[gmx-users] shear viscosity
Dear users, g_energy -f *.edr -vis I have two questions about the results of eviscoi.xvg ( derivative of Einstein relation): 1.) I dont understand the unit of y-axis. It is kg.m^(-1).s^(-1).10^(-3) in "B.Hess 2002" In eviscoi.xvg @yaxis label "(kg m\S-1\N s\S-1\N ps)" That is The unit of y-axis:kg.m^(-1).s^(-1).ps What is that? kg.m^(-1).s^(-1).ps equals to kg.m^(-1).s^(-1).10^(-3)? 2.) There are 5 columns in eviscoi.xvg. 1th is time. What are the rest? By the way, there is 216 water molecules in spc216.gro. But I want to calculate the shear viscosity of 512 water molecules. How can I get/derive 512 water molecules from spc216.gro? Can anyone give me some hint of this? Thanks in advance -- Ahmet Yıldırım -- 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: extreme projections
any one please help me out with this problem? 2013/7/10 Ahmet yıldırım > Dear users, > > I extracted separate extreme projections using g_anaeig. I have to make > pictures which show the difference. Can you help me, someone who makesthem > using pymolbefore > ? > > -- > Ahmet Yıldırım > -- Ahmet Yıldırım -- 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] Figures of PCA analysis
Can anybody help me understand these better? 2013/7/10 lloyd riggs > There vectors. Theres some good older papers explaining the whole thing > from Van Gunstern, Berendsen, and some other good ones from de Groot that > explain them well and includes combining them with other data analysis > types, but I dont remeber the actual publications. A few are in the mid > 1990's, however these explain PCA better than some of the newer ones...but > some extensive reading...or text books from van guntstern and/or Berendsen > explain the whole thing well, from the math to the actual "what it means" > aspect. > > *Gesendet:* Mittwoch, 10. Juli 2013 um 14:46 Uhr > *Von:* "Ahmet yıldırım" > *An:* "Discussion list for GROMACS users" > *Betreff:* [gmx-users] Figures of PCA analysis > Dear users, > > I have a few questions about PCA analysis. I see the figures below in the > most > of the publications: > 1.) Figure:Eigenvalues along the eigenvectors > This figure gives contribution of eigenvalues along the eigenvectors to the > overall motion of the protein??? > 2.) Figure:the projection of the MD trajectories onto the first ten > principal components > This figure gives contribution of the first 10 eigenvectors to the overall > motion of the protein??? > 3.)The projection of the MD trajectories onto the plane of the first and > the second principal components > This figure gives knowledge about conformational spaces of structures??? > > Which one gives information about the motion of the structure? > Can anyone explain to me in detail what these figure are? > -- > Ahmet Yıldırım > -- > 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 > > -- > 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 > -- Ahmet Yıldırım -- 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] extreme projections
Dear users, I extracted separate extreme projections using g_anaeig. I have to make pictures which show the difference. Can you help me, someone who makes them using pymol before? -- Ahmet Yıldırım -- 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] Figures of PCA analysis
Dear users, I have a few questions about PCA analysis. I see the figures below in the most of the publications: 1.) Figure:Eigenvalues along the eigenvectors This figure gives contribution of eigenvalues along the eigenvectors to the overall motion of the protein??? 2.) Figure:the projection of the MD trajectories onto the first ten principal components This figure gives contribution of the first 10 eigenvectors to the overall motion of the protein??? 3.)The projection of the MD trajectories onto the plane of the first and the second principal components This figure gives knowledge about conformational spaces of structures??? Which one gives information about the motion of the structure? Can anyone explain to me in detail what these figure are? -- Ahmet Yıldırım -- 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: rotation of a ligand
Dear users, I tried to calculate the order parameter of benzene ring of the ligand using g_order but I have a error as the following : make_ndx -f topol.tpr -o order.xvg > a C1 C2 C3 C4 C5 C6 Found 6 atoms with names C1 C2 C3 C4 C5 C6 26 C1_C2_C3_C4_C5_C6 : 6 atoms >q g_order -f traj.xtc -s topol.tpr -n order.ndx -order.xvg Fatal error: grp 1 does not have same number of elements as grp 1 What should I do? 2013/5/3 Ahmet yıldırım > Dear users, > > I have a ligand bound to protein. How can I calculate how much this > ligand is rotated during the simulation time? Which tool should I use? > g_order, g_chi, g_dih? > > Thanks in advance > > -- > Ahmet Yıldırım > -- Ahmet Yıldırım -- 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] rotation of a ligand
Dear users, I have a ligand bound to protein. How can I calculate how much this ligand is rotated during the simulation time? Which tool should I use? g_order, g_chi, g_dih? Thanks in advance -- Ahmet Yıldırım -- 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_analyze error bar
First column is time, second is rmsd value and third column is 0. average.xvg 10 0.3123 0 20 0.3256 0 30 0.3981 0 40 0.3512 0 50 0.3754 0 ... 2013/4/16 Justin Lemkul > > > > On 4/16/13 4:26 PM, Ahmet yıldırım wrote: >> >> Dear users, >> >> g_analyze -f rmsd.xvg -av average.xvg -errbar stddev >> Unfortunately, this command didn't produce the error bar >> How can I obtain error bar for plotting? >> > > Works fine for me. Perhaps you're just not plotting average.xvg correctly. Import as XYDY. > > -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 -- Ahmet Yıldırım -- 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_analyze error bar
Dear users, g_analyze -f rmsd.xvg -av average.xvg -errbar stddev Unfortunately, this command didn't produce the error bar How can I obtain error bar for plotting? Thanks in advance -- Ahmet Yıldırım -- 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: thermal conductivity,specific heat,enthalpy
Dear Prof. Spoel, Firstly, thanks for your reply. I looked at the paper your said. 1.) To calculate the density d in a constant pressure simulation (in npt simulation): d=M/ equation (5) M: mass of the system V:volume of the system Doesnt this formula (equation 5) use when Gromacs calculates the density of system? 2.) The classical-that is, without any quantum corrections-heat capacity cP can be obtained from the fluctuations in the enthalpy (from your paper): cP=/(kB.T^2) (equation 13) How did you calculate ? 3.)You said before " http://www.mail-archive.com/gmx-users@gromacs.org/msg37580.html"; cP = ( - ^2)/kB T^2 (NPT sim) This formula doesn't equal to equation 13. There isnt ^2 term in equation 13. Why? Thanks in advance 2013/4/12 David van der Spoel > On 2013-04-11 22:20, Ahmet yıldırım wrote: > >> could anybody help me please? >> > Check > http://pubs.acs.org/doi/abs/**10.1021/ct200731v<http://pubs.acs.org/doi/abs/10.1021/ct200731v> > > >> >> 2013/4/11 Ahmet yıldırım >> >> Dear users, >>> >>> I calculated diffusion constant of a substance using g_msd tool. I also >>> want to calculate thermal conductivity its. By the way,I did npt >>> simulation. >>> >>> Diffusion constant=alpha >>> Thermal conductivity=k >>> specific heat=Cp >>> density=d >>> alpha=k/(d.Cp) >>> and >>> k=alpha.d.Cp >>> I need d and Cp to calculate k. >>> >>> 1.) To calculate Cp: >>> Prof. Spoel:From >>> http://www.mail-archive.com/**gmx-users@gromacs.org/**msg37580.html<http://www.mail-archive.com/gmx-users@gromacs.org/msg37580.html> >>> >>> cP = ( - ^2)/kB T^2 (NPT sim) >>> >>> The .edr file gives average enthalpy . According to above formula, I >>> need both H and . How can I get H (not average)? >>> 2.) .edr file: >>>1 LJ-(SR) 2 LJ-(LR) 3 Coulomb-(SR) 4 >>> Coul.-recip. >>>5 Potential6 Kinetic-En. 7 Total-Energy 8 >>> Temperature >>>9 Pressure10 Box-X 11 Box-Y 12 >>> Box-Z >>> 13 Volume 14 Density 15 pV 16 >>> Enthalpy >>> 17 Vir-XX 18 Vir-XY 19 Vir-XZ 20 >>> Vir-YX >>> 21 Vir-YY 22 Vir-YZ 23 Vir-ZX 24 >>> Vir-ZY >>> 25 Vir-ZZ 26 Pres-XX 27 Pres-XY 28 >>> Pres-XZ >>> 29 Pres-YX 30 Pres-YY 31 Pres-YZ 32 >>> Pres-ZX >>> 33 Pres-ZY 34 Pres-ZZ 35 #Surf*SurfTen 36 >>> Mu-X >>> 37 Mu-Y38 Mu-Z39 T-System40 >>> Lamb-System >>> Firstly I calculated Entalphy (16) >>> Afterward I calculated both Etot (7) and pV (15) >>> Enthalpy=Etot+pV >>> Unfortunately, I get "Enthalpy isnt equals to Etot+pV". Why? >>> >>> >>> -- >>> Ahmet Yıldırım >>> >>> >> >> >> > > -- > David van der Spoel, Ph.D., Professor of Biology > Dept. of Cell & Molec. Biol., Uppsala University. > Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. > sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se > -- > gmx-users mailing listgmx-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. > * Can't post? Read > http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> > -- Ahmet Yıldırım -- 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] tip5p water model:Atomtype LP1 not found
The norm of force is very high. And the system converged in 3 steps For example, I got the following results for spc water model Steepest Descents converged to Fmax < 1000 in 167 steps Potential Energy = -2.1208019e+05 Maximum force = 9.8452704e+02 on atom 286 Norm of force = 4.9830578e+01 2013/4/15 Justin Lemkul > > > On 4/15/13 7:22 AM, Ahmet yıldırım wrote: > >> I did as you said. I corrected number of water molecules in the topology >> by >> hand. >> >> grompp -v -f minim.mdp -c protein-water.gro -p topol.top -o >> protein-water.tpr >> Steepest Descents converged to Fmax < 1000 in 3 steps >> Potential Energy = -1.5700267e+05 >> Maximum force = 7.2195142e+02 on atom 3761 >> Norm of force = 1.3341200e+02 >> >> I think these results isnt normal. isnt it? >> >> > What exactly do you think is wrong? > > > -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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> > > ==**== > -- > gmx-users mailing listgmx-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. > * Can't post? Read > http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> > -- Ahmet Yıldırım -- 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] tip5p water model:Atomtype LP1 not found
I did as you said. I corrected number of water molecules in the topology by hand. grompp -v -f minim.mdp -c protein-water.gro -p topol.top -o protein-water.tpr Steepest Descents converged to Fmax < 1000 in 3 steps Potential Energy = -1.5700267e+05 Maximum force = 7.2195142e+02 on atom 3761 Norm of force = 1.3341200e+02 I think these results isnt normal. isnt it? 2013/4/15 Justin Lemkul > > > On 4/15/13 6:58 AM, Ahmet yıldırım wrote: > >> I have the following files in directory >> 1.tip5p.gro >> 2.topol.top >> 3.em.mdp >> >> topol.top: >> #include "oplsaa.ff/forcefield.itp" >> #include "oplsaa.ff/tip5p.itp" >> >> [ system ] >> water >> >> [ molecules ] >> SOL 512 >> >> commands: >> editconf -f tip5p.gro -o protein-PBC.gro -bt cubic -d 1.0 >> genbox -cp protein-PBC.gro -cs tip5p.gro -p topol.top -o protein-water.gro >> >> topol.top after genbox command: >> #include "oplsaa.ff/forcefield.itp" >> #include "oplsaa.ff/tip5p.itp" >> >> [ system ] >> water >> >> [ molecules ] >> >> grompp -v -f minim.mdp -c protein-water.gro -p topol.top -o >> protein-water.tpr >> Fatal error: >> No molecules were defined in the system >> >> There isnt the number of water molecules in topol.top after genbox >> command. >> I dont understand why they have been deleted. >> >> > I cannot reproduce this problem with version 4.6, but it's trivial to just > add the correct number of water molecules in the topology by hand. > > > -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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> > > ==**== > -- > gmx-users mailing listgmx-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. > * Can't post? Read > http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> > -- Ahmet Yıldırım -- 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] tip5p water model:Atomtype LP1 not found
I have the following files in directory 1.tip5p.gro 2.topol.top 3.em.mdp topol.top: #include "oplsaa.ff/forcefield.itp" #include "oplsaa.ff/tip5p.itp" [ system ] water [ molecules ] SOL 512 commands: editconf -f tip5p.gro -o protein-PBC.gro -bt cubic -d 1.0 genbox -cp protein-PBC.gro -cs tip5p.gro -p topol.top -o protein-water.gro topol.top after genbox command: #include "oplsaa.ff/forcefield.itp" #include "oplsaa.ff/tip5p.itp" [ system ] water [ molecules ] grompp -v -f minim.mdp -c protein-water.gro -p topol.top -o protein-water.tpr Fatal error: No molecules were defined in the system There isnt the number of water molecules in topol.top after genbox command. I dont understand why they have been deleted. 2013/4/11 Justin Lemkul > On Thu, Apr 11, 2013 at 9:27 AM, Ahmet yıldırım > wrote: > > > I am simulating tip5p water. I got tip5p.gro from $GMXLIB > > 1.) editconf -f tip5p.gro -o protein.pdb > > 2.) pdb2gmx -f protein.pdb -o protein.gro -p protein.top > > > > 14 (OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)) > > > > Select the Water Model: > > 1: TIP4P TIP 4-point, recommended > > 2: TIP3P TIP 3-point > > 3: TIP5P TIP 5-point > > 4: SPCsimple point charge > > 5: SPC/E extended simple point charge > > 6: None > > > > 3 (TIP5P TIP 5-point) > > > > 3.) editconf -f protein.gro -o protein-PBC.gro -bt cubic -d 1.0 > > 4.) genbox -cp protein-PBC.gro -cs tip5p.gro -p protein.top -o > > protein-water.gro > > 5.) grompp -v -f minim.mdp -c protein-water.gro -p protein.top -o > > protein-water.tpr > > Fatal error: > > number of coordinates in coordinate file (protein-water.gro, 37090) > > does not match topology (protein.top, 34530) > > > > > > > What does the [molecules] directive of your .top say? In principle, most of > the steps carried out above are unnecessary. You've got pure water, so the > topology is easy: > > #include "oplsaa.ff/forcefield.itp" > #include "oplsaa.ff/tip5p.itp" > > [ system ] > water > > [ molecules ] > SOL X > > ...where X is the number of water molecules. > > -Justin > > -- > > > > Justin A. Lemkul, Ph.D. > Research Scientist > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) > 231-9080http://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 > -- Ahmet Yıldırım -- 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: thermal conductivity,specific heat,enthalpy
could anybody help me please? 2013/4/11 Ahmet yıldırım > Dear users, > > I calculated diffusion constant of a substance using g_msd tool. I also > want to calculate thermal conductivity its. By the way,I did npt simulation. > > Diffusion constant=alpha > Thermal conductivity=k > specific heat=Cp > density=d > alpha=k/(d.Cp) > and > k=alpha.d.Cp > I need d and Cp to calculate k. > > 1.) To calculate Cp: > Prof. Spoel:From > http://www.mail-archive.com/gmx-users@gromacs.org/msg37580.html > > cP = ( - ^2)/kB T^2 (NPT sim) > > The .edr file gives average enthalpy . According to above formula, I > need both H and . How can I get H (not average)? > 2.) .edr file: > 1 LJ-(SR) 2 LJ-(LR) 3 Coulomb-(SR) 4 > Coul.-recip. > 5 Potential6 Kinetic-En. 7 Total-Energy 8 > Temperature > 9 Pressure10 Box-X 11 Box-Y 12 > Box-Z > 13 Volume 14 Density 15 pV 16 > Enthalpy > 17 Vir-XX 18 Vir-XY 19 Vir-XZ 20 > Vir-YX > 21 Vir-YY 22 Vir-YZ 23 Vir-ZX 24 > Vir-ZY > 25 Vir-ZZ 26 Pres-XX 27 Pres-XY 28 > Pres-XZ > 29 Pres-YX 30 Pres-YY 31 Pres-YZ 32 > Pres-ZX > 33 Pres-ZY 34 Pres-ZZ 35 #Surf*SurfTen 36 > Mu-X > 37 Mu-Y38 Mu-Z39 T-System40 > Lamb-System > Firstly I calculated Entalphy (16) > Afterward I calculated both Etot (7) and pV (15) > Enthalpy=Etot+pV > Unfortunately, I get "Enthalpy isnt equals to Etot+pV". Why? > > > -- > Ahmet Yıldırım > -- Ahmet Yıldırım -- 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] tip5p water model:Atomtype LP1 not found
I am simulating tip5p water. I got tip5p.gro from $GMXLIB 1.) editconf -f tip5p.gro -o protein.pdb 2.) pdb2gmx -f protein.pdb -o protein.gro -p protein.top 14 (OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)) Select the Water Model: 1: TIP4P TIP 4-point, recommended 2: TIP3P TIP 3-point 3: TIP5P TIP 5-point 4: SPCsimple point charge 5: SPC/E extended simple point charge 6: None 3 (TIP5P TIP 5-point) 3.) editconf -f protein.gro -o protein-PBC.gro -bt cubic -d 1.0 4.) genbox -cp protein-PBC.gro -cs tip5p.gro -p protein.top -o protein-water.gro 5.) grompp -v -f minim.mdp -c protein-water.gro -p protein.top -o protein-water.tpr Fatal error: number of coordinates in coordinate file (protein-water.gro, 37090) does not match topology (protein.top, 34530) 2013/4/11 Justin Lemkul > On Thu, Apr 11, 2013 at 7:28 AM, Ahmet yıldırım > wrote: > > > There isnt tip5p.itp and tip5p.gro at newer versions of Gromacs. I > couldnt > > find them > > > > > They're there. The tip5p.gro file is in $GMXLIB and tip5p.itp is in several > force field subdirectories. > > $ ls -l *.ff/tip5p.itp > -rw-r--r-- 1 jalemkul jalemkul 1870 Nov 27 20:24 amber03.ff/tip5p.itp > -rw-r--r-- 1 jalemkul jalemkul 1870 Nov 27 20:24 amber94.ff/tip5p.itp > -rw-r--r-- 1 jalemkul jalemkul 1870 Nov 27 20:24 amber96.ff/tip5p.itp > -rw-r--r-- 1 jalemkul jalemkul 1870 Nov 27 20:24 amber99.ff/tip5p.itp > -rw-r--r-- 1 jalemkul jalemkul 1870 Nov 27 20:24 amber99sb.ff/tip5p.itp > -rw-r--r-- 1 jalemkul jalemkul 1870 Nov 27 20:24 > amber99sb-ildn.ff/tip5p.itp > -rw-r--r-- 1 jalemkul jalemkul 1870 Nov 27 20:24 amberGS.ff/tip5p.itp > -rw-r--r-- 1 jalemkul jalemkul 1870 Nov 27 20:24 charmm27.ff/tip5p.itp > -rw-r--r-- 1 jalemkul jalemkul 1434 Nov 27 20:24 oplsaa.ff/tip5p.itp > > -Justin > > > > > > 2013/4/11 Justin Lemkul > > > > > On Thu, Apr 11, 2013 at 7:12 AM, Ahmet yıldırım > > > wrote: > > > > > > > I am simulating tip5p water. I found tip5p.gro and tip5p.itp files > from > > > > gromacs 4.0.7. are they wrong? > > > > > > > > > > > Well, they trigger a fatal error... > > > > > > Yes, they are wrong and newer versions of Gromacs are correct. > > > > > > -Justin > > > > > > > > > > > > > > 2013/4/11 Justin Lemkul > > > > > > > > > On Thu, Apr 11, 2013 at 6:52 AM, Ahmet yıldırım < > ahmedo...@gmail.com > > > > > > > > wrote: > > > > > > > > > > > Dear Justin, > > > > > > > > > > > > I copied to gmx.ff it. You know the tip5p shows the general shape > > of > > > > the > > > > > > 5-site water models but the spc shows the general shape of the > > 3-site > > > > > water > > > > > > models. Therefore I need tip5p.itp. > > > > > > > > > > > > > > > > Is there going to be a protein in the system, as well? If so, > gmx.ff > > > is a > > > > > poor choice and I would still maintain that despite any possible > > > > > improvement in water model (and none of them are perfect), it's > not a > > > > > proper combination. If you're simulating pure water, the choice of > > > parent > > > > > force field is largely irrelevant. > > > > > > > > > > > > > > > > How can you get it? > > > > > > > > > > > > > > > > > I have no idea why your tip5p.itp is wrong. The atom type should be > > MW > > > > for > > > > > both LP1 and LP2, as I said before. Fix the atom types and the > > problem > > > > > should go away. > > > > > > > > > > -Justin > > > > > > > > > > > > > > > > > > > > > > 2013/4/11 Justin Lemkul > > > > > > > > > > > > > On Thu, Apr 11, 2013 at 1:56 AM, Ahmet yıldırım < > > > ahmedo...@gmail.com > > > > > > > > > > > > wrote: > > > > > > > > > > > > > > > Dear users, > > > > > > > > > > > > > > > > I am trying MD simulation of tip5p water model. I am getting > > > Fatal > > > > > > > > Error:Atomtype LP1 not found. > > > > > > > > There isnt LP in atomtypes.atp file. Which one corresponds to > > LP1 > > > > and > &g
