[gmx-users] Re: DCD can not open file 'md_0_1.xtc' for reading

file '1dx0.pdb' for reading. It seems catdcd can not work! maggin -- View this message in context: http://gromacs.5086.x6.nabble.com/DCD-can-not-open-file-md-0-1-xtc-for-reading-tp5009795p5009797.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-use

[gmx-users] Re: DCD can not open file 'md_0_1.xtc' for reading

file 'md_0_1.xtc' for reading. Something wrong in somewhere, where is it ? Thank you very much! maggin by the way, 1.Download catdcd-4.0b.tar.gz 2.tar -zxvf catdcd-4.0b.tar.gz 3. add path LINUXAMD64/bin/catdcd4.0 to .bash_profile 4. source .bash_profile 5. which catdcd ~/softwares/

[gmx-users] DCD can not open file 'md_0_1.xtc' for reading

file 'md_0_1.xtc' for reading. How to fix it ? Thank you very much! maggin -- View this message in context: http://gromacs.5086.x6.nabble.com/DCD-can-not-open-file-md-0-1-xtc-for-reading-tp5009795.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. --

[gmx-users] convert gromacs formats and xyz

Hi, Is anybody known how to convert gromacs formats and xyz? If VMD or catdcd can do it ? Thank you very much! maggin -- View this message in context: http://gromacs.5086.x6.nabble.com/convert-gromacs-formats-and-xyz-tp5009793.html Sent from the GROMACS Users Forum mailing list archive

[gmx-users] Re: g_cluster

lecular simulation" (2002) but it seems no clearly concrete answer how to operation to do convergence analysis based on cluster analysis. So, I still confused a quantitative justification for the simulations' convergence from g_cluster. Thank you very much! maggin -- View this message

[gmx-users] g_cluster

Hi, I have a qustion how to use g_cluster to judge convergence of the simulation of peptide ? Thank you very much! maggin -- View this message in context: http://gromacs.5086.x6.nabble.com/g-cluster-tp5009690.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com

[gmx-users] can extract edr and cpt of one frame?

Hi, I want extract one frame from NPT to run MD because for md need npt.gro and npt.cpt So, if can we extract cpt of one frame? and because I want to check if this frame at equilibration state, use g_energy -f npt.edr So, if can we extract edr of one frame? Thank you very much! maggin

[gmx-users] Re: How to check if one protein broke into fragments during MD?

Hi, Justin, use: trjconv -dump 19532 -pbc nojump -s md_0_1.tpr -f md_0_1.xtc get: <http://gromacs.5086.x6.nabble.com/file/n5009238/dd.png> Thank you veru much! maggin -- View this message in context: http://gromacs.5086.x6.nabble.com/How-to-check-if-one-protein-broke-into-fra

[gmx-users] Re: How to check if one protein broke into fragments during MD?

Hi, Justin the structure of 19532ps shows as <http://gromacs.5086.x6.nabble.com/file/n5009235/aa2.png> the structure of md_0_1 shows as <http://gromacs.5086.x6.nabble.com/file/n5009235/cc.png> So, how can I fix the structure of 19532ps like md_0_1 ? Thank you very m

[gmx-users] How to check if one protein broke into fragments during MD?

of MD finished <http://gromacs.5086.x6.nabble.com/file/n5009221/bb.jpg> at the bottom the number of protein is 1 So, it seems from last structure it can not tell if is this protein broken. Is there anyway to check if protein is broken during MD? Thank you very much! maggin -- View

[gmx-users] Re: a snapshot of NVT

Hi,Tsjerk, Oh, that's it ! Thank you very much for your kind help! maggin -- View this message in context: http://gromacs.5086.x6.nabble.com/a-snapshot-of-NVT-tp5009206p5009211.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-

[gmx-users] Re: NVT .gro for NPT

Hi, Tsjerk You asked me a good question. Ya, sometime it accords my imagination to tell if it right or not. That's not the correct way. Maybe it near boundary, like at the boundary of dangerous. So let me have such question. maggin -- View this message in context: http://gromacs

