[gmx-users] a plot technique question

very much best Albert -- 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 in

[gmx-users] how can we obtain replicated trajectory?

just wondering how can we generate and visualize the system at 300 K with that at 400-500 K? There is a ligand in my system, and it is expected to escape binding pocket with large loop movement thank you very much best Albert -- gmx-users mailing listgmx-users@gromacs.org http://li

Re: [gmx-users] how can we obtain replicated trajectory?

scape binding pocket coupled with some big loop movement. thank you very much. best Albert -- 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! * P

[gmx-users] 4.6.1 support double precision GPU now?

Hello: I am wondering is double precision supported in current 4.6.1 GPU version? Otherwise it would be very slow to use CPU version running free energy calculations thank you very much best Albert -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman

[gmx-users] questions about umbrella sampling tutorial

sampling answer this question? Or we should pull the ligand along X,Y and Z three direction so that it is more convinced? (2) it is said that when doing free energy calculation in gromacs, we'db better use double precision Gromacs. So probably we have to use CPU instead of GPU for this? thank

[gmx-users] Intel compiling failed

Hello: I am trying to compile gromacs with intel compiler. However, it failed when I compile FFTW3 with command: ./configure --enable-sse --enable-float --with-pic --enable-single --enable-static --enable-mpi --prefix=/home/albert/install/fftw-3.3.3 CC=icc CXX=icc F77=ifort here is the

Re: [gmx-users] Intel compiling failed

On 04/05/2013 12:38 PM, Carsten Kutzner wrote: Hi Albert, one reason for the error you see could be that you are using a non-Intel MPI compiler wrapper. I think you need to specify MPICC=mpiicc as well. Carsten thanks a lot both Carsten and Justin. I've compiled both fftw and openmpi

Re: [gmx-users] Intel compiling failed

one thank you very much best Albert -- 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

[gmx-users] problem of umbrella sampling pulling code

Hello: I am trying to run umbrella sampling, the system contains a ligand. here is the pulling setting: ; Pull code pull= umbrella pull_geometry = distance ; simple distance increase pull_dim= Y N N pull_start = yes ; define initial COM distance > 0 pull_ngro

[gmx-users] genion doesn't work in 4.6.1?

calculate. Obviously, the total charge of the system is -11.0, but genion doesn't add anything to netural it thank you very much best Albert -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at

Re: [gmx-users] genion doesn't work in 4.6.1?

On 04/05/2013 09:09 PM, Warren Gallin wrote: Don't you have to give tyne name of the positive and negative ions that will be added by genion? Otherwise, how would it know? Warren Gallin No, it doesn't work either: genion_mpi -s ions.tpr -o solv_ions.gro -p complex.top -neutral -norandom -p

[gmx-users] where is gromos54a7_lipid FF?

Hello: I saw lots of people is using gromos54a7_lipid FF and I search the gromacs webiste, but didn't find it. Would anybody tell me where can we obtain it? THX Albert -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please searc

Re: [gmx-users] amber99 with berger's lipids

On 04/06/2013 04:29 PM, Justin Lemkul wrote: And what was your basis for that decision? What makes you think that AMBER99 can even be combined with the Berger lipid force field? -Justin I think he probably read this paper which suggest the combination of Amber FF and Berger lipids FF: htt

[gmx-users] fail to pull

est Albert -- 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 se

Re: [gmx-users] fail to pull

this is too short for whole protein as COM? thank you very much best Albert -- 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&#

Re: [gmx-users] fail to pull

md_pull.mdp -c npt.gro -p topol.top -n index.ndx -t npt.cpt -o pull.tpr for pulling .tpr generating. May I ask whey shall we use option "-t npt.cpt" in this step? Usually we only need to specify .mdp, .gro and .top file for .tpr file thank you very much best Albert On 04/

Re: [gmx-users] fail to pull

IC. thanks a lot for explanations. Albert On 04/07/2013 06:08 PM, Justin Lemkul wrote: I'm assuming you're getting that line from my tutorial. You pass the .cpt file to grompp to preserve velocities from the previous equilibration phase. If you don't, what was the point o

[gmx-users] can we use GPU from another machine for calculation?

Hello: I've got two GPU workstation both of which have two GTX690 GPU. Now I am planning to run Gromacs GPU version and I am just wondering can we submit a single GPU jobs in one machine and evoke all GPU resources from both machine? thank you very much best Albert -- gmx-users ma

[gmx-users] how to extract last frame?