Re: [gmx-users] tip5p water model:Atomtype LP1 not found
There isnt tip5p.itp and tip5p.gro at newer versions of Gromacs. I couldnt find them 2013/4/11 Justin Lemkul > On Thu, Apr 11, 2013 at 7:12 AM, Ahmet yıldırım > wrote: > > > I am simulating tip5p water. I found tip5p.gro and tip5p.itp files from > > gromacs 4.0.7. are they wrong? > > > > > Well, they trigger a fatal error... > > Yes, they are wrong and newer versions of Gromacs are correct. > > -Justin > > > > > > 2013/4/11 Justin Lemkul > > > > > On Thu, Apr 11, 2013 at 6:52 AM, Ahmet yıldırım > > > wrote: > > > > > > > Dear Justin, > > > > > > > > I copied to gmx.ff it. You know the tip5p shows the general shape of > > the > > > > 5-site water models but the spc shows the general shape of the 3-site > > > water > > > > models. Therefore I need tip5p.itp. > > > > > > > > > > Is there going to be a protein in the system, as well? If so, gmx.ff > is a > > > poor choice and I would still maintain that despite any possible > > > improvement in water model (and none of them are perfect), it's not a > > > proper combination. If you're simulating pure water, the choice of > parent > > > force field is largely irrelevant. > > > > > > > > > > How can you get it? > > > > > > > > > > > I have no idea why your tip5p.itp is wrong. The atom type should be MW > > for > > > both LP1 and LP2, as I said before. Fix the atom types and the problem > > > should go away. > > > > > > -Justin > > > > > > > > > > > > > > 2013/4/11 Justin Lemkul > > > > > > > > > On Thu, Apr 11, 2013 at 1:56 AM, Ahmet yıldırım < > ahmedo...@gmail.com > > > > > > > > wrote: > > > > > > > > > > > Dear users, > > > > > > > > > > > > I am trying MD simulation of tip5p water model. I am getting > Fatal > > > > > > Error:Atomtype LP1 not found. > > > > > > There isnt LP in atomtypes.atp file. Which one corresponds to LP1 > > and > > > > LP2 > > > > > > atoms in atomtypes.atp file? > > > > > > (I am using Gromacs 4.5.5) > > > > > > > > > > > > > > > > > > usr/share/gromacs/top/gmx.ff/tip5p.itp > > > > > > ... > > > > > > [ atoms ] > > > > > > ; idat type res nr residu name at name cg nr > > > charge > > > > > > 1 OW1 SOL OW 1 > > > 0 > > > > > > 2 HW1 1 SOL HW1 > 1 > > > > > > 0.241 > > > > > > 3 HW2 1 SOL HW2 1 > > > > > 0.241 > > > > > > 4 LP1 1 SOL LP1 1 > > > > > -0.241 > > > > > > 5 LP2 1 SOL LP2 1 > > > > > -0.241 > > > > > > > > > > > > > > > > > > > > > > > It looks like someone has erroneously modified your files. The > TIP5P > > > > model > > > > > should not be included in gmx.ff (Gromos force fields should be > used > > > with > > > > > SPC), and the atom type for both LP1 and LP2 should be MW. > > > > > > > > > > -Justin > > > > > > > > > > -- > > > > > > > > > > > > > > > > > > > > Justin A. Lemkul, Ph.D. > > > > > Research Scientist > > > > > Department of Biochemistry > > > > > Virginia Tech > > > > > Blacksburg, VA > > > > > jalemkul[at]vt.edu | (540) > > > > > 231-9080http://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 l
Re: [gmx-users] tip5p water model:Atomtype LP1 not found
I am simulating tip5p water. I found tip5p.gro and tip5p.itp files from gromacs 4.0.7. are they wrong? 2013/4/11 Justin Lemkul > On Thu, Apr 11, 2013 at 6:52 AM, Ahmet yıldırım > wrote: > > > Dear Justin, > > > > I copied to gmx.ff it. You know the tip5p shows the general shape of the > > 5-site water models but the spc shows the general shape of the 3-site > water > > models. Therefore I need tip5p.itp. > > > > Is there going to be a protein in the system, as well? If so, gmx.ff is a > poor choice and I would still maintain that despite any possible > improvement in water model (and none of them are perfect), it's not a > proper combination. If you're simulating pure water, the choice of parent > force field is largely irrelevant. > > > > How can you get it? > > > > > I have no idea why your tip5p.itp is wrong. The atom type should be MW for > both LP1 and LP2, as I said before. Fix the atom types and the problem > should go away. > > -Justin > > > > > > 2013/4/11 Justin Lemkul > > > > > On Thu, Apr 11, 2013 at 1:56 AM, Ahmet yıldırım > > > wrote: > > > > > > > Dear users, > > > > > > > > I am trying MD simulation of tip5p water model. I am getting Fatal > > > > Error:Atomtype LP1 not found. > > > > There isnt LP in atomtypes.atp file. Which one corresponds to LP1 and > > LP2 > > > > atoms in atomtypes.atp file? > > > > (I am using Gromacs 4.5.5) > > > > > > > > > > > > usr/share/gromacs/top/gmx.ff/tip5p.itp > > > > ... > > > > [ atoms ] > > > > ; idat type res nr residu name at name cg nr > charge > > > > 1 OW1 SOL OW 1 > 0 > > > > 2 HW1 1 SOL HW1 1 > > > > 0.241 > > > > 3 HW2 1 SOL HW2 1 > > > 0.241 > > > > 4 LP1 1 SOL LP1 1 > > > -0.241 > > > > 5 LP2 1 SOL LP2 1 > > > -0.241 > > > > > > > > > > > > > > > It looks like someone has erroneously modified your files. The TIP5P > > model > > > should not be included in gmx.ff (Gromos force fields should be used > with > > > SPC), and the atom type for both LP1 and LP2 should be MW. > > > > > > -Justin > > > > > > -- > > > > > > > > > > > > Justin A. Lemkul, Ph.D. > > > Research Scientist > > > Department of Biochemistry > > > Virginia Tech > > > Blacksburg, VA > > > jalemkul[at]vt.edu | (540) > > > 231-9080http://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 > > > > > > > > > > > -- > > Ahmet Yıldırım > > -- > > 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 > > > > > > -- > > > > Justin A. Lemkul, Ph.D. > Research Scientist > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) > 231-9080http://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 > -- Ahmet Yıldırım -- 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] tip5p water model:Atomtype LP1 not found
Dear Justin, I copied to gmx.ff it. You know the tip5p shows the general shape of the 5-site water models but the spc shows the general shape of the 3-site water models. Therefore I need tip5p.itp. How can you get it? 2013/4/11 Justin Lemkul > On Thu, Apr 11, 2013 at 1:56 AM, Ahmet yıldırım > wrote: > > > Dear users, > > > > I am trying MD simulation of tip5p water model. I am getting Fatal > > Error:Atomtype LP1 not found. > > There isnt LP in atomtypes.atp file. Which one corresponds to LP1 and LP2 > > atoms in atomtypes.atp file? > > (I am using Gromacs 4.5.5) > > > > > > usr/share/gromacs/top/gmx.ff/tip5p.itp > > ... > > [ atoms ] > > ; idat type res nr residu name at name cg nr charge > > 1 OW1 SOL OW 1 0 > > 2 HW1 1 SOL HW1 1 > > 0.241 > > 3 HW2 1 SOL HW2 1 > 0.241 > > 4 LP1 1 SOL LP1 1 > -0.241 > > 5 LP2 1 SOL LP2 1 > -0.241 > > > > > > > It looks like someone has erroneously modified your files. The TIP5P model > should not be included in gmx.ff (Gromos force fields should be used with > SPC), and the atom type for both LP1 and LP2 should be MW. > > -Justin > > -- > > > > Justin A. Lemkul, Ph.D. > Research Scientist > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) > 231-9080http://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 > -- Ahmet Yıldırım -- 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] thermal conductivity,specific heat,enthalpy
Dear users, I calculated diffusion constant of a substance using g_msd tool. I also want to calculate thermal conductivity its. By the way,I did npt simulation. Diffusion constant=alpha Thermal conductivity=k specific heat=Cp density=d alpha=k/(d.Cp) and k=alpha.d.Cp I need d and Cp to calculate k. 1.) To calculate Cp: Prof. Spoel:From http://www.mail-archive.com/gmx-users@gromacs.org/msg37580.html cP = ( - ^2)/kB T^2 (NPT sim) The .edr file gives average enthalpy . According to above formula, I need both H and . How can I get H (not average)? 2.) .edr file: 1 LJ-(SR) 2 LJ-(LR) 3 Coulomb-(SR) 4 Coul.-recip. 5 Potential6 Kinetic-En. 7 Total-Energy 8 Temperature 9 Pressure10 Box-X 11 Box-Y 12 Box-Z 13 Volume 14 Density 15 pV 16 Enthalpy 17 Vir-XX 18 Vir-XY 19 Vir-XZ 20 Vir-YX 21 Vir-YY 22 Vir-YZ 23 Vir-ZX 24 Vir-ZY 25 Vir-ZZ 26 Pres-XX 27 Pres-XY 28 Pres-XZ 29 Pres-YX 30 Pres-YY 31 Pres-YZ 32 Pres-ZX 33 Pres-ZY 34 Pres-ZZ 35 #Surf*SurfTen 36 Mu-X 37 Mu-Y38 Mu-Z39 T-System40 Lamb-System Firstly I calculated Entalphy (16) Afterward I calculated both Etot (7) and pV (15) Enthalpy=Etot+pV Unfortunately, I get "Enthalpy isnt equals to Etot+pV". Why? -- Ahmet Yıldırım -- 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] tip5p water model:Atomtype LP1 not found
Dear users, I am trying MD simulation of tip5p water model. I am getting Fatal Error:Atomtype LP1 not found. There isnt LP in atomtypes.atp file. Which one corresponds to LP1 and LP2 atoms in atomtypes.atp file? (I am using Gromacs 4.5.5) usr/share/gromacs/top/gmx.ff/tip5p.itp ... [ atoms ] ; idat type res nr residu name at name cg nr charge 1 OW1 SOL OW 1 0 2 HW1 1 SOL HW1 1 0.241 3 HW2 1 SOL HW2 1 0.241 4 LP1 1 SOL LP1 1 -0.241 5 LP2 1 SOL LP2 1 -0.241 -- Ahmet Yıldırım -- 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] water models tip3p.gro and spce.gro
Dear users, I will run MD simulations of all water models in Gromacs. I need spce.gro and tip3p.gro files. How can I find them? Thanks in advance -- Ahmet Yıldırım -- 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: diffusion constant level off
- Expected values are estimated. For example İf the structure is reach to converge at last 100 ns ( all simulation time is 200 ns), then in theory, diffusion coefficients will dont change at last 100 ns. -I have only one diffusion coefficient for each 10 ns. I have 20 diffusion coefficients during all simulation time. -I controlled all msd.xvg. They are linear. The plot I sent is diffusion versus time. (Please see it again). It isnt msd vs time - I tried to increase sampling. The results are same approximately. Commands for trestart to 1000 ps: Command for 1.diffusion:g_msd -f traj.xtc -s topol.top -o msd1.xvg -trestart 1000 -beginfit -1 -endfit -1 -b 0 -e 1 # D[ Protein] = 0.1091 (+/- 0.0212) (1e-5 cm^2/s)=13.line from msd.xvg Command for 2.diffusion:g_msd -f traj.xtc -s topol.top -o msd2.xvg -trestart 1000 -beginfit -1 -endfit -1 -b 1 -e 2 # D[ Protein] = 0.0679(+/- 0.0013) (1e-5 cm^2/s) Command for 1.diffusion:g_msd -f traj.xtc -s topol.top -o msd3.xvg -trestart 1000 -beginfit -1 -endfit -1 -b 2 -e 3 ... Command for 3.diffusion:g_msd -f traj.xtc -s topol.top -o msd20.xvg -trestart 1000 -beginfit -1 -endfit -1 -b 19 -e 20 2013/3/29 Justin Lemkul > > > On 3/28/13 7:56 PM, Dr. Vitaly Chaban wrote: > >> The simplest advice is to increase sampling. >> >> > I think the OP needs to describe what the system is in greater detail. > For a simple liquid, I would opine that 200 ns is normally vast overkill. > For a membrane, it may not be enough. There's just no way to say. > > -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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> > > ==**== > -- > gmx-users mailing listgmx-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. > * Can't post? Read > http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> > -- Ahmet Yıldırım -- 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: diffusion constant level off
Please see plot: http://imageshack.us/photo/my-images/35/diffusion.png/ 2013/3/28 Justin Lemkul > On Thu, Mar 28, 2013 at 9:59 AM, Ahmet yıldırım > wrote: > > > Dear users, > > > > Again, I have strange results (for 10,50,100,150,200 ns). I am wondering, > > is there a bug with g_msd? > > > > > I see no evidence for a bug, and you should avoid such speculation unless > you know exactly how the program should behave. Only then, after an > analysis of known quantities or behavior, can we discuss bugginess. Do you > know how g_msd works? Do you know what all of the flags are doing, or are > you just making adjustments hoping for clarity? You may find the following > post very illuminating: > > http://lists.gromacs.org/pipermail/gmx-users/2010-July/052512.html > > -Justin > > > > Commands for trestart to 20 ps: > > g_msd -f traj.xtc -s topol.top -o msd1.xvg -trestart 20 -beginfit -1 > > -endfit -1 -b 0 -e 1 > > g_msd -f traj.xtc -s topol.top -o msd2.xvg -trestart 20 -beginfit -1 > > -endfit -1 -b 1 -e 2 > > g_msd -f traj.xtc -s topol.top -o msd3.xvg -trestart 20 -beginfit -1 > > -endfit -1 -b 2 -e 3 > > ... > > g_msd -f traj.xtc -s topol.top -o msd20.xvg -trestart 20 -beginfit -1 > > -endfit -1 -b 19 -e 20 > > > > Commands for trestart to 1000 ps: > > g_msd -f traj.xtc -s topol.top -o msd1.xvg -trestart 1000 -beginfit -1 > > -endfit -1 -b 0 -e 1 > > g_msd -f traj.xtc -s topol.top -o msd2.xvg -trestart 1000 -beginfit -1 > > -endfit -1 -b 1 -e 2 > > g_msd -f traj.xtc -s topol.top -o msd3.xvg -trestart 1000 -beginfit -1 > > -endfit -1 -b 2 -e 3 > > ... > > g_msd -f traj.xtc -s topol.top -o msd20.xvg -trestart 1000 -beginfit -1 > > -endfit -1 -b 19 -e 20 > > > > > > D1 (cm^2/s):Diffusion for trestart to 20 ps > > D2 (cm^2/s):Diffusion for trestart to 1000 ps > > Time (ns) D1 D2 > > 10 0.1616 0.1091 > > 20 0.0735 0.0679 > > 30 0.0775 0.0705 > > 40 0.1097 0.1189 > > 50 0.1471 0.1436 > > 60 0.0468 0.048 > > 70 0.0667 0.0652 > > 80 0.0727 0.086 > > 90 0.0664 0.0707 > > 100 0.1336 0.114 > > 110 0.0899 0.0841 > > 120 0.0572 0.0598 > > 130 0.0506 0.0482 > > 140 0.0723 0.0767 > > 150 0.1466 0.1439 > > 160 0.0703 0.0601 > > 170 0.081 0.0853 > > 180 0.0278 0.027 > > 190 0.1121 0.1024 > > 200 0.3136 0.2981 > > > > > > 2013/3/28 Dr. Vitaly Chaban > > > > > > > > > > > if I do as you said, I will get only one diffusion coefficient. I > want > > to > > > > calculate one diffusion coefficient for each 10 > > > > ns of the simulation time of 200 ns. That is, I want to get 20 > > diffusion > > > > values. > > > > > > > > 2013/3/28 David van der Spoel > > > > > > > >> On 2013-03-28 10:40, Ahmet yıldırım wrote: > > > >> > > > >>> Dear users, > > > >>> > > > >>> This time, I calculated the diffusion coefficients of protein for > > each 10 > > > >>> ns of the simulation providing a total simulation time of 200 ns. > > > >>> g_msd -f traj.xtc -s topol.top -o msd1.xvg -trestart 20 -beginfit > -1 > > > >>> -endfit -1 -b 0 -e 1 > > > >>> g_msd -f traj.xtc -s topol.top -o msd2.xvg -trestart 20 -beginfit > -1 > > > >>> -endfit -1 -b 10001 -e 2 > > > >>> g_msd -f traj.xtc -s topol.top -o msd3.xvg -trestart 20 -beginfit > -1 > > > >>> -endfit -1 -b 20001 -e 3 > > > >>> > > > >>> g_msd -f traj.xtc -s topol.top -o msd20.xvg -trestart 20 -beginfit > -1 > > > >>> -endfit -1 -b 190001 -e 20 > > > >>> > > > >> > > > >> Set trestart to 10001 (no restarts), or do one run with > > > >> > > > >> g_msd -f traj.xtc -s topol.top -o msd20.xvg -trestart 1 > > > >> > > > > > > > > > I believe the advice was to increase "trestart" and you can decide > > > yourself how much to increase. > > > > > > Most likely, your protein deserves better sampling than 10 ns for a > > > linear diffusion. > > > > > > Dr. Vitaly Chaban > > > -- > > > gmx-users mailing listgmx-users@gromacs.org > > > http://lists.gromacs.org/mailman/listinfo/gmx-users > > > * Please search the archive at > >
Re: [gmx-users] Re: diffusion constant level off
Dear users, Again, I have strange results (for 10,50,100,150,200 ns). I am wondering, is there a bug with g_msd? Commands for trestart to 20 ps: g_msd -f traj.xtc -s topol.top -o msd1.xvg -trestart 20 -beginfit -1 -endfit -1 -b 0 -e 1 g_msd -f traj.xtc -s topol.top -o msd2.xvg -trestart 20 -beginfit -1 -endfit -1 -b 1 -e 2 g_msd -f traj.xtc -s topol.top -o msd3.xvg -trestart 20 -beginfit -1 -endfit -1 -b 2 -e 3 ... g_msd -f traj.xtc -s topol.top -o msd20.xvg -trestart 20 -beginfit -1 -endfit -1 -b 19 -e 20 Commands for trestart to 1000 ps: g_msd -f traj.xtc -s topol.top -o msd1.xvg -trestart 1000 -beginfit -1 -endfit -1 -b 0 -e 1 g_msd -f traj.xtc -s topol.top -o msd2.xvg -trestart 1000 -beginfit -1 -endfit -1 -b 1 -e 2 g_msd -f traj.xtc -s topol.top -o msd3.xvg -trestart 1000 -beginfit -1 -endfit -1 -b 2 -e 3 ... g_msd -f traj.xtc -s topol.top -o msd20.xvg -trestart 1000 -beginfit -1 -endfit -1 -b 19 -e 20 D1 (cm^2/s):Diffusion for trestart to 20 ps D2 (cm^2/s):Diffusion for trestart to 1000 ps Time (ns) D1 D2 10 0.1616 0.1091 20 0.0735 0.0679 30 0.0775 0.0705 40 0.1097 0.1189 50 0.1471 0.1436 60 0.0468 0.048 70 0.0667 0.0652 80 0.0727 0.086 90 0.0664 0.0707 100 0.1336 0.114 110 0.0899 0.0841 120 0.0572 0.0598 130 0.0506 0.0482 140 0.0723 0.0767 150 0.1466 0.1439 160 0.0703 0.0601 170 0.081 0.0853 180 0.0278 0.027 190 0.1121 0.1024 200 0.3136 0.2981 2013/3/28 Dr. Vitaly Chaban > > > > > if I do as you said, I will get only one diffusion coefficient. I want to > > calculate one diffusion coefficient for each 10 > > ns of the simulation time of 200 ns. That is, I want to get 20 diffusion > > values. > > > > 2013/3/28 David van der Spoel > > > >> On 2013-03-28 10:40, Ahmet yıldırım wrote: > >> > >>> Dear users, > >>> > >>> This time, I calculated the diffusion coefficients of protein for each 10 > >>> ns of the simulation providing a total simulation time of 200 ns. > >>> g_msd -f traj.xtc -s topol.top -o msd1.xvg -trestart 20 -beginfit -1 > >>> -endfit -1 -b 0 -e 1 > >>> g_msd -f traj.xtc -s topol.top -o msd2.xvg -trestart 20 -beginfit -1 > >>> -endfit -1 -b 10001 -e 2 > >>> g_msd -f traj.xtc -s topol.top -o msd3.xvg -trestart 20 -beginfit -1 > >>> -endfit -1 -b 20001 -e 3 > >>> > >>> g_msd -f traj.xtc -s topol.top -o msd20.xvg -trestart 20 -beginfit -1 > >>> -endfit -1 -b 190001 -e 20 > >>> > >> > >> Set trestart to 10001 (no restarts), or do one run with > >> > >> g_msd -f traj.xtc -s topol.top -o msd20.xvg -trestart 1 > >> > > > I believe the advice was to increase "trestart" and you can decide > yourself how much to increase. > > Most likely, your protein deserves better sampling than 10 ns for a > linear diffusion. > > Dr. Vitaly Chaban > -- > 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 -- Ahmet Yıldırım -- 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: diffusion constant level off
