[gmx-users] g_rms and g_rmsdist on initial structure

is high to about 0.5nm. Can someone explain for me? Sincerely yours, Hsin-Lin -- 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

[gmx-users] Is openmp necessary?

before? Sincerely yours, Hsin-Lin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use

[gmx-users] Re: Is openmp necessary?

Hi Mark, Thank you for your reply. I understand now. Sincerely yours, Hsin-Lin I want to calculate the diffusion coefficient of a small polypeptide with g_msd (see here http://www.gromacs.org/Documentation/How-tos/Diffusion_Constant) because of periodic boundary condition, when the peptide

[gmx-users] part number in extending simulation

md100ns.trr, md100ns.gro, md100ns.edr, and md100ns.log. So, is the function of part number in extending simulation in ver.4.5.4 cancelled? Hsin-Lin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http

[gmx-users] part number in extending simulation

Hi Flo, Thank you for reply. I got it. But as you see I also indicate the new names for output files. Do I get correct result in this kind of situation? Or I need to rerun it with -noappend Sincerely yours, Hsin-Lin Hi, check the standard options of mdrun with the help flag -h of version 4.5.4

[gmx-users] part number in extending simulation

without doubt. By the way, md100ns.trr here mean from 50ns to 100ns. I just don't want the new run append to md50ns.trr to make me confused. Hsin-Lin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http

[gmx-users] increasing cut-off and PME grid spacing

Hi Justin, I understand now. The vector of box changed from 5.8 to 44 after the short MD for equilibrium. I don't know what happened during equilibrium. But that is belong to the other question now. Thank you very much for your reply. Sincerely yours, Hsin-LIn Hsin-Lin Chiang wrote: Hi

[gmx-users] increasing cut-off and PME grid spacing

;#160;#160;#160;#160;#160; =#160; 300 gen_seed#160;#160;#160;#160;#160;#160;#160;#160;#160;#160;#160; =#160; 173529 Sincerely yours, Hsin-Lin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org

[gmx-users] increasing cut-off and PME grid spacing

ref_p = 1.0 gen_vel = yes gen_temp = 300 gen_seed = 173529 Sincerely yours, Hsin-Lin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please

[gmx-users] increasing cut-off and PME grid spacing

compressibility = 5.4e-5 ref_p = 1.0 gen_vel = yes gen_temp = 300 gen_seed = 173529 Hsin-Lin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please

[gmx-users] increasing cut-off and PME grid spacing

more messages in detail? Hsin-Lin --- #160;#160;#160;#160;#160;#160;#160; Written by Emile Apol, Rossen Apostolov, Herman J.C. Berendsen, #160;#160;#160;#160;#160; Aldert van Buuren, P#228;r Bjelkmar, Rudi van Drunen, Anton Feenstra, #160

[gmx-users] reference structure of g_rms

. Could someone tell me what cause the different and which choice is better? And my version is gromacs v4.0.5 Sincerely yours, Hsin-Lin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org

[gmx-users] reference structure of g_rms

something else with our time :-) Mark Hi, I checked the result again The order of the different is less than 0.1 nm. So that means this different is caused by precision? Sincerely yours, Hsin-Lin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx

[gmx-users] reference structure of g_rms

Hi Tsjerk, It's very helpful information. Thank you very much Sincerely yours, Hsin-Lin Hi Hsin-Lin, If you use a .tpr file, you perform a mass-weighted fit and analysis. A .gro file has no masses and thus the fit and analysis are performed non-mass weighted, which will give differences

[gmx-users] disulfide bond, molecule type

/ // I doubt the chain identifiers are relevant. Both .gro and .pdb files should // display properly. The only odd instance I can think of is that without separate // chains, some programs may interpret the protein coordinates as a single // molecule, but I would think that would only

[gmx-users] disulfide bond, molecule type

to 30. // // I'm afraid VMD got confused for the repeat number 1 to 21. // So I change 1-30 in b-chain to 22-51. // Then snapshot in VMD become correct. / Then this was primarily VMD's issue. -Justin Thank you for your help. I think I have no problem now. Hsin-Lin -- gmx-users mailing list

[gmx-users] disulfide bond, molecule type

residues plus 1. And it was also strange that the number of first water molecules was equal to the number of B-chain plus 1 I thought it should be equal to the number of A-chain's residues plus the number of B-chain's residues plus 1 Is it a bug? Sincerely yours, Hsin-Lin -- gmx-users mailing

[gmx-users] disulfide bond, molecule type

Hsin-Lin Chiang wrote: / Hi, // // I'm trying to heat a protein. // There are two chains, A-chain and B-chain. // Two disulfide bonds are between A-chain and B-chain. // As I know, I should let A-chain and B-chain belong to the same [molecule // type] in .top file if I want to have the two