Hello: I am trying to extract last frame of my MD simulations with command: trjconv_mpi -f s.xtc -s P-in.gro -dump -1 -o p-out.pdb but it said: WARNING no output, last frame read at t=751.4 gcq#286: "Oh, There Goes Gravity" (Eminem) thank you very much best Albert -- gmx-users ma

[gmx-users] shall we add ions in FEP?

rgy through FEP? THX Albert -- 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 t

[gmx-users] why no. of atoms doesn't match?

gand, cholestrol, popc and water. The system contains 1 protein, 1 ligand, 42 chelostrol, 98 POPC and 10079 water molecules. Then I am trying to minimize the system with command: grompp_mpi -f em.mdp -c complex.pdb -o em.tpr However, it always failed with messages: Program grompp_mpi, VERSION

Re: [gmx-users] why no. of atoms doesn't match?

s not match topology (topol.top, 51295) " It is correct with the topology I defined at the end of topol.top file: [ molecules ] ; Compound#mols Protein 1 LIG1 CHL142 POPC98 SOL10079 thank you very much best Albert On 04/15/2013 07:45 PM, Justin Lemkul wrote: Seriou

Re: [gmx-users] why no. of atoms doesn't match?

1.00 0.00 MEMB ATOM 6423 H16Y POPA 22 -19.546 21.266 -2.437 1.00 0.00 MEMB ATOM 6424 H16Z POPA 22 -20.104 19.539 -2.286 1.00 0.00 MEMB thank you very much best Albert On 04/15/2013 08:03 PM, Albert wrote: Hello Justin and bv08ay: thanks a lot for kind

[gmx-users] new CHARMM-GUI output not supported?

very much best Albert --- Begin Message --- Hello: I obtained a POPC lipids from CHARMM-GUI and I found the initial 12 line are following: following atom name order: ATOM 6315 N POPC 22 3.580 -22.614 19.970 1.00-19.29 MEMB ATOM 6316 C12 POPC 22 4.563 -22.414

[gmx-users] new CHARMM-GUI output not supported?

very much best Albert -- 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

[gmx-users] why minimization stop so fast

of the run time was spent in domain decomposition, 6 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) gcq#154: "Rub It Right Accross Your Eyes" (F. Zappa) Thank you very much Albert -- gmx-users mail

Re: [gmx-users] why minimization stop so fast

Hi Justin: thanks for kind reply. Yes, there many atom clashes in CHARMM-GUI system, so I add very strong force on protein and ligands, and try to minimize the rest of the system do you have any idea how can I solve the issue and make it work? thanks a lot Albert On 04/16/2013 07:09

Re: [gmx-users] why minimization stop so fast

On 04/16/2013 07:28 PM, Justin Lemkul wrote: Create a more physically reasonable starting structure. -Justin the protein and ligand are already minimized, but CHARMM-GUI create the mix lipids automatically which I cannot change them. ALBERT -- gmx-users mailing listgmx-users

Re: [gmx-users] new CHARMM-GUI output not supported?

Hello Mark and Justin: thanks a lot for kind comments. I changed the atom order in forcecfiled .rtp file so that they are the same with the output from CHARMM-GUI, and it works fine now. best Albert On 04/17/2013 12:50 AM, Mark Abraham wrote: "Support" is not really the

Re: [gmx-users] Re: why minimization stop so fast

Hello Brad: thanks for advices. I've also solved the problem after I run the 6.1 minimization step in NAMD. After that, I reimport the lipids system into gromacs, and it no longer complain those issue. best Albert On 04/16/2013 09:59 PM, Brad Van Oosten wrote: Hello,I have ha

[gmx-users] how to direct log file correctly?