Dear Prof.Spoel, if I do as you said, I will get only one diffusion coefficient. I want to calculate one diffusion coefficient for each 10 ns of the simulation time of 200 ns. That is, I want to get 20 diffusion values. 2013/3/28 David van der Spoel > On 2013-03-28 10:40, Ahmet yıldırım wrote: > >> Dear users, >> >> This time, I calculated the diffusion coefficients of protein for each 10 >> ns of the simulation providing a total simulation time of 200 ns. >> g_msd -f traj.xtc -s topol.top -o msd1.xvg -trestart 20 -beginfit -1 >> -endfit -1 -b 0 -e 1 >> g_msd -f traj.xtc -s topol.top -o msd2.xvg -trestart 20 -beginfit -1 >> -endfit -1 -b 10001 -e 2 >> g_msd -f traj.xtc -s topol.top -o msd3.xvg -trestart 20 -beginfit -1 >> -endfit -1 -b 20001 -e 3 >> >> g_msd -f traj.xtc -s topol.top -o msd20.xvg -trestart 20 -beginfit -1 >> -endfit -1 -b 190001 -e 20 >> > > Set trestart to 10001 (no restarts), or do one run with > > g_msd -f traj.xtc -s topol.top -o msd20.xvg -trestart 1 > > > >> I have strange Diffusion results (especially 10,50,100,150,200 ns). How >> can >> I fix this problem? >> Results: >> Time (ns) D(cm^2/s) >> 10 0.1616 >> 20 0.0735 >> 30 0.0775 >> 40 0.1097 >> 50 0.1471 >> 60 0.0468 >> 70 0.0667 >> 80 0.0727 >> 90 0.0664 >> 100 0.1336 >> 110 0.0899 >> 120 0.0572 >> 130 0.0506 >> 140 0.0723 >> 150 0.1466 >> 160 0.0703 >> 170 0.081 >> 180 0.0278 >> 190 0.1121 >> 200 0.3136 >> >> >> >> 2013/3/27 Ahmet yıldırım >> >>> >>> Dear users, >>> >>> I used the following commands to get diffusion constants (every 10 ns) of >>> >> a simulation of 100 ns . The number of frame is 5001 (write .xtc >> trajectory >> every 20 ps). I looked at RMSD vs average structure, RMSD vs starting >> structure, Radius of gyration, RMSD matrix. This simulation has reached to >> converge at last 50 ns. >> >>> g_msd -f traj.xtc -s topol.tpr -o msd_1.xvg -b 0 -e 1 >>> g_msd -f traj.xtc -s topol.tpr -o msd_2.xvg -b 1 -e 2 >>> g_msd -f traj.xtc -s topol.tpr -o msd_3.xvg -b 2 -e 3 >>> ... >>> g_msd -f traj.xtc -s topol.tpr -o msd_10.xvg -b 9 -e 10 >>> >>> 1.) I used the above commands without the following flags ( -type, >>> >> -lateral and -ten). Which diffusion will the above comands give? is it >> bulk >> diffusion? >> >>> Gromacs manual: >>> -type:Compute diffusion coefficient in one direction:no, x, y or z >>> -lateral:Calculate the lateral diffusion in a plane perpendicular to: no, >>> >> x, y or z >> >>> -ten:Calculate the full tensor >>> 2.) I plotted diffusions (10 values) as function of time. Diffusions dont >>> >> converge. Did I do any steps by mistake? >> >>> 3.) From manual: >>> The diffusion constant is calculated by least squares fitting a straight >>> >> line (D*t + c)... >> >>> What is (D*t + c)? What are the meaning of D and c? >>> 4.) What should be "Time between restarting points in trajectory"? >>> >>> Thanks in advance >>> -- >>> Ahmet Yıldırım >>> >> >> >> >> >> -- >> Ahmet Yıldırım >> >> > > -- > David van der Spoel, Ph.D., Professor of Biology > Dept. of Cell & Molec. Biol., Uppsala University. > Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. > sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se > -- > gmx-users mailing listgmx-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. > * Can't post? Read > http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> > -- Ahmet Yıldırım -- 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: diffusion constant level off
Dear users, This time, I calculated the diffusion coefficients of protein for each 10 ns of the simulation providing a total simulation time of 200 ns. g_msd -f traj.xtc -s topol.top -o msd1.xvg -trestart 20 -beginfit -1 -endfit -1 -b 0 -e 1 g_msd -f traj.xtc -s topol.top -o msd2.xvg -trestart 20 -beginfit -1 -endfit -1 -b 10001 -e 2 g_msd -f traj.xtc -s topol.top -o msd3.xvg -trestart 20 -beginfit -1 -endfit -1 -b 20001 -e 3 g_msd -f traj.xtc -s topol.top -o msd20.xvg -trestart 20 -beginfit -1 -endfit -1 -b 190001 -e 20 I have strange Diffusion results (especially 10,50,100,150,200 ns). How can I fix this problem? Results: Time (ns) D(cm^2/s) 10 0.1616 20 0.0735 30 0.0775 40 0.1097 50 0.1471 60 0.0468 70 0.0667 80 0.0727 90 0.0664 100 0.1336 110 0.0899 120 0.0572 130 0.0506 140 0.0723 150 0.1466 160 0.0703 170 0.081 180 0.0278 190 0.1121 200 0.3136 2013/3/27 Ahmet yıldırım > > Dear users, > > I used the following commands to get diffusion constants (every 10 ns) of a simulation of 100 ns . The number of frame is 5001 (write .xtc trajectory every 20 ps). I looked at RMSD vs average structure, RMSD vs starting structure, Radius of gyration, RMSD matrix. This simulation has reached to converge at last 50 ns. > g_msd -f traj.xtc -s topol.tpr -o msd_1.xvg -b 0 -e 1 > g_msd -f traj.xtc -s topol.tpr -o msd_2.xvg -b 1 -e 2 > g_msd -f traj.xtc -s topol.tpr -o msd_3.xvg -b 2 -e 3 > ... > g_msd -f traj.xtc -s topol.tpr -o msd_10.xvg -b 9 -e 10 > > 1.) I used the above commands without the following flags ( -type, -lateral and -ten). Which diffusion will the above comands give? is it bulk diffusion? > Gromacs manual: > -type:Compute diffusion coefficient in one direction:no, x, y or z > -lateral:Calculate the lateral diffusion in a plane perpendicular to: no, x, y or z > -ten:Calculate the full tensor > 2.) I plotted diffusions (10 values) as function of time. Diffusions dont converge. Did I do any steps by mistake? > 3.) From manual: > The diffusion constant is calculated by least squares fitting a straight line (D*t + c)... > What is (D*t + c)? What are the meaning of D and c? > 4.) What should be "Time between restarting points in trajectory"? > > Thanks in advance > -- > Ahmet Yıldırım -- Ahmet Yıldırım -- 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] diffusion constant level off
Dear users, I used the following commands to get diffusion constants (every 10 ns) of a simulation of 100 ns . The number of frame is 5001 (write .xtc trajectory every 20 ps). I looked at RMSD vs average structure, RMSD vs starting structure, Radius of gyration, RMSD matrix. This simulation has reached to converge at last 50 ns. g_msd -f traj.xtc -s topol.tpr -o msd_1.xvg -b 0 -e 1 g_msd -f traj.xtc -s topol.tpr -o msd_2.xvg -b 1 -e 2 g_msd -f traj.xtc -s topol.tpr -o msd_3.xvg -b 2 -e 3 ... g_msd -f traj.xtc -s topol.tpr -o msd_10.xvg -b 9 -e 10 1.) I used the above commands without the following flags ( -type, -lateral and -ten). Which diffusion will the above comands give? is it bulk diffusion? Gromacs manual: -type:Compute diffusion coefficient in one direction:no, x, y or z -lateral:Calculate the lateral diffusion in a plane perpendicular to: no, x, y or z -ten:Calculate the full tensor 2.) I plotted diffusions (10 values) as function of time. Diffusions dont converge. Did I do any steps by mistake? 3.) From manual: The diffusion constant is calculated by least squares fitting a straight line (D*t + c)... What is (D*t + c)? What are the meaning of D and c? 4.) What should be "Time between restarting points in trajectory"? Thanks in advance -- Ahmet Yıldırım -- 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] compilation of gromacs-4.5.4 with fftw-3.3 for double precision versition
t? Any reply will be appreciated. > >> > >> > > In your last step, you're not using --enable-shared like you did in every > > preceding step. Adding that flag should fix it. > > > > http://www.gromacs.org/**Documentation/Installation_** > > Instructions_4.5#Details_for_**building_the_FFTW_prerequisite< > http://www.gromacs.org/Documentation/Installation_Instructions_4.5#Details_for_building_the_FFTW_prerequisite > > > > > > Gromacs 4.5.4 is pretty old; is there any reason you're not using a new > > version? You'll get much better performance from 4.6.1. > > > > -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< > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> > > > > ==**== > > -- > > gmx-users mailing listgmx-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. > > * Can't post? Read http://www.gromacs.org/**Support/Mailing_Lists< > http://www.gromacs.org/Support/Mailing_Lists> > > > > > > -- > Best Regards, > > Qinghua > -- > 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 > -- Ahmet Yıldırım -- 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] regarding the cosine content analysis
Then, these cosine content's results are all normal? 2013/2/25 Tsjerk Wassenaar > Because it fits a little bit better to a cosine with full period than > the first one fits a cosine with half period and the third one fits a > cosine with 1.5 period. > > Tsjerk > > On Mon, Feb 25, 2013 at 1:23 PM, Ahmet yıldırım > wrote: > > Hi, > > > > I think my question was misunderstood. > > My question is: > > Why is second cosine content greater than the other values? > > > > Regards > > > > 2013/2/25 Thomas Evangelidis > > > >> On 25 February 2013 12:14, Tsjerk Wassenaar wrote: > >> > >> > Hi Thomas, > >> > > >> > As I've explained previously, the cosine content does not allow such > >> > inferences. Besides, taking the relaxation from the start into account > >> > in PCA is pretty nonsensical, unless you aim to characterize that > >> > relaxation in the first place. Looking at the cosine content to infer > >> > > >> > >> Yes, that's what I meant, to identity those ns where the protein does > >> unidirectional motion before it starts exploring the energy landscape, > and > >> exclude them from the final analysis (whatever this is). At least this > is > >> what I've seen doing in publications and this is what I have understood > >> from our previous conversations. I think your objection is about the > way I > >> use the term "equilibration" to refer to what you call "relaxation" (I > >> presume it is not the same as energy minimization). Perhaps it would be > >> helpful to have your definition of the terms "equilibration" and > >> "relaxation. > >> > >> > >> > equilibration from that is blatantly fooling yourself. > >> > If you feel you must use cosine content to support any claim on > >> > equilibration, then it is a much better approach to start from the end > >> > of the simulation and check that the stretch of the trajectory you > >> > take does not yield high cosine contents, in which case you have some > >> > reason to argue that that part of the simulation is sampled in a local > >> > equilibrium. > >> > > >> > Cheers, > >> > > >> > Tsjerk > >> > > >> > > >> > On Mon, Feb 25, 2013 at 10:56 AM, Thomas Evangelidis < > teva...@gmail.com> > >> > wrote: > >> > > You don't do it the right way. You must start the analysis from the > >> > > beginning not from the end of your trajectory. I.e. > >> > > > >> > > 0-20ns > >> > > 0-30ns > >> > > 0-40ns > >> > > ... > >> > > 0-100ns > >> > > > >> > > Until the cosine content of the first 3 principal components that > >> account > >> > > for most of the variance in the atomic fluctuation have been > dropped at > >> > > least once below 0.5. This is the point where theoretically the > system > >> > has > >> > > equilibrated enough. > >> > > > >> > > Thomas > >> > > > >> > > > >> > > On 22 February 2013 13:43, Ahmet yıldırım > wrote: > >> > > > >> > >> Dear users, > >> > >> > >> > >> I performed MD simulation of 400 ns of a structure. I used the > cosine > >> > >> content to check whether the simulation is not converged. I used > last > >> > 100 > >> > >> and 50 ns of trajectory to the analysis, respectively. The results > >> were > >> > >> very similar to each other.The cosine contents of the first ten > >> > principal > >> > >> components are as follows. The cosine contents of the principal > >> > components > >> > >> are very small but one. Why is the second cosine content differs > from > >> > the > >> > >> others? What could be the reason for this? And do you think > simulation > >> > has > >> > >> reached convergence? > >> > >> > >> > >> The cosine contents of last 50 ns: > >> > >> 1 0.00685769 > >> > >> 2 0.137028 > >> > >> 3 0.00139929 > >> > >> 4 0.00903137 > >> > >> 5 0.0180072 > >> > >> 6 0.0128686 &g
Re: [gmx-users] regarding the cosine content analysis
Hi, I think my question was misunderstood. My question is: Why is second cosine content greater than the other values? Regards 2013/2/25 Thomas Evangelidis > On 25 February 2013 12:14, Tsjerk Wassenaar wrote: > > > Hi Thomas, > > > > As I've explained previously, the cosine content does not allow such > > inferences. Besides, taking the relaxation from the start into account > > in PCA is pretty nonsensical, unless you aim to characterize that > > relaxation in the first place. Looking at the cosine content to infer > > > > Yes, that's what I meant, to identity those ns where the protein does > unidirectional motion before it starts exploring the energy landscape, and > exclude them from the final analysis (whatever this is). At least this is > what I've seen doing in publications and this is what I have understood > from our previous conversations. I think your objection is about the way I > use the term "equilibration" to refer to what you call "relaxation" (I > presume it is not the same as energy minimization). Perhaps it would be > helpful to have your definition of the terms "equilibration" and > "relaxation. > > > > equilibration from that is blatantly fooling yourself. > > If you feel you must use cosine content to support any claim on > > equilibration, then it is a much better approach to start from the end > > of the simulation and check that the stretch of the trajectory you > > take does not yield high cosine contents, in which case you have some > > reason to argue that that part of the simulation is sampled in a local > > equilibrium. > > > > Cheers, > > > > Tsjerk > > > > > > On Mon, Feb 25, 2013 at 10:56 AM, Thomas Evangelidis > > wrote: > > > You don't do it the right way. You must start the analysis from the > > > beginning not from the end of your trajectory. I.e. > > > > > > 0-20ns > > > 0-30ns > > > 0-40ns > > > ... > > > 0-100ns > > > > > > Until the cosine content of the first 3 principal components that > account > > > for most of the variance in the atomic fluctuation have been dropped at > > > least once below 0.5. This is the point where theoretically the system > > has > > > equilibrated enough. > > > > > > Thomas > > > > > > > > > On 22 February 2013 13:43, Ahmet yıldırım wrote: > > > > > >> Dear users, > > >> > > >> I performed MD simulation of 400 ns of a structure. I used the cosine > > >> content to check whether the simulation is not converged. I used last > > 100 > > >> and 50 ns of trajectory to the analysis, respectively. The results > were > > >> very similar to each other.The cosine contents of the first ten > > principal > > >> components are as follows. The cosine contents of the principal > > components > > >> are very small but one. Why is the second cosine content differs from > > the > > >> others? What could be the reason for this? And do you think simulation > > has > > >> reached convergence? > > >> > > >> The cosine contents of last 50 ns: > > >> 1 0.00685769 > > >> 2 0.137028 > > >> 3 0.00139929 > > >> 4 0.00903137 > > >> 5 0.0180072 > > >> 6 0.0128686 > > >> 7 0.00154502 > > >> 8 9.71793e-05 > > >> 9 0.00485945 > > >> 10 0.00202377 > > >> > > >> Thanks in advance > > >> -- > > >> Ahmet Yıldırım > > >> -- > > >> 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 > > >> > > > > > > > > > > > > -- > > > > > > == > > > > > > Thomas Evangelidis > > > > > > PhD student > > > University of Athens > > > Faculty of Pharmacy > > > Department of Pharmaceutical Chemistry > > > Panepistimioupoli-Zografou > > > 157 71 Ath
[gmx-users] Re: regarding the cosine content analysis
Dear users, I did not get any response in my last email. Any help will be appreciated. Thanks in advance 2013/2/22 Ahmet yıldırım > Dear users, > > I performed MD simulation of 400 ns of a structure. I used the cosine > content to check whether the simulation is not converged. I used last 100 > and 50 ns of trajectory to the analysis, respectively. The results were > very similar to each other.The cosine contents of the first ten principal > components are as follows. The cosine contents of the principal components > are very small but one. Why is the second cosine content differs from the > others? What could be the reason for this? And do you think simulation > has reached convergence? > > The cosine contents of last 50 ns: > 1 0.00685769 > 2 0.137028 > 3 0.00139929 > 4 0.00903137 > 5 0.0180072 > 6 0.0128686 > 7 0.00154502 > 8 9.71793e-05 > 9 0.00485945 > 10 0.00202377 > > Thanks in advance > -- > Ahmet Yıldırım > -- Ahmet Yıldırım -- 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] regarding the cosine content analysis