[gmx-users] disulfide bond, molecule type

of snapshot was just because chain identifiers were lacked before. Do I have any commend can use instead of chain identifier A and B mannually? Sincerely yours, Hsin-Lin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive

[gmx-users] disulfide bond, molecule type

don't need to separate chains manually. Hsin-Lin -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

[gmx-users] About -chainsep and -ter

於 2011/7/21 上午 03:19, gmx-users-requ...@gromacs.org 提到: Hi everyone, My pdb file is consist of two chains with one intra- two inter-disulfide bonds. So I used pdb2gmx in this way pdb2gmx -f protein.pdb -o protein.gro -p protein.top -n -q -chainsep ter (I have deleted the TER and

[gmx-users] About -chainsep and -ter

not sure if I can post all here. Do we have another way to discuss? Sincerely yours, Hsin-Lin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting

[gmx-users] About -chainsep and -ter

not. -Justin I get success in pdb2gmx, but I not only delete ter line but also all OXT lines according to this mailing list, http://www.mail-archive.com/gmx-users@gromacs.org/msg33251.html But I'm failed when I used mdrun in -chainsep ter case. Hsin-Lin -- gmx-users mailing listgmx

[gmx-users] About -chainsep and -ter

. -Justin I understand now. Thank you very much for your help. Sincerely yours, Hsin-Lin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please

[gmx-users] About -chainsep and -ter

protein.pdb -o protein.gro -p protein.top -n -q -chainsep interactive#160; and selected y. Then everything is OK in mdrun step. I don't know what the different in -chainsep interactive and -chainsep ter is in my case. They seems to the same in my two chain system. Sincerely yours, Hsin-Lin

[gmx-users] Can't unfold the protein

and the other 2ns for 400K only, then the protein is still stable and the value is almost the same in radius of gyration. Below is the mdp file of the heating. What's wrong with my system? regards, Hsin-Lin - title#160;#160;#160;#160;#160;#160;#160; = ttt cpp#160;#160;#160

[gmx-users] Can't unfold the protein

But it also useless to me. And in my mdp I use thermostat and barostat, which means my system is NPT. Does anything wrong in my methods? Sincerely yours, Hsin-Lin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive

[gmx-users] mdrun -nc

is employed by mdrun_mpi? (Exactly I never use mdrun_mpi more than one machine since the ethernet between machines is very slow here.) If mdrun -nc is available. Do we have another commend support CPUs more than one in the same machine. Sincerely yours, Hsin-Lin -- gmx-users mailing listgmx-users

[gmx-users] Re: gmx-users Re: Error of installing gromacs v4.5.4

Hi, Thank you. I use gcc v4.4 and complete the installing. Sincerely yours, Hsin-Lin Hi, That compiler is ancient (thought it might have SSE2 support) as well as the OS, I guess (RHEL 3?). Still, the CPU does support SSE2 so if you can get a gcc 4.1 or later on it you should still

[gmx-users] Re: Error of installing gromacs v4.5.4

Hi, Thank you for your reply. I'm not so good in computer. I think the platform you ask me is Linux, and kernel is 2.4.21-60.ELsmp The compiler is gcc v3.2.3 in the machine in my institute. Sincerely yours, Hsin-Lin Message: 1 Date: Thu, 26 May 2011 18:03:09 +0200 From: Szil?rd P?ll

[gmx-users] different output generated by continue and discontinue simulation

. The interaction energy within protein also fluctuate in an unstable way. On the contrary, the second method generate a stable movie and fluctuation of interaction energy. Theotically these two should be the same, right? Is anything wrong in my work? Sincerely yours, Hsin-Lin -- gmx-users mailing list

[gmx-users] different output generated by continue and discontinue simulation

be the same, right? Is anything wrong in my work? Sincerely yours, Hsin-Lin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post

[gmx-users] different output generated by continue and discontinue simulation

be the same, right? Is anything wrong in my work? Sincerely yours, Hsin-Lin --- End of Forwarded Message --- -- 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

[gmx-users] different output generated by continue and discontinue simulation

convergence you mean here? Does It mean I can try to find mutual convergence in output of second way? I'm sorry for my stupid and poor English. Sincerely yours, Hsin-Lin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search

[gmx-users] Inaccurate time frame

Hi, Mark, I'll adopt your suggestion. Thank you for your reply again. Sincerely yours, Hsin-Lin On 7/12/2010 6:01 PM, Hsin-Lin Chiang wrote: / // Ah, sorry, I didn't read you well enough. // // I've just seen that GROMACS 4.5 introduced trjconv -round to address // this kind of issue. I

[gmx-users] Inaccurate time frame

, 2000.00012, 3000.00024, and t= 4000.00024. I know I can add -timestep 1 to solve this problem and let file can be truncated at t= 1000.6. How does this kind of inaccurate time frames happen? Is this trajectory a wrong result? Sincerely yours, Hsin-Lin -- gmx-users mailing listgmx-users