? Meanwhile tho job won't have any problem going to next step (I am running all the steps in one script). thank you very much best Albert -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromac

Re: [gmx-users] Announcement: new version of GridMAT-MD available

eaving directory `/home/albert/Desktop/matpack/source/3rdparty/libpng' make[3]: Leaving directory `/home/albert/Desktop/matpack/source/3rdparty/libpng' (cd Matutil ; make ) make[3]: Entering directory `/home/albert/Desktop/matpack/source/Matutil' g++ -ansi -std=c++0x -m64 -DXPM_INCL

Re: [gmx-users] how to direct log file correctly?

and: mpirun -np 2 mdrun_mpi -v -s md.tpr -c md.gro -x md.xtc -g md.log & > md.info but it said: Invalid null command. thanks a lot Albert On 04/17/2013 05:33 PM, Justin Lemkul wrote: On 4/17/13 11:30 AM, Albert wrote: Hello: I found that each time I submit gromacs job in GPU w

Re: [gmx-users] GROMACS 4.6 with GPU acceleration (double

On 04/22/2013 08:40 AM, Mikhail Stukan wrote: Could you explain which hardware do you mean? As far as I know, K20X supports double precision, so I would assume that double precision GROMACS should be realizable on it. Really? But many people have discussed that the GPU version ONLY support s

Re: [gmx-users] using CHARMM force field for organic molecule

On 04/22/2013 01:43 PM, Justin Lemkul wrote: There are several options, all external to Gromacs: https://www.paramchem.org/ http://www.swissparam.ch/ -Justin did paramchem support gromacs? As far as I know it only export in CHARMM format. Albert -- gmx-users mailing listgmx

[gmx-users] compile error

Dear: I've installed gromacs-4.6.1 in a GPU workstation with two GTX690. Here is my step: ./configure --prefix=/home/albert/install/openmpi-1.4.5 CC=icc CXX=icpc F77=ifort FC=ifort make make install cmake .. -DGMX_MPI=ON -DGMX_GPU=ON -DBUILD_SHARED_LIBS=OFF -DCUDA_TOOLKIT_ROO

Re: [gmx-users] compile error

IC. it works very well now. thanks a lot Albert On 04/26/2013 08:01 PM, Szilárd Páll wrote: You got a warning at configure-time that the nvcc host compiler can't be set because the mpi compiler wrapper are used. Because of this, nvcc is using gcc to compile CPU code whick chokes on th

[gmx-users] GPU efficiency question

e cap.: 3.0, ECC: no, stat: compatible why the "-np 2" and "-np 4" are the same efficiency? shouldn't it be faster for "-np 4" ? thank you very much Albert -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-us

[gmx-users] _gpu_id failed

Hello: I am going to run gromacs with command: mpirun -np 4 mdrun_mpi -s em.tpr -c em.gro -v -g em.log -gpu_id #0, #2, #3, #4 but it failed with messages: Program mdrun_mpi, VERSION 4.6.1 Source code file: /home/albert/install/source/gromacs-4.6.1/src/gmxlib/statutil.c, line: 364 Fatal

[gmx-users] can we use large timestep for membrane GPU simulation?

? What's more, Eric also shown the GLIC ion channel simulation with 150,000 atoms. E5-2690+GTX Titan can get up to 38ns/day. But he didn't talked about what's the timestep and cutoff. could anybody comment on this? thank you very much best Albert -- gmx-users mailing li

[gmx-users] why files are so large?

file size is negative? Moreover, my nstxout is very large, I don't know why the file is so big and no matter how did I change nstxout, nstvout, the files size doesn't change at all. it always claimed: This run will generate roughly 2791985478365075968 Mb of data thank you very m

Re: [gmx-users] why files are so large?

. best Albert -- 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 interfa

[gmx-users] GPU job often stopped

). -- I can continue the jobs with mdrun option "-append -cpi", but it still stopped from time to time. I am just wondering what's the problem? thank you very much Albert -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx

Re: [gmx-users] GPU job often stopped

em in another GTX690 machine, it also goes well. I compiled Gromacs with the same options in that machine. thank you very much best Albert On 04/29/2013 01:19 PM, Szilárd Páll wrote: Have you tried running on CPUs only just to see if the issue persists? Unless the issue does not occur wit

Re: [gmx-users] GPU job often stopped

time? best Albert -- 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 in

Re: [gmx-users] GPU job often stopped

On 04/29/2013 03:31 PM, Szilárd Páll wrote: The segv indicates that mdrun crashed and not that the machine was restarted. The GPU detection output (both on stderr and log) should show whether ECC is "on" (and so does the nvidia-smi tool). Cheers, -- Szilárd yes it was on: Reading file heavy.