Dear users, I performed MD simulation of 400 ns of a structure. I used the cosine content to check whether the simulation is not converged. I used last 100 and 50 ns of trajectory to the analysis, respectively. The results were very similar to each other.The cosine contents of the first ten principal components are as follows. The cosine contents of the principal components are very small but one. Why is the second cosine content differs from the others? What could be the reason for this? And do you think simulation has reached convergence? The cosine contents of last 50 ns: 1 0.00685769 2 0.137028 3 0.00139929 4 0.00903137 5 0.0180072 6 0.0128686 7 0.00154502 8 9.71793e-05 9 0.00485945 10 0.00202377 Thanks in advance -- Ahmet Yıldırım -- 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] virtual sites in reference structure
Dear Tsjerk, Do the virtual sites cause incorrect calculations of SASA, RMSD or something else? Regards 2013/2/21 Tsjerk Wassenaar > Hi Ahmet, > > You can always use suitable index groups for analysis. > > Cheers, > > Tsjerk > > On Thu, Feb 21, 2013 at 7:08 AM, Ahmet yıldırım > wrote: > > I thought the virtual sites can affect analysis.For example, dont they > cause > > incorrect calculations of SASA, RMSD or something else? > > > > Thanks in advance > > > > 2013/2/20 Justin Lemkul > > > >> > >> > >> On 2/20/13 9:18 AM, Ahmet yıldırım wrote: > >> > >>> Dear users, > >>> > >>> I have the virtual sites in reference structure and all trajectory. > When > >>> analyzing simulation, do I have to get rid of those(virtual sites)? If > >>> yes/no, why? > >>> > >>> > >> Why do you think you need to remove 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< > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> > >> > >> ==**== > >> -- > >> gmx-users mailing listgmx-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. > >> * Can't post? Read http://www.gromacs.org/**Support/Mailing_Lists< > http://www.gromacs.org/Support/Mailing_Lists> > >> > > > > > > > > -- > > Ahmet Yıldırım > > -- > > 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 > > > > -- > Tsjerk A. Wassenaar, Ph.D. > > post-doctoral researcher > Biocomputing Group > Department of Biological Sciences > 2500 University Drive NW > Calgary, AB T2N 1N4 > Canada > -- > 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 > -- Ahmet Yıldırım -- 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] virtual sites in reference structure
I thought the virtual sites can affect analysis.For example, dont they cause incorrect calculations of SASA, RMSD or something else? Thanks in advance 2013/2/20 Justin Lemkul > > > On 2/20/13 9:18 AM, Ahmet yıldırım wrote: > >> Dear users, >> >> I have the virtual sites in reference structure and all trajectory. When >> analyzing simulation, do I have to get rid of those(virtual sites)? If >> yes/no, why? >> >> > Why do you think you need to remove 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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> > > ==**== > -- > gmx-users mailing listgmx-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. > * Can't post? Read > http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> > -- Ahmet Yıldırım -- 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] the meaning of the dummy atom
Dear users, What is the meaning of the dummy atom in Gromacs? Regards -- Ahmet Yıldırım -- 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] virtual sites in reference structure
Dear users, I have the virtual sites in reference structure and all trajectory. When analyzing simulation, do I have to get rid of those(virtual sites)? If yes/no, why? Regards -- Ahmet Yıldırım -- 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: Reference structure for PCA.
s the average > of > >> >> the > >> >>> same time window (there must not be large deviation) while I get low > >> >> cosine > >> >>> for the first case where deviations are calculated from the full > >> >> trajectory > >> >>> average (large deviation) ? > >> >>> > >> >>> Any help is appreciated. > >> >>> > >> >>> Thanks, > >> >>> > >> >>> -Vivek Modi > >> >>> Graduate Student > >> >>> IITK. > >> >>> -- > >> >>> 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 > >> >>> > >> >> > >> >> > >> >> > >> >> -- > >> >> *--- > >> >> Thanks and Regards, > >> >> Bipin Singh* > >> >> -- > >> >> 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 > >> >> > >> > > >> > > >> > > >> > -- > >> > Tsjerk A. Wassenaar, Ph.D. > >> > > >> > post-doctoral researcher > >> > Biocomputing Group > >> > Department of Biological Sciences > >> > 2500 University Drive NW > >> > Calgary, AB T2N 1N4 > >> > Canada > >> > -- > >> > 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 > >> > > >> -- > >> Antonio M. Baptista > >> Instituto de Tecnologia Quimica e Biologica, Universidade Nova de Lisboa > >> Av. da Republica - EAN, 2780-157 Oeiras, Portugal > >> phone: +351-214469619 email: bapti...@itqb.unl.pt > >> fax: +351-214411277 WWW: http://www.itqb.unl.pt/~baptista > >> > -- > >> > >> > >> > >> -- > >> > >> > >> > > -- > > 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 > > > > -- > Tsjerk A. Wassenaar, Ph.D. > > post-doctoral researcher > Biocomputing Group > Department of Biological Sciences > 2500 University Drive NW > Calgary, AB T2N 1N4 > Canada > -- > 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 > -- Ahmet Yıldırım -- 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] suffice of position restraints
Dear users, I usually apply the positions restraint of 100 ps on system. Does it produce a problem to apply the positions restraint for long time (100 or 200 ps)? cant it cause strain on structure? Thanks in advance -- Ahmet Yıldırım -- 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] activation energy
It is the minimum energy required to start a chemical reaction. I have a structure complexed A and B ligands. I want to calculate how these ligands changed the activation energy. 2013/1/14 Felipe Pineda, PhD > I would first explain what do you mean with activation energy. What > definition do you use? > > > On 01/14/2013 01:15 PM, Ahmet yıldırım wrote: > >> Dear users, >> >> Is it possible to calculate the activation energy of a structure using >> Gromacs? if OK, how? >> >> Thanks in advance >> > -- > gmx-users mailing listgmx-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. > * Can't post? Read > http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> > -- Ahmet Yıldırım -- 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] activation energy
Dear users, Is it possible to calculate the activation energy of a structure using Gromacs? if OK, how? Thanks in advance -- Ahmet Yıldırım -- 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] coordinates obtained from the Automated Topology Builder
Dear users, I get topology (A.itp) and structure (A.gro) files of a ligand using Automated Topology Builder. A.gro file has optimised geometry. That is, the coordinates of the atoms have been changed according to the initial file .pdb. I am confused. When I do simulation related to protein-ligand interactions, which coordinates I use? Optimised coordinates obtained from the Automated Topology Builder or original coordinates in .pdb? Thanks in advance -- Ahmet Yıldırım -- 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] increase of temperature or pressure
Dear users, When analyzing some of the simulations; I get 312 K, 310 K or 308 K instead of 300K (the t_ref value for the whole system). 1. What is the reason for the increase of temperature? For example it can be cutoff artifacts. What else can be? 2. To get the the error small tau_t can be reduced. What is the minimum value for tau_t? Sometimes, the pressure in the output files is high ( 7 bar, 6 bar or 1.5 bar instead of 1 bar). I.The reason for this? II. tau_p can be reduced as temperature. And what is the minimum value for tau_p? Briefly, what could be the reasons for the increase in temperature or pressure? What are your suggestions for the solution? Thanks in advance -- Ahmet Yıldırım -- 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] cosine content and nonconverged trajectory
Dear users, The cosine content of the principal components is an effective indicator for predicting whether or not a trajectory has been convergent. A high cosine content typically indicates a nonconverged trajectory (Chapter 5: Normal Modes and Essential Dynamics Steven Hayward and Bert L. de Groot). What is a high cosine content? 0.2, 0.5 or 0.7 What is the value? Thanks in advance -- Ahmet Yıldırım -- 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] regarding converge of system
Dear Christopher, Firstly thanks for your reply. RMSD is a measure related with whether or not converge of particles in the structures versus the starting structure. In other word, it is the difference (average distance) between the positions of particles in two structures. Conformational changes is not only on the change of the position of atoms/particles in the structure but also depend on other parameters (dihedral angle, formation of a hydrogen bond, tilt/rotation of a protein/peptide in a lipid bilayer, solvation patterns, ligand binding, system volume, etc). Am I wrong? RMSD matrix is also used to control the convergence of the structure. What is the main difference between RMSD and RMSD matrix? Thanks in advance 2012/11/1 Christopher Neale > RMSD of what? Probably you mean RMSD from the starting (or crystal) > structure. First, consider that your profile > of RMSD vs. crystal structure levels off at 0.4 nm with increasing > simulation time. Consider how many possible > conformations are 0.4 nm RMSD away from the crystal structure. A stable > RMSD does not necessarily indicate > that you have obtained Boltzmann sampling of a particular conformational > basin. Very generally, it is the > degeneracy of RMSD with respect to conformational space that makes RMSD an > insufficient indicator of > convergence. There are other ways to look at this though. For instance, > there might be an important degree of > freedom that is important for your system but does not greatly affect the > global conformation (and thus the > RMSD). This might be a dihedral angle, formation of a hydrogen bond, > tilt/rotation of a protein/peptide in a > lipid bilayer, solvation patterns, ligand binding, system volume, etc. > > Also, and I presume that this is not what Tsjerk meant (but you should > check whatever reference you are referring > to) it is always possible that you remain stuck within a conformational > basin that is locally favourable but globally > unfavourable. > > For other measures of convergence, first think about what you are trying > to study for your system and use that > to guide your selection of properties for which you can evaluate > convergence. This should include both global > and local structural measures. There are loads of papers available that > discuss this. See papers by Grossfield, > Zuckerman, and others. A colleague of mine has also shown that some > properties converge faster than others > (meaning that some properties, like the RMSD, converge before the > partition function has converged: > http://pubs.acs.org/doi/abs/10.1021/ct900302n ). > > Chris. > > -- original message -- > > I have two questions: > > 1-We can say "The RMSD is commonly used as an indicator of convergence > of the structure towards an equilibrium state (Tsjerk W.)". RMSD is > not sufficient to determine whether or not converge of > structure/system. Why? > > 2-Radius of gyration, RMSD, rmsd matrix are used as an indicator of > convergence of the structure. are there other indicators of > convergence of the structure? > > Thanks in advance > > -- > Ahmet Yıldırım > -- > 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 > -- Ahmet Yıldırım -- 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] regarding converge of system
Hi, I have two questions: 1-We can say "The RMSD is commonly used as an indicator of convergence of the structure towards an equilibrium state (Tsjerk W.)". RMSD is not sufficient to determine whether or not converge of structure/system. Why? 2-Radius of gyration, RMSD, rmsd matrix are used as an indicator of convergence of the structure. are there other indicators of convergence of the structure? Thanks in advance -- Ahmet Yıldırım -- 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] tpr file
Hi, I converted a .tpr file to .pdb using editconf. editconf -f md.tpr -o new-md.pdb I visualised new-topol.pdb using pymol. It has the virtual sites. Furthermore, the molecule(s) does not stay in the centre of the box. I need a proper .tpr or .pdb file for analysis. How can these problems fixed? Thanks in advance -- Ahmet Yıldırım -- 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] Regarding RMSD analysis result
Hi, trjconv -s top.tpr -f traj.xtc -o traj-nojump.xtc -pbc nojump I hope it helps 2012/9/25 Archana Sonawani > Hi, > > Your RMSD graph is ok but is represented wrong due to pbc problem. Use > whole and nojump options of trjconv. > > On Tue, Sep 25, 2012 at 2:15 PM, Felipe Pineda, PhD < > luis.pinedadecas...@lnu.se> wrote: > > > On 09/25/2012 10:08 AM, naga sundar wrote: > > > >> Dear Felipe > >> > >> Thanks for ur reply. > >> > >> The system is a protein-protein complex. Like u r saying its > due > >> to pbc problem then why any abnormality doesn't happened to the native > >> complex (Black line)?. > >> > > Maybe because MD is stochastic ... > > > > > >As already suggest by justin i checked the pbc > >> conditions upto my knowledge everything is fine. > >> > > As Justin said, it's not about the pbc conditions as they appear in the > > mdp file, but about pbc effects due to a chain, probably the ligand, > > leaving the box and being reflected to the opposite side. Have you > checked > > out visually how the weird frames look like? > > > > > > -- > > gmx-users mailing listgmx-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. > > * Can't post? Read http://www.gromacs.org/**Support/Mailing_Lists< > 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 > -- Ahmet Yıldırım -- 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] Regarding RMSD analysis result
emkul, 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< > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> > >> > > >> > ==**== > >> > -- > >> > gmx-users mailing listgmx-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. > >> > * Can't post? Read > >> http://www.gromacs.org/**Support/Mailing_Lists< > http://www.gromacs.org/Support/Mailing_Lists> > >> > > >> > >> > >> > >> -- > >> 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 > > > > -- > Tsjerk A. Wassenaar, Ph.D. > > post-doctoral researcher > Biocomputing Group > Department of Biological Sciences > 2500 University Drive NW > Calgary, AB T2N 1N4 > Canada > -- > 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 > -- Ahmet Yıldırım -- 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] content of secondary structure output file
Dear users, I am using the command as the following. A part of output file (secondary-structure.xvg) is as follows. 1.column: time 2.column:structure 3.column:coil ... I do not understand the meaning of 2.column. What is "structure"? What is the meaning of value there? Greetings secondary-structure.xvg: # This file was created Mon Sep 24 09:55:49 2012 # by the following command: # do_dssp -s protein-RUN.tpr -f traj-nojump.xtc -o secondary-structure.xpm -sc secondary-structure.xvg # # do_dssp is part of G R O M A C S: # # Grunge ROck MAChoS # @title "Secondary Structure" @xaxis label "Time (ps)" @yaxis label "Number of Residues" @TYPE xy @ subtitle "Structure = A-Helix + B-Sheet + B-Bridge + Turn" @ view 0.15, 0.15, 0.75, 0.85 @ legend on @ legend box on @ legend loctype view @ legend 0.78, 0.8 @ legend length 2 @ s0 legend "Structure" @ s1 legend "Coil" @ s2 legend "B-Sheet" @ s3 legend "B-Bridge" @ s4 legend "Bend" @ s5 legend "Turn" @ s6 legend "A-Helix" @ s7 legend "5-Helix" @ s8 legend "3-Helix" @ s9 legend "Chain_Separator" 0 34174 131 44338 168 0 0 1 20 33184 119 63741 165 0 6 1 40 33378 121 84139 165 0 6 1 ... -- Ahmet Yıldırım -- 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: the effect of ligand on protein
Dear users, any suggestion? Thanks in advance 2012/7/2 ahmet yıldırım > > Dear users, > > Which analysis do you suggest to examine the effect of ligand on protein? > > 1.)For quality assurance: > RMSD,RMSF and Radius of gyration for free and complex form > > 2.)For structural analysis: > ISA (interface surface area), the number of hydrogen bonds between > protein and ligand, secondary structure for free and complex form > > 3.)Principial component analysis: > The eigenvalues versus the first 30, 40 or 50 eigenvectors > Projection of trajectory onto onto the first five or ten eigenvectors > Projection of trajectory onto the plane of first two eigenvectors > Cosine Content of some eigenvectors > > Are these analyzes adequate? > > Thanks in advance > > -- > Ahmet Yıldırım -- Ahmet Yıldırım -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] the effect of ligand on protein
Dear users, Which analysis do you suggest to examine the effect of ligand on protein? 1.)For quality assurance: RMSD,RMSF and Radius of gyration for free and complex form 2.)For structural analysis: ISA (interface surface area), the number of hydrogen bonds between protein and ligand, secondary structure for free and complex form 3.)Principial component analysis: The eigenvalues versus the first 30, 40 or 50 eigenvectors Projection of trajectory onto onto the first five or ten eigenvectors Projection of trajectory onto the plane of first two eigenvectors Cosine Content of some eigenvectors Are these analyzes adequate? Thanks in advance -- Ahmet Yıldırım -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] try2
try2 -- Ahmet Yıldırım -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] the RMSD of Bond lengths, Bond angles, Dihedrals and Impropers
Dear users I calculated the backbone/all protein RMSD versus the starting structure or the average structure. I couldnt calculate some RMSDs. How can I calculate the RMSD of Bond lengths, Bond angles, Dihedrals and Impropers versus the starting structure or the average structure Do I need to create index files? Cheers -- Ahmet Yıldırım -- 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] renumber charge group
Dear user, Please see attached file. I renumbered the "cgnr" of a ligand. Is there any mistake related to renumbered of "cgnr"? I get the following error when I run position restrain (pr.mdp) mdrun -deffnm pr Fatal error: A charge group moved too far between two domain decomposition steps This usually means that your system is not well equilibrated [ moleculetype ] ; Name nrexcl TRIS 3 [ atoms ] ; nr type resnr resid atom cgnr chargemasstotal_charge 1 CH01TRIS C10.143 12.0110 2NL1TRIS N1 -0.590 14.0067 3 H1TRIS H10.399 1.0080 4 H1TRIS H10.399 1.0080 5 H1TRIS H10.399 1.0080 6 CH21TRIS C20.257 14.0270 7OA1TRIS O2 -0.637 15.9994 8 H1TRIS H20.463 1.0080 9 CH21TRIS C30.257 14.0270 10OA1TRIS O3 -0.637 15.9994 11 H1TRIS H30.463 1.0080 12 CH21TRIS C40.257 14.0270 13OA1TRIS O4 -0.636 15.9994 14 H1TRIS H40.463 1.0080 ; 1.000 ; total charge of the molecule: 1.000 -- Ahmet Yıldırım <>-- 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] parameters of em.mdp
Dear Justin, Thanks for your reply. You said "You should avoid ad hoc changes." You used different parameters for energy minimization at tutorial called "Tutorial 5: Protein-Ligand Complex". *a part of your em.mdp* nstlist = 1 rlist = 1.0 rcoulomb = 1.0 rvdw = 1.0 *a part of your md.mdp* nstlist = 5 rlist = 0.9 rcoulomb = 0.9 rvdw = 1.4 Then, Why did you change some parameters (nstlist,rlist,rcoulomb,rvdw) for energy minimization? Thanks in advance 23 Mart 2012 19:31 tarihinde Justin A. Lemkul yazdı: > > > ahmet yıldırım wrote: > >> Dear users, >> >> I am using the Reaction-Field method for electrostatics interactions. I >> used the following parameters for all input files (em.mdp, pr.mdp, nvt.mdp, >> npt.mdp, md.mdp). I just changed as an epsilon_rf=78 in md.mdp. If I set >> nstlist=rlist=rcoulomb=rvdw=1.**0 for energy minimization, would not it >> be better? What is your suggestions? >> >> > Why do you think making such changes to the cutoffs would be better? > These settings, for the most part, are a fixed part of the force field > you're using. Unless you have proof (either by your own demonstration or > one that is published) that making such changes result in better results, > you should avoid ad hoc changes. > > ; Neighbor Searching Parameters >> nstlist = 5 ns-type = Grid pbc >>= xyz rlist = 0.9 ; >> Electrostatics >> coulombtype = Reaction-Field rcoulomb= 1.4 >> epsilon_rf = 54 ; VdW >> vdw-type= Cut-off rvdw= 1.4 >> * >> Another question:* I used 200 K (in pr.mdp) and 300 K (in nvt.mdp, >> npt.mdp and md.mdp) the reference temperature for coupling. I analysed the >> temperature after production run. I get "Temperature=312.646" (g_energy -f >> md.edr -o temperature.xvg). that is, The temperature has increased >> (approximately 12 K) during the simulation. What could be the reason for >> the increase in temperature? I had setted to 200 K the reference >> temperature for coupling in pr.mdp. it can cause? >> >> > This outcome is precisely what you would expect, simply because you're > using the reaction field method and it introduces cutoff artifacts. > Interestingly, this same outcome (an increase of exactly 12K) has been > reported before: > > http://lists.gromacs.org/**pipermail/gmx-users/2009-**January/039113.html<http://lists.gromacs.org/pipermail/gmx-users/2009-January/039113.html> > > -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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> > > ==**== > -- > gmx-users mailing listgmx-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. > Can't post? Read > http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> > -- Ahmet Yıldırım -- 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] parameters of em.mdp
Dear users, I am using the Reaction-Field method for electrostatics interactions. I used the following parameters for all input files (em.mdp, pr.mdp, nvt.mdp, npt.mdp, md.mdp). I just changed as an epsilon_rf=78 in md.mdp. If I set nstlist=rlist=rcoulomb=rvdw=1.0 for energy minimization, would not it be better? What is your suggestions? ; Neighbor Searching Parameters nstlist = 5 ns-type = Grid pbc= xyz rlist = 0.9 ; Electrostatics coulombtype = Reaction-Field rcoulomb= 1.4 epsilon_rf = 54 ; VdW vdw-type= Cut-off rvdw= 1.4 * Another question:* I used 200 K (in pr.mdp) and 300 K (in nvt.mdp, npt.mdp and md.mdp) the reference temperature for coupling. I analysed the temperature after production run. I get "Temperature=312.646" (g_energy -f md.edr -o temperature.xvg). that is, The temperature has increased (approximately 12 K) during the simulation. What could be the reason for the increase in temperature? I had setted to 200 K the reference temperature for coupling in pr.mdp. it can cause? My em.mdp file is as the following: *em.mdp:* title= Energy Minimization ; Title of run cpp= /lib/cpp ; Preprocessor: Line tell the program the standard locations where to find certain files define = -DFLEXIBLE ; defines to pass to the preprocessor ; Run Control integrator= steep; steep integrator (steep = steepest descent minimization) nsteps= 2500; maximum number of steps to integrate ; Energy Minimization emtol= 1000.0 ; [kJ/mol/nm] minimization is converged when max force is < emtol emstep = 0.01 ; [nm] initial step-size ; Output Control nstxout = 0 ; [steps] freq to write coordinates to trajectory nstvout = 0 ; [steps] freq to write velocities to trajectory nstfout = 0 ; [steps] freq to write forces to trajectory nstlog = 1 ; [steps] freq to write energies to log file nstenergy= 1; [steps] freq to write energies to energy file energygrps= System; group(s) to write to energy file ; Neighbor Searching Parameters nstlist = 5 ; [steps] freq to update neighbor list ns-type = Grid ; method of updating neighbor list pbc= xyz; periodic boundary conditions (yes/no)in all directions rlist = 0.9 ; [nm] cut-off distance for the short-range neighbor list ; Electrostatics coulombtype = Reaction-Field ; Reaction-Field electrostatics rcoulomb= 1.4 ; [nm] distance for Coulomb cut-off epsilon_rf = 54 ; The relative dielectric constant of the reaction field ; VdW vdw-type= Cut-off ; twin-range cut-off with rlist where rvdw >= rlist rvdw= 1.4 ; [nm] distance for LJ cut-off ; Bonds constraints = none ; convert all bonds to constraints -- Ahmet Yıldırım -- 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: Neigborsearching, Electrostatics and vdw options
Hi, *quote from a paper: A twin range cut-off for van der Waals (0.9/1.4 nm) and a smooth particle mesh Ewald algorithm for Coulomb interactions (switching distance of 0.9 nm) were used.* i.e.this means: ; NEIGHBORSEARCHING PARAMETERS . rlist = 0.9 ; OPTIONS FOR ELECTROSTATICS AND VDW coulombtype = PME rcoulomb = 0.9 vdw-type = Cut-off rvdw = 1.4 Am I wrong? A twin range cut-off for van der Waals (0.9/1.4 nm) means rlist/rvdw. isnt it?* * Thanks in advance* * 22 Mart 2012 01:32 tarihinde Oliver Stueker yazdı: > Hi Ahmet, > > > Let's imagine a sphere(two concentric spheres): > > radius of the inside small sphere=rvdw > > radius of the big sphere=rcoulomb > > distance between two of our nested spheres:rlist > > is this approach correct? > > No. I suggest you read section 4.6.3 (and probably also 4.6.2) in the > Gromacs Manual. > The Difference between rcoulomb (or rvdw) and rlist is a buffer-zone > for the fact that the > neighbor-lists are only updated every nstlist steps (often nstlist = 5). > > Oliver > > 2012/3/21 ahmet yıldırım : > > Dear users, > > > > Berk Hess says: > > [gmx-users] a) rlist vs rvdw/rcoulomb size confusion, and b) reduced > units > > Mon Jul 16 14:17:12 CEST 2007 > > > > There are three options in Gromacs. > > > > The option you want is rcoulomb < rlist and rvdw < rlist. > > This works and gives the most accurate and also the most costly > integration. > > > > A faster and very commonly used setting is: rlist=rcoulomb=rvdw. > > With PME the Coulomb interactions are very small at the cut-off, > > as are the LJ interactions. > > So with a small sacrifice in integration accuracy one can gain a lot > > of performance, also because analytical LJ is cheaper than tabulated. > > > > The last option is rcoulomb > rlist and/or rvdw > rlist. > > Then the energies and forces beyond rlist are only updated every nslist > > steps. > > This gives less integration accuracy but can give a lot of "interaction" > > accuracy > > at a small computational cost. > > > > Justin A. Lemkul says: > > [gmx-users] Twin-range cut-off > > Tue Sep 13 01:25:28 CEST 2011 > > > > > > A twin-range cutoff just means that your short-range cutoffs aren't all > the > > same > > value, such that they form two interaction zones. Within the shortest, > the > > neighbor list is updated every step. Between the shortest and longest > > cutoffs, > > the neighbor list is updated every nstlist steps. For instance: > > > > rlist = 0.9 > > rcoulomb = 0.9 > > rvdw = 1.4 > > > > are common settings for Gromos96 force fields (in conjunction with PME). > > Thus > > there are two interaction zones - the first is if two atoms (or charge > > groups, > > depending on the algorithm) are within 0.9 nm, and the second is if the > two > > interacting species are beyond 0.9 nm but within 1.4 nm of each other. > > > > rcoulomb: distance for Coulomb cut-off (nm) > > rvdw:distance for LJ or Buckingham cut-off (nm) > > nstlist: neighbor list update frequency > > rlist: cut-off distance of the short-range neighbor > > Twin range cutoff consists of rcoulomb and rvdw, isnt it? > > > > Let's imagine a sphere(two concentric spheres): > > radius of the inside small sphere=rvdw > > radius of the big sphere=rcoulomb > > distance between two of our nested spheres:rlist > > is this approach correct? > > I could not understand the fourierspacing and rlist. > > > > > > Thanks in advance > > > > > > > > 21 Mart 2012 20:53 tarihinde ahmet yıldırım yazdı: > > > >> Dear users, > >> > >> I have two configuration as the following related to Neigborsearching, > >> Electrostatics and vdw options. I checked the literature: > >> Generally the rlist, rcoulomb and rvdw have used as the following. > >> rlist=1 > >> rcoulomb=0.8 > >> rvdw=1.4 > >> > >> Is there much difference between the following two options in the > >> calculation/the results? Is there one significant difference between > the two > >> options. If yes, then what is it? What is relationship between rlist, > >> nstlist and rvdw/rcoulomb? > >> > >> Furthermore, > >> fourierspacing = 0.16 > >> or > >> fourierspacing = 0.12 > >> difference between these two options? > >> > >> 1.choice
[gmx-users] Re: Neigborsearching, Electrostatics and vdw options
Dear users, *Berk Hess says: [gmx-users] a) rlist vs rvdw/rcoulomb size confusion, and b) reduced units Mon Jul 16 14:17:12 CEST 2007* There are three options in Gromacs. The option you want is rcoulomb < rlist and rvdw < rlist. This works and gives the most accurate and also the most costly integration. A faster and very commonly used setting is: rlist=rcoulomb=rvdw. With PME the Coulomb interactions are very small at the cut-off, as are the LJ interactions. So with a small sacrifice in integration accuracy one can gain a lot of performance, also because analytical LJ is cheaper than tabulated. The last option is rcoulomb > rlist and/or rvdw > rlist. Then the energies and forces beyond rlist are only updated every nslist steps. This gives less integration accuracy but can give a lot of "interaction" accuracy at a small computational cost. *Justin A. Lemkul says: [gmx-users] Twin-range cut-off Tue Sep 13 01:25:28 CEST 2011* A twin-range cutoff just means that your short-range cutoffs aren't all the same value, such that they form two interaction zones. Within the shortest, the neighbor list is updated every step. Between the shortest and longest cutoffs, the neighbor list is updated every nstlist steps. For instance: rlist = 0.9 rcoulomb = 0.9 rvdw = 1.4 are common settings for Gromos96 force fields (in conjunction with PME). Thus there are two interaction zones - the first is if two atoms (or charge groups, depending on the algorithm) are within 0.9 nm, and the second is if the two interacting species are beyond 0.9 nm but within 1.4 nm of each other. rcoulomb: distance for Coulomb cut-off (nm) rvdw:distance for LJ or Buckingham cut-off (nm) nstlist: neighbor list update frequency rlist: cut-off distance of the short-range neighbor Twin range cutoff consists of rcoulomb and rvdw, isnt it? Let's imagine a sphere(two concentric spheres): radius of the inside small sphere=rvdw radius of the big sphere=rcoulomb distance between two of our nested spheres:rlist is this approach correct? I could not understand the fourierspacing and rlist. Thanks in advance 21 Mart 2012 20:53 tarihinde ahmet yıldırım yazdı: > Dear users, > > I have two configuration as the following related to Neigborsearching, > Electrostatics and vdw options. I checked the literature: > Generally the rlist, rcoulomb and rvdw have used as the following. > rlist=1 > rcoulomb=0.8 > rvdw=1.4 > > *Is there much difference between the following two options in the > calculation/the results? Is there one significant difference between the > two options. If yes, then what is it? What is relationship between rlist, > nstlist and rvdw/rcoulomb?* > > Furthermore, > fourierspacing = 0.16 > or > fourierspacing = 0.12 > *difference between these two options?* > > *1.choice* > . > ; NEIGHBORSEARCHING PARAMETERS > nstlist = 5 > ns-type = Grid > pbc= xyz > *rlist= 1.0 * > > ; OPTIONS FOR ELECTROSTATICS AND VDW > coulombtype = PME > pme_order= 4 > fourierspacing = 0.16 > *rcoulomb = 1.0* > vdw-type = Cut-off > *rvdw = 1.0* > ... > > *2.choice* > .. > ; NEIGHBORSEARCHING PARAMETERS > nstlist = 5 > ns-type= Grid > pbc = xyz > *rlist = 0.9 * > > ; OPTIONS FOR ELECTROSTATICS AND VDW > coulombtype = PME > pme_order = 4 > fourierspacing = 0.16 > *rcoulomb = 0.9 * > vdw-type = Cut-off > *rvdw = 1.4* > ... > > Thanks in advance > -- > Ahmet Yıldırım > > -- Ahmet Yıldırım -- 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] Neigborsearching, Electrostatics and vdw options
Dear users, I have two configuration as the following related to Neigborsearching, Electrostatics and vdw options. I checked the literature: Generally the rlist, rcoulomb and rvdw have used as the following. rlist=1 rcoulomb=0.8 rvdw=1.4 *Is there much difference between the following two options in the calculation/the results? Is there one significant difference between the two options. If yes, then what is it? What is relationship between rlist, nstlist and rvdw/rcoulomb?* Furthermore, fourierspacing = 0.16 or fourierspacing = 0.12 *difference between these two options?* *1.choice* . ; NEIGHBORSEARCHING PARAMETERS nstlist = 5 ns-type = Grid pbc= xyz *rlist= 1.0 * ; OPTIONS FOR ELECTROSTATICS AND VDW coulombtype = PME pme_order= 4 fourierspacing = 0.16 *rcoulomb = 1.0* vdw-type = Cut-off *rvdw = 1.0* ... *2.choice* .. ; NEIGHBORSEARCHING PARAMETERS nstlist = 5 ns-type= Grid pbc = xyz *rlist = 0.9 * ; OPTIONS FOR ELECTROSTATICS AND VDW coulombtype = PME pme_order = 4 fourierspacing = 0.16 *rcoulomb = 0.9 * vdw-type = Cut-off *rvdw = 1.4* ... Thanks in advance -- Ahmet Yıldırım -- 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] pme note
Dear users, I get the following note: The optimal PME mesh load for parallel simulations is below 0.5 and for highly parallel simulations between 0.25 and 0.33, for higher performance, increase the cut-off and the PME grid spacing What should I do? Thanks in advance -- Ahmet Yıldırım -- 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] one ligand in ATB
Hi, I have a pdb file containing only one ligand. There is already .gro and .itp files of this ligand at Automated Topology Builder (ATB). I want to use the gro and .itp files of this ligand from ATB. The ligand coordinates in my pdb file is different than at ATB. i.e. ATB have used another coordinates when it obtains .gro and .itp files. can I use these files obtained from ATB? If ok, doesn't the location/position of the ligand change in the enzyme? Greetings -- Ahmet Yıldırım -- 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] rerun problem
Dear users, I am using Gromacs 4.5.4. I rerun the simulation using the following command: mdrun -s protein-RUN.tpr -cpi protein-RUN.cpt -append Unfortunately remaining output didnt append to existing files (protein-RUN.xtc, protein-RUN.edr, protein-RUN.log). On the contrary remaining output appended to new files (traj.xtc, ener.edr, md.log). What should I do? Cheers, -- Ahmet Yıldırım -- 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] overheating problem
Hi, I put a new cooler (Thermaltake Friock) on the CPU. The problem is solved. 2012/2/4 Mark Abraham > On 4/02/2012 11:15 PM, ahmet yıldırım wrote: > > Hi, > The problem might caused by X58 chipset. > Now I am using ubuntu. Which operating system do you recommend? > > > I doubt it is relevant at all. > > Mark > > > 2012/2/4 David van der Spoel > >> On 2012-02-03 23:49, ahmet yıldırım wrote: >> >>> Dear Mark, >>> >>> >>> Believe me, I tried all methods that you said but unfortunately the >>> result doesnt change :( >>> >> >> It used to be like this that GROMACS ran more efficient on AMD cpus than >> the official AMD burn-in code, and therefore also hotter. You could run >> gromacs on fewer cores to see if that helps, but it seems like a hardware >> problem. Have any warranty on your computers? >> >> >>> 2012/2/4 Mark Abraham >> <mailto:mark.abra...@anu.edu.au>> >>> >>> >>>On 4/02/2012 8:24 AM, ahmet yıldırım wrote: >>> >>>>Dear users, >>>> >>>>I am using ubuntu 11.1 (64 bit). The Ubuntu normally runs when I >>>>dont run the Gromacs program. i.e there is not heating problem. >>>>But the CPU is excessive heating (82 degree) when I run the gromacs. >>>> >>> >>>There are various "stress test" programs you can get if you Google >>>around. I expect these will produce the same symptoms. >>> >>> >>> I am using the all cores at 100%. Now I have 2 PC.I use them >>>> >>>>separately >>>>1.first: It has Intel i7 920 CPU and Asus P6T SE motherboard >>>>2.second: It has Intel I7 960 and Gıgabyte x58A-UD5 LGA 1366 >>>>motherboard >>>>I have the problem of warming/overheating on both computers. I >>>>could not figure out this problem for two weeks :( >>>>By the way: >>>>-I dont use an older compiler to get the binary. I am using gcc >>>>4.6 and I am using Gromacs 4.5.4 >>>>-I watch the temperatures by "lm sensor" program >>>>-I installed ubuntu 32-bit but the result didnt change again >>>>-I have sufficient cooling on both PC >>>> >>> >>>I'd say this is evidence that you don't have sufficient cooling. >>> >>> >>>It is likely something related to the program because no problem >>>>with any hardware related to computers according to experts say. >>>> >>> >>>If things are installed correctly. For example, cheap thermal paste >>>between the CPU and heat sink can cause these symptoms. >>> >>> >>> >>>>what do you suggest? :( >>>> >>> >>>Get more cooling. Maybe lower the clock speed (if possible). Run a >>>less efficient MD code! >>> >>>Mark >>> >>> >>> >>>>*atk0110-acpi-0 >>>> >>>>Adapter: ACPI interface >>>>Vcore Voltage: +1.22 V (min = +0.80 V, max = +1.60 V) >>>> +3.3 Voltage: +3.31 V (min = +2.97 V, max = +3.63 V) >>>> +5 Voltage: +5.00 V (min = +4.50 V, max = +5.50 V) >>>> +12 Voltage: +12.03 V (min = +10.20 V, max = +13.80 V) >>>>CPU FAN Speed: 2163 RPM (min = 600 RPM) >>>>CHASSIS1 FAN Speed:0 RPM (min = 600 RPM) >>>>CHASSIS2 FAN Speed: 2033 RPM (min = 600 RPM) >>>>POWER FAN Speed: 0 RPM (min =0 RPM) >>>>CPU Temperature: +82.0°C (high = +60.0°C, crit = +75.0°C) >>>>MB Temperature: +45.0°C (high = +45.0°C, crit = +75.0°C) >>>> >>>>radeon-pci-0200 >>>>Adapter: PCI adapter >>>> temp1:+60.5°C * >>>> >>>> >>>>-- >>>>Ahmet Yıldırım >>>> >>>> >>>> >>>> >>> >>>-- >>>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 t
Re: [gmx-users] overheating problem
Hi, The problem might caused by X58 chipset. Now I am using ubuntu. Which operating system do you recommend? 2012/2/4 David van der Spoel > On 2012-02-03 23:49, ahmet yıldırım wrote: > >> Dear Mark, >> >> >> Believe me, I tried all methods that you said but unfortunately the >> result doesnt change :( >> > > It used to be like this that GROMACS ran more efficient on AMD cpus than > the official AMD burn-in code, and therefore also hotter. You could run > gromacs on fewer cores to see if that helps, but it seems like a hardware > problem. Have any warranty on your computers? > > >> 2012/2/4 Mark Abraham > <mailto:mark.abra...@anu.edu.**au >> >> >> >>On 4/02/2012 8:24 AM, ahmet yıldırım wrote: >> >>>Dear users, >>> >>>I am using ubuntu 11.1 (64 bit). The Ubuntu normally runs when I >>>dont run the Gromacs program. i.e there is not heating problem. >>>But the CPU is excessive heating (82 degree) when I run the gromacs. >>> >> >>There are various "stress test" programs you can get if you Google >>around. I expect these will produce the same symptoms. >> >> >>I am using the all cores at 100%. Now I have 2 PC.I use them >>> >>>separately >>>1.first: It has Intel i7 920 CPU and Asus P6T SE motherboard >>>2.second: It has Intel I7 960 and Gıgabyte x58A-UD5 LGA 1366 >>>motherboard >>>I have the problem of warming/overheating on both computers. I >>>could not figure out this problem for two weeks :( >>>By the way: >>>-I dont use an older compiler to get the binary. I am using gcc >>>4.6 and I am using Gromacs 4.5.4 >>>-I watch the temperatures by "lm sensor" program >>>-I installed ubuntu 32-bit but the result didnt change again >>>-I have sufficient cooling on both PC >>> >> >>I'd say this is evidence that you don't have sufficient cooling. >> >> >>It is likely something related to the program because no problem >>>with any hardware related to computers according to experts say. >>> >> >>If things are installed correctly. For example, cheap thermal paste >>between the CPU and heat sink can cause these symptoms. >> >> >> >>>what do you suggest? :( >>> >> >>Get more cooling. Maybe lower the clock speed (if possible). Run a >>less efficient MD code! >> >>Mark >> >> >> >>>*atk0110-acpi-0 >>> >>>Adapter: ACPI interface >>>Vcore Voltage: +1.22 V (min = +0.80 V, max = +1.60 V) >>> +3.3 Voltage: +3.31 V (min = +2.97 V, max = +3.63 V) >>> +5 Voltage: +5.00 V (min = +4.50 V, max = +5.50 V) >>> +12 Voltage: +12.03 V (min = +10.20 V, max = +13.80 V) >>>CPU FAN Speed: 2163 RPM (min = 600 RPM) >>>CHASSIS1 FAN Speed:0 RPM (min = 600 RPM) >>>CHASSIS2 FAN Speed: 2033 RPM (min = 600 RPM) >>>POWER FAN Speed: 0 RPM (min =0 RPM) >>>CPU Temperature: +82.0°C (high = +60.0°C, crit = +75.0°C) >>>MB Temperature: +45.0°C (high = +45.0°C, crit = +75.0°C) >>> >>>radeon-pci-0200 >>>Adapter: PCI adapter >>>temp1:+60.5°C * >>> >>> >>>-- >>>Ahmet Yıldırım >>> >>> >>> >>> >> >>-- >>gmx-users mailing list gmx-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-request@**gromacs.org>. >> >> >>Can't post? Read >> http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> >> >> >> >> >> -- >> Ahmet Yıldırım >> >> >> >> > > -- > David van der Spoel, Ph.D., Professor of Biology > Dept. of Cell & Molec. Biol., Uppsala University. > Box 596, 75124 Uppsala, Sweden. Phone
Re: [gmx-users] overheating problem
Dear Mark, Believe me, I tried all methods that you said but unfortunately the result doesnt change :( 2012/2/4 Mark Abraham > On 4/02/2012 8:24 AM, ahmet yıldırım wrote: > > Dear users, > > I am using ubuntu 11.1 (64 bit). The Ubuntu normally runs when I dont run > the Gromacs program. i.e there is not heating problem. But the CPU is > excessive heating (82 degree) when I run the gromacs. > > > There are various "stress test" programs you can get if you Google around. > I expect these will produce the same symptoms. > > > I am using the all cores at 100%. Now I have 2 PC. I use them separately > 1.first: It has Intel i7 920 CPU and Asus P6T SE motherboard > 2.second: It has Intel I7 960 and Gıgabyte x58A-UD5 LGA 1366 motherboard > I have the problem of warming/overheating on both computers. I could not > figure out this problem for two weeks :( > By the way: > -I dont use an older compiler to get the binary. I am using gcc 4.6 and I > am using Gromacs 4.5.4 > -I watch the temperatures by "lm sensor" program > -I installed ubuntu 32-bit but the result didnt change again > -I have sufficient cooling on both PC > > > I'd say this is evidence that you don't have sufficient cooling. > > > It is likely something related to the program because no problem with any > hardware related to computers according to experts say. > > > If things are installed correctly. For example, cheap thermal paste > between the CPU and heat sink can cause these symptoms. > > > > what do you suggest? :( > > > Get more cooling. Maybe lower the clock speed (if possible). Run a less > efficient MD code! > > Mark > > > > *atk0110-acpi-0 > Adapter: ACPI interface > Vcore Voltage: +1.22 V (min = +0.80 V, max = +1.60 V) > +3.3 Voltage: +3.31 V (min = +2.97 V, max = +3.63 V) > +5 Voltage: +5.00 V (min = +4.50 V, max = +5.50 V) > +12 Voltage: +12.03 V (min = +10.20 V, max = +13.80 V) > CPU FAN Speed: 2163 RPM (min = 600 RPM) > CHASSIS1 FAN Speed:0 RPM (min = 600 RPM) > CHASSIS2 FAN Speed: 2033 RPM (min = 600 RPM) > POWER FAN Speed: 0 RPM (min =0 RPM) > CPU Temperature: +82.0°C (high = +60.0°C, crit = +75.0°C) > MB Temperature: +45.0°C (high = +45.0°C, crit = +75.0°C) > > radeon-pci-0200 > Adapter: PCI adapter > temp1:+60.5°C * > > > -- > Ahmet Yıldırım > > > > > > -- > 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 > -- Ahmet Yıldırım -- 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 in installation
Hi, 1.method: You can install it from Synaptic package manager. 2.method: sudo apt-get install libfftw3-dev Later, in gromacs directory ./configure sudo make sudo make install sudo make mdrun sudo make links 2012/1/18 Mark Abraham > On 18/01/2012 7:30 PM, kumud agarwal wrote: > > Hi > > I have been trying to install Gromacs on ubuntu. > > After make command I got the following error > > */usr/bin/ld: /usr/local/lib/libfftw3f.a(alloc.o): relocation R_X86_64_32 > against `.rodata.str1.1' can not be used when making a shared object; > recompile with -fPIC* > > > See > http://www.gromacs.org/Downloads/Installation_Instructions#Details_for_building_the_FFTW_prerequisite > > Mark > > */usr/local/lib/libfftw3f.a: could not read symbols: Bad value* > > *collect2: ld returned 1 exit status* > > *make[3]: *** [libmd.la] Error 1* > > *make[3]: Leaving directory `/home/ankit/gromacs/gromacs-4.5.5/src/mdlib'* > > *make[2]: *** [all-recursive] Error 1* > > *make[2]: Leaving directory `/home/ankit/gromacs/gromacs-4.5.5/src'* > > *make[1]: *** [all] Error 2* > > *make[1]: Leaving directory `/home/ankit/gromacs/gromacs-4.5.5/src'* > > *make: *** [all-recursive] Error 1* > > *ankit@ubuntu:~/gromacs/gromacs-4.5.5$ > * > > How can I solve this error? > > Thanks > > Kumud Agarwal > > > > > > > > -- > 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 > -- Ahmet Yıldırım -- 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] multi file input for index files
Thanks Mark and Marzinek, The Problem is solved: g_hbond -f traj.xtc -s run.tpr -num AB.xvg -n AB.ndx > chain A Found 1234 atoms with chain identifier A 19 chA : 1234 atoms > name 19 chainA > chain B Found 1234 atoms with chain identifier B 20 chB : 1234 atoms > name 20 chainB > q 2012/1/10 Marzinek, Jan > So as you can see Gromacs does not support multi file input :) Create > one index file and specify there your two groups. Then g_hbond will ask you > to choose two groups from this file. > > > > Jan > > > > === > Jan Marzinek > PhD Candidate > Centre for Process Systems Engineering > Department of Chemical Engineering > Imperial College London > South Kensington Campus > London SW7 2AZ > E: j.marzine...@imperial.ac.uk > M: +44(0)7411 640 552 > -- > *From:* gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on > behalf of ahmet yıldırım [ahmedo...@gmail.com] > *Sent:* Tuesday, January 10, 2012 8:13 AM > *To:* Discussion list for GROMACS users > *Subject:* [gmx-users] multi file input for index files > > Dear users, > > I created two different index files (A.ndx and B.ndx). I want to run the > two files at the same time. > e.g. > g_hbond -f traj.xtc -s run.tpr -num A-B.xvg -n A.ndx -n B.ndx > where, I want to calculate the hydrogen bonds between A and B. > This command is giving the error as it expected. "Gromacs tools do not > support multi file input for index files" from > http://sbcb.bioch.ox.ac.uk/users/oliver/software/GromacsWrapper/html/gromacs/core/tools.html. > Is this correct? If no, what should I do? > > Thanks in advance > -- > Ahmet Yıldırım > > > -- > 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 > -- Ahmet Yıldırım -- 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] multi file input for index files
Hi, But I want to calculate the hydrogen bonds between A and B groups. If I do as you said, I will have calculated intra hydrogen bonds of a group AB (merged A and B). 2012/1/10 Mark Abraham > On 10/01/2012 7:13 PM, ahmet yıldırım wrote: > >> Dear users, >> >> I created two different index files (A.ndx and B.ndx). I want to run the >> two files at the same time. >> e.g. >> g_hbond -f traj.xtc -s run.tpr -num A-B.xvg -n A.ndx -n B.ndx >> where, I want to calculate the hydrogen bonds between A and B. >> This command is giving the error as it expected. "Gromacs tools do not >> support multi file input for index files" from >> http://sbcb.bioch.ox.ac.uk/**users/oliver/software/** >> GromacsWrapper/html/gromacs/**core/tools.html<http://sbcb.bioch.ox.ac.uk/users/oliver/software/GromacsWrapper/html/gromacs/core/tools.html>. >> Is this correct? If no, what should I do? >> > > You can put your two groups in the same index file. > > Run make_ndx and quit to see the format for index.ndx that it generates by > default. You can do that too. > > Mark > -- > gmx-users mailing listgmx-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. > Can't post? Read > http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> > -- Ahmet Yıldırım -- 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] multi file input for index files
Dear users, I created two different index files (A.ndx and B.ndx). I want to run the two files at the same time. e.g. g_hbond -f traj.xtc -s run.tpr -num A-B.xvg -n A.ndx -n B.ndx where, I want to calculate the hydrogen bonds between A and B. This command is giving the error as it expected. "Gromacs tools do not support multi file input for index files" from http://sbcb.bioch.ox.ac.uk/users/oliver/software/GromacsWrapper/html/gromacs/core/tools.html. Is this correct? If no, what should I do? Thanks in advance -- Ahmet Yıldırım -- 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] calculation time
Thanks for your reply I dont understand "step number is at least as large as nstlist". can you some explain? Furthermore, if the file system doesnt write the buffer to the destination screen/file, then does that mean there is a problem? for example if it shows as the following: 1500 steps, 3.0 ps. 2011/10/19 Mark Abraham > On 19/10/2011 5:04 PM, ahmet yıldırım wrote: > > For example; > > grompp -f run.mdp -p topol.top -c pr.gro -n index.ndx -o run.tpr > mdrun -v -deffnm run > > ... > 1500 steps, 3.0 ps. > step 100, will finish Sun Nov 27 19:11:00 2011 > > Sometimes it shows as the following: > 1500 steps, 3.0 ps. > That is, there is not "will finish Sun Nov 27 19:11:00 2011" sentence > > > It only writes it when certain conditions are true (e.g. step number is at > least as large as nstlist), and it only appears when the file system decides > to write the buffer to the destination screen/file. > > Mark > > > > > 2011/10/19 Emanuel Birru > >> You can get them in the log file. (At the bottom) >> >> Cheers, >> >> >> >> >> >> >> >> = >> Emanuel Birru >> PhD Candidate >> >> Faculty of Pharmacy and Pharmaceutical Sciences >> Monash University (Parkville Campus) >> 381 Royal Parade, Parkville >> Victoria 3052, Australia >> >> Tel: Int + 61 3 9903 9187 <%2B%2061%203%209903%209187> >> E-mail: emanuel.bi...@monash.edu >> www.pharm.monash.edu.au >> >> -Original Message- >> From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] >> On Behalf Of Mark Abraham >> Sent: Wednesday, 19 October 2011 3:08 PM >> To: Discussion list for GROMACS users >> Subject: Re: [gmx-users] calculation time >> >> On 19/10/2011 5:26 AM, ahmet yıldırım wrote: >> > Dear users, >> > >> > Sometimes, in the end ( in production simulation), Gromacs doesn't >> > show calculation/finish time on screen, why? How can we show it? >> >> I don't know what you mean. >> >> 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 >> >> -- >> 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 >> > > > > -- > Ahmet YILDIRIM > > > > > -- > 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 > -- Ahmet YILDIRIM -- 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] calculation time
For example; grompp -f run.mdp -p topol.top -c pr.gro -n index.ndx -o run.tpr mdrun -v -deffnm run ... 1500 steps, 3.0 ps. step 100, will finish Sun Nov 27 19:11:00 2011 Sometimes it shows as the following: 1500 steps, 3.0 ps. That is, there is not "will finish Sun Nov 27 19:11:00 2011" sentence 2011/10/19 Emanuel Birru > You can get them in the log file. (At the bottom) > > Cheers, > > > > > > > > = > Emanuel Birru > PhD Candidate > > Faculty of Pharmacy and Pharmaceutical Sciences > Monash University (Parkville Campus) > 381 Royal Parade, Parkville > Victoria 3052, Australia > > Tel: Int + 61 3 9903 9187 > E-mail: emanuel.bi...@monash.edu > www.pharm.monash.edu.au > > -Original Message- > From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] > On Behalf Of Mark Abraham > Sent: Wednesday, 19 October 2011 3:08 PM > To: Discussion list for GROMACS users > Subject: Re: [gmx-users] calculation time > > On 19/10/2011 5:26 AM, ahmet yıldırım wrote: > > Dear users, > > > > Sometimes, in the end ( in production simulation), Gromacs doesn't > > show calculation/finish time on screen, why? How can we show it? > > I don't know what you mean. > > 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 > > -- > 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 > -- Ahmet YILDIRIM -- 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] calculation time
Dear users, Sometimes, in the end ( in production simulation), Gromacs doesn't show calculation/finish time on screen, why? How can we show it? Thanks in advance -- Ahmet YILDIRIM -- 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] RMSD bonds and angles
No, it calculates with respect to the positions atom. but I want to calculate the RMSD bonds (A˚ ) and RMSD angles (o). 2011/10/4 Mark Abraham > On 4/10/2011 7:05 PM, ahmet yıldırım wrote: > > any hints? :( > > > You didn't find something useful in the section titled "Root mean square > deviations in structure"? > > Mark > > > 03 Ekim 2011 22:32 tarihinde ahmet yıldırım yazdı: > >> I look at chapter 8 but I didnt found that I want. can you give a hint? >> Thanks >> >> >> 2011/10/3 Mark Abraham >> >>> On 3/10/2011 10:29 PM, ahmet yıldırım wrote: >>> >>>> Dear users, >>>> >>>> How can I calculate the RMSD bonds (A˚ ) and RMSD angles (o)? >>>> >>> >>> Please start your search in chapter 8 of the manual, and consider doing >>> some tutorial material. Someone is likely to have covered some similar >>> procedures. >>> >>> 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 >>> >> >> >> >> -- >> Ahmet YILDIRIM >> > > > > -- > Ahmet YILDIRIM > > > > > -- > 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 > -- Ahmet YILDIRIM -- 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] RMSD bonds and angles
any hints? :( 03 Ekim 2011 22:32 tarihinde ahmet yıldırım yazdı: > I look at chapter 8 but I didnt found that I want. can you give a hint? > Thanks > > > 2011/10/3 Mark Abraham > >> On 3/10/2011 10:29 PM, ahmet yıldırım wrote: >> >>> Dear users, >>> >>> How can I calculate the RMSD bonds (A˚ ) and RMSD angles (o)? >>> >> >> Please start your search in chapter 8 of the manual, and consider doing >> some tutorial material. Someone is likely to have covered some similar >> procedures. >> >> Mark >> -- >> gmx-users mailing listgmx-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. >> Can't post? Read >> http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> >> > > > > -- > Ahmet YILDIRIM > -- Ahmet YILDIRIM -- 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] heteroatom not to be a ligand
Dear users, I have a xxx .pdb including enzyme+X. But X is a cryoprotectant, that is heteroatom, it is not a ligand. I think I shouldn't use a way as Justin tutorial 5. Because X is not a ligand. what should I do? Thanks -- Ahmet YILDIRIM -- 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] RMSD bonds and angles
I look at chapter 8 but I didnt found that I want. can you give a hint? Thanks 2011/10/3 Mark Abraham > On 3/10/2011 10:29 PM, ahmet yıldırım wrote: > >> Dear users, >> >> How can I calculate the RMSD bonds (A˚ ) and RMSD angles (o)? >> > > Please start your search in chapter 8 of the manual, and consider doing > some tutorial material. Someone is likely to have covered some similar > procedures. > > Mark > -- > gmx-users mailing listgmx-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. > Can't post? Read > http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> > -- Ahmet YILDIRIM -- 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] RMSD bonds and angles
Dear users, How can I calculate the RMSD bonds (A˚ ) and RMSD angles (o)? Thanks in advance -- Ahmet YILDIRIM -- 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] if PRODRG calculate incorrectly
Dear users, If I obtain/generate the topology file for a ligand using another program (except PRODRG); 1) How can I arrange .itp file? Because it seems very complicate. 2) Justin tutorial: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/02_topology.html We will make use of two files that PRODRG gives us. Save the output of the field "The GROMOS87/GROMACS coordinate file (polar/aromatic hydrogens)" into a text file called "jz4.gro" and "The GROMACS topology" into a file called "drg.itp." Then how can I generate .gro file using another program? I was obtaining .gro and .itp files using PRODRG but PRODRG is giving improper results/output. best regards 2011/9/17 Mark Abraham > On 17/09/2011 11:28 PM, ahmet yıldırım wrote: > >> Dear Tsjerk and Justin, >> >> Thanks for your reply. I will contact the PRODRG developers. >> can you suggest anyway/anytool for generating ligand >> coordinates/topologies? >> > > http://www.gromacs.org/**Documentation/How-tos/Steps_** > to_Perform_a_Simulation<http://www.gromacs.org/Documentation/How-tos/Steps_to_Perform_a_Simulation> > > Mark > > -- > gmx-users mailing listgmx-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. > Can't post? Read > http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> > -- Ahmet YILDIRIM -- 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] meaning of minus potential and buried surface area
Dear Justin, If possible, can you some explain "net attraction"? Best regards 2011/9/22 Justin A. Lemkul > > > ahmet yıldırım wrote: > >> Dear users, >> >> 1.) During the simulation the mean potential energy is minus (-) value. >> What does this mean? Why minus? >> > > Net attraction. > > > 2.) let's say, Interface/Buried Surace Area (ISA) between protein and >> ligand was calculated and hydrophobic ISA obtained greater than hydrophilic >> ISA. What does this mean? >> >> > That, as you might expect, hydrophobic groups are shielded from the solvent > to a greater extent than polar groups. > > -Justin > > > No one is my special advisor but If you help me, I will be happy. >> >> Thanks in advance >> >> -- >> Ahmet YILDIRIM >> >> > -- > ==**== > > 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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> > > ==**== > -- > gmx-users mailing listgmx-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. > Can't post? Read > http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> > -- Ahmet YILDIRIM -- 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] what difference between RMSF and RMDEV
Dear Justin, Thanks for your reply. Tsjerk: http://lists.gromacs.org/pipermail/gmx-users/2009-October/045884.html There are two things to distinguish: > > 1. The reference structure used to remove translational and rotational > degrees of freedom > 2. The reference against which the deviations (on a per atom base) are > calculated that are then squared, averaged and taken the root of (root > mean square fluctuation). > > These two need not be the same. It is common, and most sensible, to > calculate the deviations against the average structure, after fitting > all structures in the trajectory against a certain reference > structure. With option -od the deviations against the reference used > for fitting are calculated rather than against the average. You do > need a reference for fitting, since otherwise you include overall > rotation and translation in the calculation of the RMSF, which you > usually wouldn't want. > 1.) For RMSD, You said (i.e. the one present in the .tpr file). which one? How do Gromacs select the reference structure? 2.) Tsjerk: RMSF calculate the deviations against the average structure, after fitting all structures in the trajectory against a certain reference structure. the reference structure is taken as average over the trajectory. That is, it is the average structure (please look at example). isn't it? *For example:* coordinates of N atom: x y z 2 4 6 8 7 1 8 1 2 the average structure of N atom:[(x1+x2+x3)/3, (y1+y2+y3)/3, (z1+z2+z3)/3]. isnt it? x y z 6 4 3 3.) This "The reference structure used to remove translational and rotational degrees of freedom" is RMSD??? 2011/9/21 Justin A. Lemkul > > > ahmet yıldırım wrote: > >> Dear users, >> >> g_rmsf -s run.tpr -f run.xtc -od rmsdev.xvg -o rmsf.xvg -res >> >> With the option -od the root mean square deviation with respect to the >> reference structure is calculated. >> Then, >> RMSDEV is the RMSD per residue (the root mean square deviation with >> respect to the reference structure is calculated). >> >> and >> RMSF is the RMSD per residue (the root mean square fluctuation (RMSF, i.e. >> standard deviation) of atomic positions after (optionally) fitting to a >> reference frame). That is, it is the measurement averaged over all atoms in >> each residue. >> >> Now what difference? >> >> > The RMSD is measured relative to the reference structure (i.e. the one > present in the .tpr file). RMSF is measured with respect to average > coordinates. > > -Justin > > > I am confused. >> >> -- >> Ahmet YILDIRIM >> >> > -- > ==**== > > 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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> > > ==**== > -- > gmx-users mailing listgmx-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. > Can't post? Read > http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> > -- Ahmet YILDIRIM -- 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] meaning of minus potential and buried surface area
Dear users, 1.) During the simulation the mean potential energy is minus (-) value. What does this mean? Why minus? 2.) let's say, Interface/Buried Surace Area (ISA) between protein and ligand was calculated and hydrophobic ISA obtained greater than hydrophilic ISA. What does this mean? No one is my special advisor but If you help me, I will be happy. Thanks in advance -- Ahmet YILDIRIM -- 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] what difference between RMSF and RMDEV
Dear users, g_rmsf -s run.tpr -f run.xtc -od rmsdev.xvg -o rmsf.xvg -res With the option -od the root mean square deviation with respect to the reference structure is calculated. Then, RMSDEV is the RMSD per residue (the root mean square deviation with respect to the reference structure is calculated). and RMSF is the RMSD per residue (the root mean square fluctuation (RMSF, i.e. standard deviation) of atomic positions after (optionally) fitting to a reference frame). That is, it is the measurement averaged over all atoms in each residue. Now what difference? I am confused. -- Ahmet YILDIRIM -- 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] if PRODRG calculate incorrectly
Dear Tsjerk and Justin, Thanks for your reply. I will contact the PRODRG developers. can you suggest anyway/anytool for generating ligand coordinates/topologies? Thanks in advance 17 Eylül 2011 15:58 tarihinde Justin A. Lemkul yazdı: > > > ahmet yıldırım wrote: > >> Dear users, >> I have a problem related to PRODRG. >> >> Chirality:NO >> Full charges: YES >> Energy minimization: NO >> >> _*İnput file name:TRS.pdb*_ >> HETATM 1803 C TRS B 232 38.588 -4.733 65.956 1.00 17.99 >> C ANISOU 1803 C TRS B 232 2126 1948 2760 -378 45-81 >> C HETATM 1804 C1 TRS B 232 40.103 -5.057 65.899 1.00 16.81 >> C ANISOU 1804 C1 TRS B 232 1642 1577 3168 -531171 >> 120 C HETATM 1805 C2 TRS B 232 37.795 -5.994 66.343 1.00 >> 20.76 C ANISOU 1805 C2 TRS B 232 2790 2021 3077 67 >> 141 -408 C HETATM 1806 C3 TRS B 232 38.160 -3.717 67.031 >> 1.00 16.86 C ANISOU 1806 C3 TRS B 232 2240 1557 2611 >> -491 8 -192 C HETATM 1807 N TRS B 232 38.227 -4.154 >> 64.652 1.00 18.26 N ANISOU 1807 N TRS B 232 2336 2520 >> 2083 -166 46 -112 N HETATM 1808 O1 TRS B 232 40.741 >> -4.020 65.158 1.00 17.53 O ANISOU 1808 O1 TRS B 232 1921 >> 1579 3163 -225147197 O HETATM 1809 O2 TRS B 232 >> 37.871 -6.803 65.211 1.00 23.91 O ANISOU 1809 O2 TRS B 232 >> 3018 2456 3610-48-86 -450 O HETATM 1810 O3 TRS B 232 >> 38.871 -2.531 66.874 1.00 18.28 O ANISOU 1810 O3 TRS B >> 232 2677 1594 2673197 -4-52 O >> >> I get the output _as the following file1.itp_ from your PRODRG server for >> TRS ligand before 3-4 months. I think this calculate is correct: >> *_file1.itp_* >> >> [ moleculetype ] >> ; Name nrexcl >> TRS 3 >> >> [ atoms ] >> ; nr type resnr resid atom cgnr charge mass >> 1OA 1 TRS O1 1 -0.240 15.9994 2 >> H 1 TRS HAA 10.052 1.0080 3 CH2 1 TRS >> C1 10.061 14.0270 4 CH1 1 TRS C 1 >> 0.127 12.0110 5 CH2 1 TRS C3 20.090 14.0270 >> 6OA 1 TRS O3 2 -0.165 15.9994 7 >> H 1 TRS HAC 20.075 1.0080 8NL 1 TRS >> N 30.876 14.0067 9 H 1 TRS HAE 3 >> 0.041 1.0080 10 H 1 TRS HAF 30.042 1.0080 >> 11 H 1 TRS HAD 30.041 1.0080 12 >> CH2 1 TRS C2 40.090 14.0270 13OA 1 TRS >> O2 4 -0.165 15.9994 14H 1 TRS HAB 4 >> 0.075 1.0080 >> >> >> But Now, That is, today, I get the output _as the following file2.itp_ >> from your PRODRG server for TRS ligand. >> *_file2.itp_* >> . >> [ moleculetype ] >> ; Name nrexcl >> TRS 3 >> >> [ atoms ] >> ; nr type resnr resid atom cgnr charge mass >> 1OA 1 TRS O1 1 -0.173 15.9994 2 >> H 1 TRS H13 10.061 1.0080 3 CH2 1 TRS >>C1 10.165 14.0270 4 CCL4 1 TRS C 1 >> 0.177 12.0110 5 CH2 1 TRS C3 10.165 14.0270 >> 6OA 1 TRS O3 1 -0.174 15.9994 7 >> H 1 TRS H33 10.062 1.0080 8NL 1 TRS >> N 10.675 14.0067 9 H 1 TRS H2 1 >> 0.014 1.0080 10 H 1 TRS H3 10.014 1.0080 >> 11 H 1 TRS H1 10.014 1.0080 12 >> CH2 1 TRS C2 20.144 14.0270 13OA 1 TRS >> O2 2 -0.198 15.9994 14 H 1 TRS H23 2 >> 0.054 1.0080 >> >> Now, I think PRODRG calculate incorrectly cgnr charge >> >> > I agree with Tsjerk that you should contact the PRODRG developers regarding > the differences, but I would also say that neither of these files is > correct. PRODRG has never given reliable charges. See, for instance > (something I posted dozens of times before): > > http://pubs.acs.org/doi/abs/**10.1021/ci100335w<http://pubs.acs.org/doi/abs/10.1021/ci100335w> > > -Ju
[gmx-users] if PRODRG calculate incorrectly
Dear users, I have a problem related to PRODRG. Chirality:NO Full charges: YES Energy minimization: NO *İnput file name:TRS.pdb* HETATM 1803 C TRS B 232 38.588 -4.733 65.956 1.00 17.99 C ANISOU 1803 C TRS B 232 2126 1948 2760 -378 45-81 C HETATM 1804 C1 TRS B 232 40.103 -5.057 65.899 1.00 16.81 C ANISOU 1804 C1 TRS B 232 1642 1577 3168 -531171120 C HETATM 1805 C2 TRS B 232 37.795 -5.994 66.343 1.00 20.76 C ANISOU 1805 C2 TRS B 232 2790 2021 3077 67141 -408 C HETATM 1806 C3 TRS B 232 38.160 -3.717 67.031 1.00 16.86 C ANISOU 1806 C3 TRS B 232 2240 1557 2611 -491 8 -192 C HETATM 1807 N TRS B 232 38.227 -4.154 64.652 1.00 18.26 N ANISOU 1807 N TRS B 232 2336 2520 2083 -166 46 -112 N HETATM 1808 O1 TRS B 232 40.741 -4.020 65.158 1.00 17.53 O ANISOU 1808 O1 TRS B 232 1921 1579 3163 -225147197 O HETATM 1809 O2 TRS B 232 37.871 -6.803 65.211 1.00 23.91 O ANISOU 1809 O2 TRS B 232 3018 2456 3610-48-86 -450 O HETATM 1810 O3 TRS B 232 38.871 -2.531 66.874 1.00 18.28 O ANISOU 1810 O3 TRS B 232 2677 1594 2673197 -4-52 O I get the output *as the following file1.itp* from your PRODRG server for TRS ligand before 3-4 months. I think this calculate is correct: *file1.itp* [ moleculetype ] ; Name nrexcl TRS 3 [ atoms ] ; nr type resnr resid atom cgnr charge mass 1OA 1 TRS O1 1 -0.240 15.9994 2H 1 TRS HAA 10.052 1.0080 3 CH2 1 TRS C1 10.061 14.0270 4 CH1 1 TRS C 10.127 12.0110 5 CH2 1 TRS C3 20.090 14.0270 6OA 1 TRS O3 2 -0.165 15.9994 7H 1 TRS HAC 20.075 1.0080 8NL 1 TRS N 30.876 14.0067 9 H 1 TRS HAE 30.041 1.0080 10 H 1 TRS HAF 30.042 1.0080 11 H 1 TRS HAD 30.041 1.0080 12 CH2 1 TRS C2 40.090 14.0270 13OA 1 TRS O2 4 -0.165 15.9994 14H 1 TRS HAB 40.075 1.0080 But Now, That is, today, I get the output *as the following file2.itp* from your PRODRG server for TRS ligand. *file2.itp* . [ moleculetype ] ; Name nrexcl TRS 3 [ atoms ] ; nr type resnr resid atom cgnr charge mass 1OA 1 TRS O1 1 -0.173 15.9994 2 H 1 TRS H13 10.061 1.0080 3 CH2 1 TRS C1 10.165 14.0270 4 CCL4 1 TRS C 10.177 12.0110 5 CH2 1 TRS C3 10.165 14.0270 6OA 1 TRS O3 1 -0.174 15.9994 7 H 1 TRS H33 10.062 1.0080 8NL 1 TRS N 10.675 14.0067 9 H 1 TRS H2 10.014 1.0080 10 H 1 TRS H3 10.014 1.0080 11 H 1 TRS H1 10.014 1.0080 12 CH2 1 TRS C2 20.144 14.0270 13OA 1 TRS O2 2 -0.198 15.9994 14 H 1 TRS H23 20.054 1.0080 Now, I think PRODRG calculate incorrectly cgnr charge What should I do? can you help me? -- Ahmet YILDIRIM -- 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] residue SASA
There are hydrophilic and hydrophobic SASA values versus simulation time in the output file (area.xvg). I want to hydrophilic and hydrophobic SASA values versus residue. 2011/7/7 Justin A. Lemkul > > > ahmet yıldırım wrote: > >> Dear users, >> >> I want to calculate hydrophilic and hyrophobic SASA value of each residue >> in protein. I used a command as the following: >> >> g_sas -f run.xtc -s run.tpr -or protein_protein.xvg >> Select a group for calculation of surface and a group for output >> select a group: 1 (protein) >> select a group: 2 (protein) >> >> But there is SASA value of each residue in the output file. How can I >> seperate the residues as a hydrophilic and hyrophobic SASA? >> >> > This is already in the output file. Check the legends of area.xvg and you > will see. > > -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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> > > ==**== > -- > gmx-users mailing listgmx-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. > Can't post? Read > http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> > -- Ahmet YILDIRIM -- 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] residue SASA
Dear users, I want to calculate hydrophilic and hyrophobic SASA value of each residue in protein. I used a command as the following: g_sas -f run.xtc -s run.tpr -or protein_protein.xvg Select a group for calculation of surface and a group for output select a group: 1 (protein) select a group: 2 (protein) But there is SASA value of each residue in the output file. How can I seperate the residues as a hydrophilic and hyrophobic SASA? Thanks in advance -- Ahmet YILDIRIM -- 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_sas calculation
Dear Justin, Firstly thanks for your valuable information. Now, is there any error? Please see the following commands: protein and ligand are merged by make_ndx g_sas -f run.xtc -s run.tpr -o area_protein.xvg -n protein_ligand.ndx Select a group for calculation of surface and a group for output *select a group: 1 (protein_ligand)* *select a group: 2 (protein)* *I have protein SASA.* g_sas -f run.xtc -s run.tpr -o area_ligand.xvg -n protein_ligand.ndx Select a group for calculation of surface and a group for output *select a group: 1 (protein_ligand)* *select a group: 2 (ligand) I have ligand SASA.* g_sas -f run.xtc -s run.tpr -o area_protein_ligand.xvg -n protein_ligand.ndx Select a group for calculation of surface and a group for output *select a group: 1 (protein_ligand)* *select a group: 2 (protein_ligand) I have protein_ligand SASA.* *(SASA between protein and ligand)=(protein)+(ligand)-(protein_ligand)* Thanks 2011/7/3 Justin A. Lemkul > > > ahmet yıldırım wrote: > >> Dear users, >> >> I want to compute SASA between protein and ligand. >> *1.)* >> protein and ligand are merged by make_ndx >> g_sas -f run.xtc -s run.tpr -o protein_ligand.xvg -n protein_ligand.ndx >> Select a group for calculation of surface and a group for output >> select a group: 1 (protein+ligand) >> select a group: 2 (ligand) >> is this correct? >> >> *2.)* >> or >> g_sas -f run.xtc -s run.tpr -o protein_protein.xvg >> Select a group for calculation of surface and a group for output >> select a group: 1 (protein) >> select a group: 2 (protein) >> I have protein SASA. >> >> g_sas -f run.xtc -s run.tpr -o ligand_ligand.xvg >> Select a group for calculation of surface and a group for output >> select a group: 1 (ligand) >> select a group: 2 (ligand) >> I have ligand SASA. >> >> protein and ligand are merged by make_ndx >> g_sas -f run.xtc -s run.tpr -o protein_ligand.xvg -n protein_ligand.ndx >> Select a group for calculation of surface and a group for output >> select a group: 1 (protein_ligand) >> select a group: 2 (protein_ligand) >> I have protein_ligand SASA. >> >> (SASA between protein and ligand)=(protein)+(ligand)-(**protein_ligand) >> >> I am confused. which of choices is correct? >> >> > Neither. Your equation is right, but your method of calculating each of > the quantities is not. The group for the surface calculation should always > be all non-solvent atoms (per the instructions in g_sas -h). The output > group can then be whatever you like, a subset of that surface. So you will > need three calculations (sort of like option #2), but in each case the > calculation group should always be the protein-ligand merged group. > > -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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> > > ==**== > -- > gmx-users mailing listgmx-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. > Can't post? Read > http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> > -- Ahmet YILDIRIM -- 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_sas calculation