[gmx-users] a snapshot of NVT

Hi, all When I run a small peptide at NVT stage, I get a snapshot like this: <http://gromacs.5086.x6.nabble.com/file/n5009209/next6_gro2.bmp> I am not sure if it right, and can I use it for NPT ? Thank you very much! maggin -- View this message in context: http://gromacs.5

[gmx-users] a snapshot of NVT

Hi, all When I run a small peptide at NVT stage, I get a snapshot like this: <http://gromacs.5086.x6.nabble.com/file/n5009206/next6_gro2.bmp> I am not sure if it right, and can I use it for NPT ? Thank you very much! maggin -- View this message in context: http://gromacs.5

[gmx-users] NVT .gro for NPT

non? Thank you very much! maggin -- View this message in context: http://gromacs.5086.x6.nabble.com/NVT-gro-for-NPT-tp5009205.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinf

[gmx-users] Re: Gromacs 4.5.5

Hi, Alaina Before you install GMX4.5.5, did you install cmake-2.8.8 and fftw-3.3.2 ? maggin -- View this message in context: http://gromacs.5086.x6.nabble.com/Gromacs-4-5-5-tp5009198p5009203.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing

[gmx-users] Re: System equilibrium problems

reached equilibrium. maggin -- View this message in context: http://gromacs.5086.x6.nabble.com/System-equilibrium-problems-tp5009137p5009157.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org

[gmx-users] Re: Steepest Descents in vacuo

Hi, Justin, If I use Pymol to set up a mutation of 1dx0.pdb, If it best do Steepest Descents in vacuo first ? Thank you very much! maggin -- View this message in context: http://gromacs.5086.x6.nabble.com/Steepest-Descents-in-vacuo-tp5009143p5009153.html Sent from the GROMACS Users Forum

[gmx-users] Re: Steepest Descents in vacuo

Hi, Justin, Thank you very much for your help! Another question is when we do steep minimization, if it will be better first do steep with constraint, then do steep without constraint? Thank you very much! maggin -- View this message in context: http://gromacs.5086.x6.nabble.com/Steepest

[gmx-users] Re: refcoord_scaling = com

Hi, Justin, At md step, protein run out of box, if it will better that set position constraint, let protein at center of box? Thank you very much! maggin -- View this message in context: http://gromacs.5086.x6.nabble.com/refcoord-scaling-com-tp5009141p5009150.html Sent from the GROMACS

[gmx-users] Re: distance_restraints

Hi, Tsjerk, Oh, so that's it . Thank you very much! maggin -- View this message in context: http://gromacs.5086.x6.nabble.com/distance-restraints-tp5008938p5009146.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromac

[gmx-users] Re: distance_restraints

Hi, Tsjerk, I have one question that in what situation people do constraint ? Thank you very much! maggin -- View this message in context: http://gromacs.5086.x6.nabble.com/distance-restraints-tp5008938p5009144.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com

[gmx-users] Steepest Descents in vacuo

Before do Steepest with water, we first do Steepest Descents in vacuo, if such way will better to only do Steepest with water ? Thank you very much! maggin -- View this message in context: http://gromacs.5086.x6.nabble.com/Steepest-Descents-in-vacuo-tp5009143.html Sent from the GROMACS

[gmx-users] refcoord_scaling = com

, in bar compressibility = 4.5e-5; isothermal compressibility of water, bar^-1 refcoord_scaling = com at lysozyme tutorial there is no refcoord_scaling set. I'm not sure if it could do that set refcoord_scaling = com at md stage Thank you very much! maggin -- View this me

[gmx-users] Re: distance_restraints

again do steep, cg without constraint. I hope after such steps my system will not collapse again in the next NVT, NPT and MD. Good energy minimization will contribute to simulation a lot. maggin -- View this message in context: http://gromacs.5086.x6.nabble.com/distance-restraints

