On 03/12/2011 19:50, "Sanku M" wrote: Hi, It might be a very minor issue but I find in versions of gromacs 4.5.4, the output log file ( in verbose mode) writes the progress of the simulation in a single line ( unlike in previous gromacs 4.0.7 version) where it used to write the progress in a new lines. As a result, in gromacs4.5.4, opening a logfile or issuing unix 'tail' command to see last few lines becomes a bit time-consuming as the progress is written in a single line. An example is shown below for gromacs 4.5.4: ^Mstep 2100, will finish Sat Dec 3 19:55:12 2011vol 0.79 imb F 0% ^Mstep 2200, will finish Sat Dec 3 19:54:59 2011vol 0.80 imb F 1% ^Mstep 2300, will finish Sat Dec 3 19:54:49 2011vol 0.79 imb F 1% ^Mstep 2400, will finish Sat Dec 3 19:54:40 2011vol 0.80 imb F 0% ^Mstep 2500, will finish Sat Dec 3 19:54:31 2011vol 0.80 imb F 1% ^Mstep 2600, will finish Sat Dec 3 19:54:22 2011vol 0.80 imb F 1% ^Mstep 2700, will finish Sat Dec 3 I wonder whether there is an fix for this minor issue. Thanks Sanku -- 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: grompp error for CNT simulation
> Dear gmx users, > I am using gromacs 4.5.3 to simulate CNT in water. up to now I have done > these things: > 1. I used packmol to create my PDB file and the used editconf to change PDB > to gro file. > 2. I copied oplsaa.ff folder in my working directory > 3. I added following lines to atomname2type.n2t > C opls_995 0 12.011 2 C 0.142 C 0.142 > C opls_996 0 12.011 3 C 0.142 C 0.142 C 0.142 > C opls_997 0 12.011 4 C 0.142 C 0.142 C 0.142 C 0.142 > C opls_998 0 12.011 5 C 0.142 C 0.142 C 0.142 C 0.142 C > 0.142 > 4. I added these to atomtypes.atp > opls_995 12.01100 > opls_996 12.01100 > opls_997 12.01100 > opls_998 12.01100 > > 5. I added these to ffbonded.itp > [ bondtypes ] > C C 1 0.14210 478900 > > [ angletypes ] > C C C 1 120.000 397.480 > > [ dihedraltypes ] > C C 1 0.000 167.360 1 > 6. I used g_x2top to create topology for CNT. > Command line was: > > g_x2top -f CNT.gro -o CNT.top -pbc -nopairs -name CNT -nexcl 5 > > 7. I wrote a .top file given below, > ; Include forcefield parameters > #include "./oplsaa.ff/forcefield.itp" > ; Include topology for water > #include "oplsaa.ff/spc.itp" > ; Include topology for CNT > #include "oplsaa.ff/CNT.itp" > > [ system ] > ; Name > SDS and CNT in water > [ molecules ] > ; Compound #mols > water 9000 > CNT 1 > 8. when I run grompp for EM with this command line :grompp -f md.mdp -c > cnt_alone.gro -p topol.top -o em.tpr > it gave me the following error:Atomtype opls_995 not found. > I would be pleased if anyone could help me how to fix this. Maybe the non-found atomtype is really absent? On the gromacs website, there should be some examples for the CNT topologies based on the GROMOS FF. Independently, check your angles once again. It seems, there should be more angles which are to be defined for a tube. Dr. Vitaly V. Chaban, 430 Hutchison Hall, Chem. Dept. Univ. Rochester, Rochester, New York 14627-0216 THE UNITED STATES OF AMERICA -- 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] Convert xpm to matrix
Dear all, I'd like to convert an xpm file to delimited CSV , because I need to import values in excel. Any suggestion? Thanks-- 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