Dear users, I want to compute SASA between protein and ligand. *1.)* protein and ligand are merged by make_ndx g_sas -f run.xtc -s run.tpr -o protein_ligand.xvg -n protein_ligand.ndx Select a group for calculation of surface and a group for output select a group: 1 (protein+ligand) select a group: 2 (ligand) is this correct? *2.)* or g_sas -f run.xtc -s run.tpr -o protein_protein.xvg Select a group for calculation of surface and a group for output select a group: 1 (protein) select a group: 2 (protein) I have protein SASA. g_sas -f run.xtc -s run.tpr -o ligand_ligand.xvg Select a group for calculation of surface and a group for output select a group: 1 (ligand) select a group: 2 (ligand) I have ligand SASA. protein and ligand are merged by make_ndx g_sas -f run.xtc -s run.tpr -o protein_ligand.xvg -n protein_ligand.ndx Select a group for calculation of surface and a group for output select a group: 1 (protein_ligand) select a group: 2 (protein_ligand) I have protein_ligand SASA. (SASA between protein and ligand)=(protein)+(ligand)-(protein_ligand) I am confused. which of choices is correct? Thanks in advance -- Ahmet YILDIRIM -- 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_mindist
Dear Justin, can you suggest me published paper related to about hydrophobic and hydrophilic contacts? 03 Temmuz 2011 00:24 tarihinde Justin A. Lemkul yazdı: > > > ahmet yıldırım wrote: > >> Dear Justin, >> >> You said before "you can obtain some idea by using g_mindist to calculate >> hydrophobic and hydrophilic contacts between the protein and ligand". >> >> That is, I can explore whether there is hydrophobic or hydrophilic feature >> of ligand using g_mindist tool. is this correct? >> I did the calculations related to protein_ligand interactions (protein >> contains two ligand). I plotted the graphs of distance and numcount versus >> simulation time for each ligand. The number of contacts in ligand x is more >> than the other ligand y. Which of this ligands are hydrophobic? Which is >> hydrophilic? I know you are not private tutor. Please don't be angry :( >> >> > I certainly hope I haven't given the impression that I'm some angry tyrant. > I'm happy to answer reasonable questions across the list, time permitting. > > To obtain information about hydrophobic and hydrophilic contacts, you need > to use special index groups that tell g_mindist (or any other tool) which > atoms to consider. In this way, you can count how many of each type of > contact evolve over time. > > -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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> > > ==**== > -- > gmx-users mailing listgmx-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. > Can't post? Read > http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> > -- Ahmet YILDIRIM -- 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_mindist
Dear Justin, You said before "you can obtain some idea by using g_mindist to calculate hydrophobic and hydrophilic contacts between the protein and ligand". That is, I can explore whether there is hydrophobic or hydrophilic feature of ligand using g_mindist tool. is this correct? I did the calculations related to protein_ligand interactions (protein contains two ligand). I plotted the graphs of distance and numcount versus simulation time for each ligand. The number of contacts in ligand x is more than the other ligand y. Which of this ligands are hydrophobic? Which is hydrophilic? I know you are not private tutor. Please don't be angry :( Thanks in advance -- Ahmet YILDIRIM -- 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] the effect of the ligand on each residue
Dear Justin, Thanks for your reply. Well, to explore the effect of the ligand on protein g_mindist -f run.xtc -s run.tpr -od mindist.xvg -on numcont.xvg Select a group: 1 Selected 1: 'Protein' Select a group: 13 Selected 13: 'LİGAND' Does this choice make sense? 30 Haziran 2011 14:43 tarihinde Justin A. Lemkul yazdı: > > > ahmet yıldırım wrote: > >> Dear users, >> >> I want to see the effect of the ligand on each residue using the following >> command: >> g_rmsf -s run.tpr -f run.xtc -od rmsdev.xvg -o rmsf.xvg -res >> >> Select group(s) for root mean square calculation >> Select a group: ? >> Which group should I choose? >> >> > The group that is most meaningful to you, based on the behavior observed in > the trajectory. You can analyze backbone, sidechain, or all protein atoms > separately. Several iterations may be informative, using several different > groups. > > -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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> > > ==**== > -- > gmx-users mailing listgmx-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. > Can't post? Read > http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> > -- Ahmet YILDIRIM -- 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] the effect of the ligand on each residue
Dear users, I want to see the effect of the ligand on each residue using the following command: g_rmsf -s run.tpr -f run.xtc -od rmsdev.xvg -o rmsf.xvg -res Select group(s) for root mean square calculation Select a group: ? Which group should I choose? Thanks in advance -- Ahmet YILDIRIM -- 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-ligand interaction
Dear users, I am getting pairs of values in the output files as I said before. What is this mean? Furthermore, though my system have 451 residue, it seems as 230 residue ( and 1th residue does not seem in the out files). What could be the problem? * output file:* # This file was created Sun May 29 22:33:05 2011 # by the following command: # g_rmsf -s run.tpr -f run.xtc -od rmsdev.xvg -o rmsf.xvg -res # # g_rmsf is part of G R O M A C S: # # GROwing Monsters And Cloning Shrimps # @title "RMS fluctuation" @xaxis label "Residue" @yaxis label "(nm)" @TYPE xy 2 0.1217 3 0.0952 4 0.0760 5 0.0740 6 0.0613 7 0.0565 . 227 0.0785 228 0.0955 229 0.1254 230 0.1352 2 0.1181 3 0.0851 4 0.0713 5 0.0674 6 0.0645 7 0.0631 8 0.0707 9 0.0699 228 0.1034 229 0.1161 230 0.1206 29 Mayıs 2011 19:28 tarihinde ahmet yıldırım yazdı: > Dear Justin, > > I used -res flag with the following command but I get pairs of values in > the output files. is there any mistake related with the command I used? > g_rmsf -s run.tpr -f run.xtc -o rmsf.xvg -od rmsdev.xvg -res > > > > 2011/5/29 > > Quoting ahmet y?ld?r?m : >> >> Dear Justin, >>> >>> You said " You can get a per-residue RMSD by using g_rmsf -od to see the >>> effect of the ligand on each residue." >>> 1. Can you explain the difference between what goes into the -o file, and >>> what goes into the -od file? >>> >> >> The -o output is RMSF; the -od output is RMSD. >> >> >> 2. How should I create a index file to see the effect of the ligand on >>> each >>> residue? Do I have to create the index file? >>> g_rmsf -s run.tpr -f run.xtc -od rmsdev.xvg >>> Is this command sufficient to see the effect of the ligand on each >>> residue? >>> >> >> An index file should not be necessary. By default, the output is per >> atom, so use the -res flag if you want the measurements averaged over all >> atoms in each residue. The command is sufficient to measure the RMSD per >> residue. Whether or not that is sufficient is up to you. >> >> 3. Furthermore, can you suggest the other analysis tools to see the >>> effect >>> of the ligand *on protein*? >>> >>> >> You should identify the quantities you wish to measure, then read in the >> Gromacs manual about the different utility programs available. You'll learn >> far more that way. >> >> -Justin >> >> >> Thanks in advance >>> >>> 2011/5/28 >>> >>> Quoting ahmet y?ld?r?m : >>>> >>>> Dear users, >>>> >>>>> >>>>> I want to investigate *Ligand effect *on the protein . >>>>> To investigation the interaction of protein-ligand: >>>>> *RMSD calculations:* >>>>> 1. >>>>> a) RMSD of Backbone >>>>> b) RMSD of Backbone+ligand >>>>> 2. >>>>> a) RMSD of Protein >>>>> b) RMSD of Protein+ligand >>>>> 3. >>>>> a) RMSD of Protein-H >>>>> b) RMSD of Protein-H+ligand >>>>> Which one would you recommend ( 1., 2., and 2.choice)? >>>>> >>>>> >>>>> Unless the effect of your ligand is very large (i.e., the whole >>>> protein is >>>> significantly more or less stable in the presence of the ligand), then >>>> likely none of these analyses will be particularly illustrative as they >>>> are >>>> not very sensitive to small changes. You can get a per-residue RMSD by >>>> using g_rmsf -od to see the effect of the ligand on each residue. >>>> Otherwise, the most common quantity measured is backbone RMSD. >>>> >>>> -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
Re: [gmx-users] protein-ligand interaction
Dear Justin, I used -res flag with the following command but I get pairs of values in the output files. is there any mistake related with the command I used? g_rmsf -s run.tpr -f run.xtc -o rmsf.xvg -od rmsdev.xvg -res 2011/5/29 > Quoting ahmet y?ld?r?m : > > Dear Justin, >> >> You said " You can get a per-residue RMSD by using g_rmsf -od to see the >> effect of the ligand on each residue." >> 1. Can you explain the difference between what goes into the -o file, and >> what goes into the -od file? >> > > The -o output is RMSF; the -od output is RMSD. > > > 2. How should I create a index file to see the effect of the ligand on >> each >> residue? Do I have to create the index file? >> g_rmsf -s run.tpr -f run.xtc -od rmsdev.xvg >> Is this command sufficient to see the effect of the ligand on each >> residue? >> > > An index file should not be necessary. By default, the output is per atom, > so use the -res flag if you want the measurements averaged over all atoms in > each residue. The command is sufficient to measure the RMSD per residue. > Whether or not that is sufficient is up to you. > > 3. Furthermore, can you suggest the other analysis tools to see the effect >> of the ligand *on protein*? >> >> > You should identify the quantities you wish to measure, then read in the > Gromacs manual about the different utility programs available. You'll learn > far more that way. > > -Justin > > > Thanks in advance >> >> 2011/5/28 >> >> Quoting ahmet y?ld?r?m : >>> >>> Dear users, >>> I want to investigate *Ligand effect *on the protein . To investigation the interaction of protein-ligand: *RMSD calculations:* 1. a) RMSD of Backbone b) RMSD of Backbone+ligand 2. a) RMSD of Protein b) RMSD of Protein+ligand 3. a) RMSD of Protein-H b) RMSD of Protein-H+ligand Which one would you recommend ( 1., 2., and 2.choice)? Unless the effect of your ligand is very large (i.e., the whole protein >>> is >>> significantly more or less stable in the presence of the ligand), then >>> likely none of these analyses will be particularly illustrative as they >>> are >>> not very sensitive to small changes. You can get a per-residue RMSD by >>> using g_rmsf -od to see the effect of the ligand on each residue. >>> Otherwise, the most common quantity measured is backbone RMSD. >>> >>> -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 thewww >>> interface >>> or send it to gmx-users-requ...@gromacs.org. >>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>> >>> >> >> >> -- >> Ahmet YILDIRIM >> >> > > > -- > > > 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 thewww interface > or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- Ahmet YILDIRIM -- 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-ligand interaction
Dear Justin, You said " You can get a per-residue RMSD by using g_rmsf -od to see the effect of the ligand on each residue." 1. Can you explain the difference between what goes into the -o file, and what goes into the -od file? 2. How should I create a index file to see the effect of the ligand on each residue? Do I have to create the index file? g_rmsf -s run.tpr -f run.xtc -od rmsdev.xvg Is this command sufficient to see the effect of the ligand on each residue? 3. Furthermore, can you suggest the other analysis tools to see the effect of the ligand *on protein*? Thanks in advance 2011/5/28 > Quoting ahmet y?ld?r?m : > > Dear users, >> >> I want to investigate *Ligand effect *on the protein . >> To investigation the interaction of protein-ligand: >> *RMSD calculations:* >> 1. >> a) RMSD of Backbone >> b) RMSD of Backbone+ligand >> 2. >> a) RMSD of Protein >> b) RMSD of Protein+ligand >> 3. >> a) RMSD of Protein-H >> b) RMSD of Protein-H+ligand >> Which one would you recommend ( 1., 2., and 2.choice)? >> >> > Unless the effect of your ligand is very large (i.e., the whole protein is > significantly more or less stable in the presence of the ligand), then > likely none of these analyses will be particularly illustrative as they are > not very sensitive to small changes. You can get a per-residue RMSD by > using g_rmsf -od to see the effect of the ligand on each residue. > Otherwise, the most common quantity measured is backbone RMSD. > > -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 thewww interface > or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- Ahmet YILDIRIM -- 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] protein-ligand interaction
Dear users, I want to investigate *Ligand effect *on the protein . To investigation the interaction of protein-ligand: *RMSD calculations:* 1. a) RMSD of Backbone b) RMSD of Backbone+ligand 2. a) RMSD of Protein b) RMSD of Protein+ligand 3. a) RMSD of Protein-H b) RMSD of Protein-H+ligand Which one would you recommend ( 1., 2., and 2.choice)? Thanks ** -- Ahmet YILDIRIM -- 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] NPT and NVT ensembles
Dear Justin, In the first tutorial You said "After we arrive at the correct temperature (based on kinetic energies), we will apply pressure to the system until it reaches the proper density." That is, you apply each NVT and NPT ensembles when you did the position restraints. Would not it only be sufficient to implement NPT ensemble on the system? Is it compulsory to apply both the x and y? For example: I get proper density and stabilized the temperature of the system though I implement NPT ensemble on the system (not your tutorial sample). Thanks in advance -- Ahmet YILDIRIM -- 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] index file
Dear users, Firstly thanks for your replies. I have two ligands as I said before. I will analyze the system together ligands after the simulation is finished. For example: I want to plot potential energy of all system (that is, protein+LİGA+LİGB) by g_energy. Then, Should I create the groups as the following? *energygrps = ProteinLİGA_LİGB* tc-grps = Protein_LİGA_LİGBWater_and_ions OR *energygrps = ProteinLİGALİGB* tc-grps = Protein_LİGA_LİGBWater_and_ions Thanks 12 Mayıs 2011 18:29 tarihinde lina yazdı: > 2011/5/12 Justin A. Lemkul : > > > > > > lina wrote: > >> > >> make_ndx -f your.gro/pdb -n your.ndx -o your.ndx > >> > >> LiGA & LİGB: > > > > This is not correct. You need to use | rather than &. Using logical and > > (&) means the index group will contain atoms that are common to both LIGA > > and LIGB. If they are distinct entities, the group will be empty. > Logical > > or (|) says merge the two different groups to create one unified group. > > Ooops > > > > > > -Justin > > > >> q > >> > >> in grompp add -n your.ndx > >> > >> > >> 2011/5/12 ahmet yıldırım : > >>> > >>> Dear users, > >>> > >>> I have two ligands. I created a special index group that merges the > >>> protein, > >>> LiGA and LİGB. > >>> > >>> I have the pr.mdp file as the following: > >>> ... > >>> energygrps = ProteinLİGA_LİGB > >>> tc-grps = Protein_LİGA_LİGBWater_and_ions > >>> ... > >>> > >>> grompp -f pr.mdp -p topol.top -c em.gro -n index.ndx -o pr.tpr > >>> Fatal error: > >>> Group LİGA_LİGB not found in indexfile. > >>> > >>> I get the fatal error since I dont have a special index group that > merges > >>> LiGA and LİGB. should I create two different index file? > >>> > >>> Thanks in advance > >>> -- > >>> Ahmet YILDIRIM > >>> > >>> -- > >>> 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 > >>> > >> > >> > >> > > > > -- > > > > > > 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 > > > > > > -- > Best Regards, > > lina > -- > 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 > -- Ahmet YILDIRIM -- 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] index file
Dear users, I have two ligands. I created a special index group that merges the protein, LiGA and LİGB. I have the pr.mdp file as the following: ... energygrps = ProteinLİGA_LİGB tc-grps = Protein_LİGA_LİGBWater_and_ions ... grompp -f pr.mdp -p topol.top -c em.gro -n index.ndx -o pr.tpr Fatal error: Group LİGA_LİGB not found in indexfile. I get the fatal error since I dont have a special index group that merges LiGA and LİGB. should I create two different index file? Thanks in advance -- Ahmet YILDIRIM -- 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] principal moments of ellipsoid
Hi, BioVEC is a tool for visualizing molecular dynamics simulation data while allowing coarse-grained residues to berendered as ellipsoids. http://www.phas.ubc.ca/~steve/BioVEC/BioVECindex.html 2011/5/10 Mark Abraham > On 10/05/2011 8:23 PM, lammps lammps wrote: > >> Hi, >> I want to study the shape change of a macromolecule which seems like a >> ellipsoid. So, I need obtain the three principal moments of the molecules. >> Is the command of g_gyrate helpful for me? The sum of the three principal >> moments should be equal to the . However, I used the command g_gyrate >> -f traj.gro -s nvt.tpr -n anly.ndx -o shape.xvg -p obtain the Rg and other >> three qualities. >> It seems that the sum of the last three qualities is not equal to the >> Rg^2. Is there something wrong? >> > > Why should that sum equal Rg^2? > > 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 > -- Ahmet YILDIRIM -- 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