[gmx-users] Re: distance_restraints

seems for this group, atoms are far away, they are not form bond, but it looks cg take they as bonds, so it cause LINCS WARNING At such situation, what is the best way to deal with these LINCS WARNINGS? Thank you very much! maggin -- View this message in conte

[gmx-users] Re: distance_restraints

om/file/n5009124/PRO165.png> <http://gromacs.5086.x6.nabble.com/file/n5009124/VAL166.png> When I check other place, find they are same with the problematic areas, amino acid lose some H atoms connect with C So, it's unlike lose H atomes cause these LINCS WARNING. maggin -- View

[gmx-users] Re: distance_restraints

WARNING ? Thank you very much! maggin -- View this message in context: http://gromacs.5086.x6.nabble.com/distance-restraints-tp5008938p5009076.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org

[gmx-users] distance_restraints

1.24 1.0 685 688 1 0 2 0.0 0.19 1.19 1.0 775 776 1 0 2 0.0 0.20 1.20 1.0 994 995 1 2 2 0.0 0.24 1.24 1.0 #endif But things not changed, same warning How should I do to fix it? Thank you very much! maggin -- View this message in context: http://gromacs.5086.x6.nabble.com/distance-restrai

[gmx-users] Re: Steepest LINCS WARNING

no idea what can I do, to kill this LINCS WARNING? Thank you very much! maggin -- View this message in context: http://gromacs.5086.x6.nabble.com/Steepest-LINCS-WARNING-tp5008919p5008920.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-us

[gmx-users] Steepest LINCS WARNING

to find it out? Thank you very much! maggin -- View this message in context: http://gromacs.5086.x6.nabble.com/Steepest-LINCS-WARNING-tp5008919.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gro

[gmx-users] energ minimization: cg and I-bfgs

RUN gen-vel = no gen-temp = 293 gen-seed = 173529 So, I have the question that why for cg, it take place fatal error? and another question for steep, if the result is reasonable? Thank you very much! maggin -- View this message in context: http://grom

[gmx-users] Re: cg Fatal error--DD cell

. Anybody could tell me how to fix this problem! Thank you very much! maggin -- View this message in context: http://gromacs.5086.x6.nabble.com/cg-Fatal-error-DD-cell-tp5008859p5008875.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users

[gmx-users] cg Fatal error--DD cell

are doing you can adjust the lincs warning threshold in your mdp file or set the environment variable GMX_MAXCONSTRWARN to -1, but normally it is better to fix the problem So, is anyway to resolve it ? I have try, but can not find the way. Thank you very much! maggin -- View this message in

[gmx-users] Re: how to add sodium acetate

Hi, Justin It's work ! Thank you very much! maggin -- View this message in context: http://gromacs.5086.x6.nabble.com/how-to-add-sodium-acetate-tp5008786p5008831.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromac

[gmx-users] how to add sodium acetate

Hi, when we add Nacl, can use -pname NA -nname cl in GMX so for sodium acetate, how to display it ? Thank you very much! maggin -- View this message in context: http://gromacs.5086.x6.nabble.com/how-to-add-sodium-acetate-tp5008786.html Sent from the GROMACS Users Forum mailing list archive

[gmx-users] Re: frame

hi, Wagner It works! Thank you very much! maggin -- View this message in context: http://gromacs.5086.x6.nabble.com/frame-and-pdb-tp5008727p5008768.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http

[gmx-users] frame in VMD

Hi, I use VMD to see GROMACS trajectory, I run 20ns md, there are 10,000,000 step, when load to VMD, it total 2777 frames. I don't known if there something wrong in it ? How to get the frame about 19532ps? Thank you very much! maggin -- View this message in context: http://gromacs

[gmx-users] Re: frame

How to convert ur frames in a time (ps)? Thank you very much! -- View this message in context: http://gromacs.5086.x6.nabble.com/frame-and-pdb-tp5008727p5008735.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http:/