[gmx-users] Inaccurate time frame

). Would you please teach how to use -skip -sep to get the same kind of file which include all of 1000ps time frames together in a 1ns gro file? I'll appreciate to any helps. Sincerely yours, Hsin-Lin /Hi, // // My time unit is 1ps and today I have 300ns data generated by parallel

[gmx-users] Inaccurate time frame

-sep and write a shell script to combine frames together. Sincerely yours, Hsin-Lin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't

Re: [gmx-users] extending simulation without cpt file

. Am I right to use lines above to do extending simulation? Hsin-Lin - Original Message - From: Yongchul Chung yxc...@case.edu Date: Thursday, November 4, 2010 10:28 Subject: [gmx-users] extending simulation without cpt file To: Discussion list for GROMACS users gmx-users

Re: [gmx-users] extending simulation without cpt file

Hi, Mark So, You mean I can get correct extending simulation without using -e ede and -t trr in GROMACS ver.4. Then I can set my mind at rest. Thank you for your reply. Hsin-Lin Hi, Today I use serach and find this topic. I got confused. http://www.gromacs.org/Documentation/How-tos

[gmx-users] g_ hbond on two peptides

. How should I do to exclude the intra-H-bond on one peptide? Hsin-Lin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list

[gmx-users] Re: g_ hbond on two peptides

-bonds in my last message. So I think maybe it's just because the manners of two programs are different. regards, Hsin-Lin Hsin-Lin Chiang skrev: Hi, I use g_hbond to analyze the system with two peptide. And I introduce the ndx file which include two group for the two peptides

[gmx-users] Re: gmx-users Digest, Vol 73, Issue 177

Hi ,Mark: I had announced my system is a dimer with each peptides have 6 residues. I'm sorry if I didn't express it to be understood easily. Can you please tell me why 13 coils are reasonable if my systems is a dimer? regards, Hsin-Lin Hi, Justin: I post my coordinate with protein translated

[gmx-users] Re: the output of do_dssp

Hi ,Mark: I had announced that my system is a dimer with each peptides have 6 residues in my first post. I'm sorry if I didn't express it to be understood easily. Can you please tell me why 13 coils are reasonable if my systems is a dimer? regards, Hsin-Lin Hi, Justin: I post my coordinate

[gmx-users] Re: the output of do_dssp

Hi, Justin: I post my coordinate with protein translated by trjconv By this gro file, I get 0 structure and 13 coils. regards, Hsin-Lin Generated by trjconv : Protein in water t= 0.0 144 1LEU N1 2.499 1.707 2.735 -0.1664 0.1749 0.5034 1LEU H12 2.496

[gmx-users] Re: the output of do_dssp

are dicided by O, C, H, and N four atoms. How can we get dssp analysis by backbone that includes only NCCNCCNCC.? Sincerely yours, Hsin-Lin Hsin-Lin wrote: Hi, I use do_dssp to generate xvg file collect the last line to make a plot. There are something written in this way

[gmx-users] Re: the output of do_dssp

Hi, Justin Thank you for your patience. According your reply, I used trjconv to write only protein group into another file. I execute do_dssp again in group proteinand mainchain respectively but still get coils more than total residues. Why? Hsin-Lin Hsin-Lin wrote: Hi, Justin: Thank

[gmx-users] the output of do_dssp

. And the number I choose to analyze is 1. Protein. Now I have a question, if I want to calculate the percentage of secondary structure. In the example above, is it calculated in this way 5/12=42%? Hsin-Lin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users

[gmx-users] parallel simulation in dual core PC

200ns.gro. When the simulation starts, I use the commend, top, to check the utility of CPU. I found there is only one core which is used by GROMACS. And the utility of this core is separated to 52% and 48% for two mdrun_mpi jobs. How can I do for that? Any and all assistance is greatly appreciated. Hsin

[gmx-users] output of dssp

. And in my analysis I only need xvg file. How can I do to get xvg output without the others accompanied? Hsin-Lin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't

[gmx-users] gromacs, lam and condor

to mehave been 100% loading, and the CPU source availble to me is less then 10%. I think there is something wrong with my submit script or executable script, and I post them in my previous message. How should I correct my script? Hsin-Lin Hi, how many CPUs do you try to use? How big

[gmx-users] Re: gmx-users Digest, Vol 72, Issue 13

to mehave been 100% loading, and the CPU source availble to me is less then 10%. I think there is something wrong with my submit script or executable script, so I post them in my question before.(please see those below) Hsin-Lin Hi, how many CPUs do you try to use? How big is your system. What

[gmx-users] gromacs, lam and condor

/200ns.trr \ -g /stathome/jiangsl/simulation/gromacs/2OMP/2OMP_1_1/md/200ns.log \ -c /stathome/jiangsl/simulation/gromacs/2OMP/2OMP_1_1/md/200ns.gro - Hsin-Lin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive