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

Hi, I met some problem on installing gromacs 4.5.4 Below is the log. I'm soory I can't distinguish the important part and I post all of them. I'll appreciate for any help. Hsin-Lin - Making all in include make[1]: Entering directory `/stathome/jiangsl/src/gromacs-4.5.4/include' Makin

[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] Re: Error of installing gromacs v4.5.4

.@vt.edu> > Content-Type: text/plain; charset=UTF-8; format=flowed > > Hsin-Lin Chiang wrote: > > 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

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

ou should still be able compile > and run the code without a problem. > > -- > Szil獺rd > > 2011/5/26 Hsin-Lin Chiang : > > Hi, > > > > Thank you for your reply. > > I'm not so good in computer. > > I think the platform you ask me is &q

[gmx-users] mdrun -nc

Hi, I tried gromacs 4.5.4 in these days and last version I used is 4.0.5. I found when I add --enable-threads in installation. I can use mdrun -nc 12 to run 12 CPUs together within one machine. It also amazing me when I type "top" to check the job, only one process in computer and the CPU utilit

[gmx-users] Re: mdrun -nc

>/ Hi, />/ />/ I tried gromacs 4.5.4 in these days and last version I used is 4.0.5. />/ I found when I add --enable-threads in installation. />/ I can use mdrun -nc 12 to run 12 CPUs together within one machine. / I assume you mean -nt? Sorry, -nc is a typo of -nt. >/ It also amazing me w

[gmx-users] Can't unfold the protein

Hi, I have question about unfolding. I use three different ways respectively but all failed. The three way is, 1. 600K in 20ns, then the system explode. 2. 400K in 10ns, the protein is very stable and the value is almost the same in radius of gyration. 3. heating up from 300K to 400K in 2ns and

[gmx-users] Can't unfold the protein

Dear Chris, Thank you for your reply. My protein is very stable. I simulated it in 300ns in 300K before but there was almost no change. That's why I want to do denaturation now. I want to start a new simulation on the protein which is unfolded. And I'll read the paper you told me. Thank you.

[gmx-users] g_rms and g_rmsdist on initial structure

Hi, For example, I have a A.pdb as a initial structure file. And I just used pdb2gmx on it to generate another B.pdb file with GROMOS96 43a1 as its force filed. Then I select C-alpha atoms to calculate RMSD. echo 3 | g_rms -f B.pdb -s A.pdb I suppose the RMSD value should be 0, but the value is

[gmx-users] About -chainsep and -ter

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 OXT lines of A-chain.) I'm not sure if I need to use -ter here, I don't

[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

[gmx-users] About -chainsep and -ter

> Please post a diff of the two topologies (the one that failed and the one > that > worked). > > -Justin I use diff bash commend on the two top file and save to log file. The different was long but they both have three inter-disulfide bond There are 3973 lines in different log file.  I'm not

[gmx-users] About -chainsep and -ter

>I suspect this is a bug, so I have filed an issue on redmine: > >http://redmine.gromacs.org/issues/784 > >In a previous issue (http://redmine.gromacs.org/issues/544), the "-chainsep >interactive" option did not work, but now it does. Conversely, "-chainsep ter" >(which should also work in this c

[gmx-users] About -chainsep and -ter

Right. Even if you somehow force pdb2gmx to write a topology in this case, the bonds are not correct and the termini are incomplete. That will hopefully be resolved when the bug is fixed. For now, you have a workaround. Just use "-chainsep interactive" and you will get a proper topology. -Jus

[gmx-users] disulfide bond, molecule type

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 inter-bonds. So, I delete the TER line between

[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 .

[gmx-users] disulfide bond, molecule type

If you have heated your system severely, you may have generated an unstable system that is on the verge of crashing. VMD seems to allude to some weird geometry and PyMOL would seem to confirm that. I don't know why Rasmol appears OK. If you've somehow "lost" residues then they probably have inf

[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 happen in the rarest of

[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

[gmx-users] disulfide bond, molecule type

No. You said before you had broken chains. Applying trjconv -pbc mol fixes this issue. Molecules can be "broken" across periodic boundaries and is an entirely normal phenomenon. http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions >/ And I tried another way. />/ I c

[gmx-users] reference structure of g_rms

Hi, I got confused about the choice of reference structure of g_rms. (g_rms -s) For example, I run MD after PR. That's means md.tpr was generated from pr.gro I tried to use pr.gro and md.tpr to be the reference structure but get different result. I think these two should cause the same result.

[gmx-users] reference structure of g_rms

> On 17/08/11, Hsin-Lin Chiang wrote: > > > Hi, > > > > I got confused about the choice of reference structure of g_rms. (g_rms -s) > > For example, > > I run MD after PR. > > That's means md.tpr was generated from pr.gro > > I tried t

[gmx-users] reference structure of g_rms

> > Hi, > > > > I got confused about the choice of reference structure of g_rms. (g_rms -s) > > For example, > > I run MD after PR. > > That's means md.tpr was generated from pr.gro > > I tried to use pr.gro and md.tpr to be the reference structure but get > > different result. > > I think

[gmx-users] reference structure of g_rms

ences, depending on the selection for the analysis. Hope it helps, Tsjerk 2011/8/17 Hsin-Lin Chiang : >> > Hi, >> > >> > I got confused about the choice of reference structure of g_rms. (g_rms >> > -s) >> > For example, >> > I run MD aft

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

Hi, I want to run mdrun -nt 12 on our cluster. When I execute, grompp -f test.mdp -o test.tpr -c ../3eq/eq.gro -t ../3eq/eq.trr -p ../initial/insulin.top -n ../initial/index.ndx I got the message, Estimate for the relative computational load of the PME mesh part: 1.00 NOTE 1 [file test.mdp]:

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

Sorry for the confusing symbol. I tried to change it in this new mail. Hi, I want to run mdrun -nt 12 on our cluster. When I execute, grompp -f test.mdp -o test.tpr -c ../3eq/eq.gro -t ../3eq/eq.trr -p ../initial/insulin.top -n ../initial/index.ndx I got the message, Estimate for the relativ

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

>If the simulation is even stable, it will be horribly inaccurate. 12 nm >cutoffs >are unheard of and 2-nm grid spacing is about 20 times too large. > >Without seeing the original .mdp file that gave the high PME load, and without >a >further description about how large the system is (number of

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

Hi, Justin Sorry for the unclear message. My box vector in .gro file are 44.22834  44.22834  44.22834 and the number of atoms is 20171 The output of grompp is shown below, I don't know if it is enough and I'm sorry I don't know how should I do after you reply. Could you please give me more messa

[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:

[gmx-users] part number in extending simulation

Hi, Is part number in extending simulation in ver.4.5.4 cancelled? Below is my shell script, #!/bin/bash a=/stathome/jiangsl/simulation/gromacs/d1GUJ_AB/4md #running GROMACS /stathome/jiangsl/soft/gromacs-4.5.4/bin/mdrun \ -nt 12 \ -s ${a}/md100ns.tpr \ -o ${a}/md100ns.trr \ -e ${a}/md100ns.edr \

[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

[gmx-users] part number in extending simulation

>I am not sure, but I assume if you set new names, new files will be >created. The checkpoint input files contains important information about >your coordinates, velocities, states of random number generators for the >NH coupling That is the reason, why it is necessary for a >continuous extens

[gmx-users] Is openmp necessary?

Hi, For mdrun, the option -nt means "Number of threads to start (0 is guess)". Is this option executed by openmp? I used this option every time. But today my technology stuff told me that we don't have openmp installed in our computer. It make me confused. Why can I compile and run mdrun -nt 12

[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 goe

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

Hi, Today I use serach and find this topic. I got confused. http://www.gromacs.org/Documentation/How-tos/Extending_Simulations According the page of "extending simulation", in GROMACS ver.4, the commend is: tpbconv -s previous.tpr -extend timetoextendby -o next.tpr mdrun -s next.tpr -cpi prev

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/Ext

[gmx-users] Inaccurate time frame

Hi, My time unit is 1ps and today I have 300ns data generated by parallel simulation. I use trjconv -split 1000 on my trajectory but get the truncated end at t= 5000.0 Theoretically it should stop at t= 1000.000 I found that I don't have t= 1000.0 frame but have t= 1000.6, 2000.0

[gmx-users] Inaccurate time frame

Hi, Mark Thank you for your reply. I know -skip -sep is more robust. Since the definition talked about nr-th frame but not nr-th ps. -skip int 1 Only write every nr-th frame -[no]sep bool no Write each frame to a separate .gro, .g96 or .pdb file The problem is that -s

[gmx-users] Inaccurate time frame

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 suppose you will find trjconv -round -split works for you. Mark Hi, Mark Thank you for your suggestion. I'm sorry that my version is 4.0.5 I think I can use -

[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

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

Hi, My gromacs version is 4.0.5. I used grompp to generate tpr for 1ps simulation in this way grompp -f md1.mdp -n index.ndx  -p topol.top -c 0ps.gro  -t 0ps.trr -o 1ps.tpr mdrun -s 1ps.tpr -e 1ps.edr -o 1ps.trr -g 1ps.log -c 1ps.gro Here is my md1.mdp file: ; title    = ttt cpp  

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

Sorry for the abnormal code. I have fixed that. --- Hi, My gromacs version is 4.0.5. I used grompp to generate tpr for 1ps simulation in this way grompp -f md1.mdp -n index.ndx  -p topol.top -c 0ps.gro  -t 0ps.trr -o 1ps.tpr mdrun -s 1ps.tpr -e 1ps.edr -o 1ps.trr -g 1ps.log -c 1ps.gro Here i

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

Sorry for the abnormal code. I have fixed that. --- Hi, My gromacs version is 4.0.5. I used grompp to generate tpr for 1ps simulation in this way grompp -f md1.mdp -n index.ndx  -p topol.top -c 0ps.gro  -t 0ps.trr -o 1ps.tpr mdrun -s 1ps.tpr -e 1ps.edr -o 1ps.trr -g 1ps.log -c 1ps.gro Here i

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

Hi, Mark > > tc-grps > > =  A-chain B-chain drug SOL  NA+ > > > > > > > > > > > This is bad - see http://www.gromacs.org/Documentation/Terminology/Thermostats Thank you for your website.  I understand now. > > grompp -f md2.mdp -n index.ndx  -p topol.top -c ${n-1}ps.gro  -t > >

[gmx-users] gromacs, lam and condor

Hi, Do someone use gromacs, lam, and condor together here? I use gromacs with lam/mpi on condor system. Everytime I submit the parallel job. I got the node which is occupied before and the performance of each cpu is below 10%. How should I change the script? Below is one submit script and two exe

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

big is your system. What kind of > interconnect? Since you use condor probably some pretty slow interconnect. > Than you can't aspect it to work on many CPUs. If you want to use many CPUs > for MD you need a faster interconnect. > > Roland > > 2010/4/2 Hsin-Lin

[gmx-users] gromacs, lam and condor

try to use? How big is your system. What kind of > interconnect? Since you use condor probably some pretty slow interconnect. > Than you can't aspect it to work on many CPUs. If you want to use many CPUs > for MD you need a faster interconnect. > > Roland > > 2010/4

[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 1

[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] g_ hbond on two peptides

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 respectively. For the first prompt of g_hbond, I choose the group of the first peptide. For the second prompt, I choose the other peptide. I got the data that ann

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

umber of H-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 nd