[gmx-users] frame

Hi, if I run 20ns MD, and want to get the pdb at 19532ps trjconv -s md_0_1.tpr -f md_0_1.xtc -o bovin19532.gro -dt 1 -b 19532 -e 19532 editconf -f bovin19532.gro -o bovin19532.pdb If is it right? Thank you very much! -- View this message in context: http://gromacs.5086.x6.nabble.com/fram

[gmx-users] Re: FEP of ion binding protein

Hi, Steven, http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy/index.html and there is one paper"Good Practices in Free-Energy Calculations J. Phys. Chem. B, 2010, 114 (32), pp 10235–10253" Hope this data could help you! maggin -- View this

[gmx-users] Re: g_hbond

Hi, Erik Thank you very much!Thank you! maggin -- View this message in context: http://gromacs.5086.x6.nabble.com/g-hbond-tp5008507p5008548.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org

[gmx-users] Re: residue labeling in g_rmsf

Hi, you can use Matlab software to do it! maggin -- View this message in context: http://gromacs.5086.x6.nabble.com/residue-labeling-in-g-rmsf-tp5008474p5008514.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http

[gmx-users] Re: g_hbond

Hi, Pan Thank you very much for your kind help! Thank you! maggin -- View this message in context: http://gromacs.5086.x6.nabble.com/g-hbond-tp5008507p5008513.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http

[gmx-users] Re: NVT and NPT for small peptide

Thank you very much! -- View this message in context: http://gromacs.5086.x6.nabble.com/NVT-and-NPT-for-small-peptide-tp5008461p5008508.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman

[gmx-users] g_hbond

ybody can tell me at here if Hydrogen bonds Refers to the middle column: 74,73,69,69,78,74,68,68,71 Thank you ! maggin -- View this message in context: http://gromacs.5086.x6.nabble.com/g-hbond-tp5008507.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gm

[gmx-users] tpr of extend simulation

Hi, I run MD production 10ns, and get file: md_0_1.trr, md_0_1.tpr but simulation time is not enough, so I extend the time to 20ns, tpbconv -s md_0_1.tpr -extend 1 -o md_0_1_next1.tpr and get file: traj.trr, md_0_1_next1.tpr trajectory cconnection : trjcat -f md_0_1.trr traj.trr -o traj_

[gmx-users] NVT and NPT for small peptide

Hi, when simulation small peptideS, 6 or 10 amino acid, how long it is need for NVT and NPT? -- View this message in context: http://gromacs.5086.x6.nabble.com/NVT-and-NPT-for-small-peptide-tp5008461.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailin

[gmx-users] Free energy of solvation's .mdp of peptide

(the previous state B is now A) couple-lambda1= vdw-q ; all nonbonded interactions are on in state B Thank you very much! maggin -- View this message in context: http://gromacs.5086.x6.nabble.com/Free-energy-of-solvation-s-mdp-of-peptide-tp5008445.html Sent from the GROMACS Users

[gmx-users] Re: Free energy of solvation about peptide

The BAR method calculates a ratio of weighted average of the Hamiltonian difference of state B given state A and vice versa. So, for different peptides, can this method apply to compare the stability of peptides? Thank you very much! -- View this message in context: http://gromacs.5086.x6.nab

[gmx-users] Re: Fatal error: Failed to lock: md.log. Function not implemented.

hi, Justin, Thank you very much! Thank you! Ya, it's works! great! cool! Thank you very much for your suggestion, this time I also not use -reprod ,it doesn't effect simulation. Work also can go on! Thank you very much for your kind help! maggin -- View this message in cont

[gmx-users] Fatal error: Failed to lock: md.log. Function not implemented.

RSION 4.5.5 Source code file: checkpoint.c, line: 1757 Fatal error: Failed to lock: md.log. Function not implemented. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors How could fix it? Thank you very much! m