Re: [gmx-users] GPU job often stopped

Btw, were there any other processes using the GPU while mdrun was running? Cheers, -- Szilárd thanks for kind reply. There is no any other process when I am running Gromacs. do you mean I should set GMX_CUDA_STREAMSYNC in the job script like: export GMX_CUDA_STREAMSYNC=/opt/cuda-5.0 ? THX A

[gmx-users] where can be obtain circled lipids bilayer?

Hello: I've got a question about where can be obtain circled lipids bilayer? like shown here: http://wwwuser.gwdg.de/~ggroenh/membed/vesicle.png thank you very much Albert -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please s

Re: [gmx-users] GPU job often stopped

the problem is still there... :-( On 04/29/2013 06:06 PM, Szilárd Páll wrote: On Mon, Apr 29, 2013 at 3:51 PM, Albert wrote: >On 04/29/2013 03:47 PM, Szilárd Páll wrote: >> >>In that case, while it isn't very likely, the issue could be caused by >>some implem

[gmx-users] g_select question

there is only max. 12 water near 6A. However, I found that in almost all my trajectories, there are at least 16 water from the g_select output. I am just wondering, is there anything wrong of my defenition in selection.dat? thank you very much best Albert -- gmx-users mailing listgmx-users

[gmx-users] how to distribute CPU in GPU workstation?

b? thank you very much best Albert -- 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 lis

Re: [gmx-users] GROMACS 4.6.2 released

it seems that Gromacs update quite frequently these days.. On 05/30/2013 05:42 PM, Mark Abraham wrote: Hi GROMACS users, GROMACS 4.6.2 is officially released. It contains numerous bug fixes, some simulation performance enhancements and some documentation updates. We encourage all users to u

Re: [gmx-users] Question about Thermodynamic Integration

you have to run 10X times with different random seeds to confirm your results. Most importantly, you have to do biochemistry mutagenis to fully support your hypothesis otherwise nobody will believe your theoretical results good luck On 08/08/2012 09:11 AM, Asaf Farhi wrote: Dear Gromacs user

Re: [gmx-users] a residue move in extremely large scale in MD

luck Albert On 08/08/2012 08:55 AM, Acoot Brett wrote: Dear Catch ya, I have watched the trajectory of the simulation. Besdies, I got the PDb file for the whole 10 ns MD every 500 ps. Then I compared all the PDB files generated, and it confirms that 1 specific residues moves in an extremely

[gmx-users] when?

hello: Does anybody have any idea for the new version? when would it be reachable? and what's new? thx Albert -- 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

Re: [gmx-users] when?

hat's new comparing with current 4.5.5? thx best A. On 08/15/2012 04:39 PM, Elton Carvalho wrote: On Wed, Aug 15, 2012 at 4:31 PM, Albert wrote: hello: Does anybody have any idea for the new version? when would it be reachable? and what's new? You can always try the current

[gmx-users] how to check total charge by command?

Dear: I am going to check the total charge of my system from a gro file. I am wondering which command should I use? I check the manual and found nothing for it. thank you very much best A -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users

[gmx-users] very strange area/lipid value for POPC membrane system

m the POPC real area/lipids which should be something around 64. Does anybody knows what happen? thank you very much best Albert here is paramters: ## Input file and input file parameters bilayereq-withProtein.gro solventSOL ionsNA+,CL- resname

Re: [gmx-users] very strange area/lipid value for POPC membrane system

simulation for the pure lipids itself (but as I saw that few people will did the test with such big protein inserted in a membrane)? thank you very much best Albert On 08/19/2012 08:14 PM, Justin Lemkul wrote: If you tell GridMAT-MD that there is no protein, it will assign the "empty"

[gmx-users] double precision or single precision?

Dear: I am going to run a very long time simulation with Gromacs CHARMM36 FF. I am wondering, is single precision compiled version would be good enough for such kind of purpose or I should use double precision? thank you very much Albert -- gmx-users mailing listgmx-users@gromacs.org

[gmx-users] any alternative methods?

but GridMAT give me something 72. I am just wondering is there any alternative methods? thank you very much best Albert -- 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

[gmx-users] when new FF would be available in Gromacs website?

Hello: I found that recently both Amber and CHARMM FF have been updated including CHARMM 37 (or so called c36_aug12 ?) http://mackerell.umaryland.edu/CHARMM_ff_params.html , Amber 12SB, Amber Lipid FF. Does anybody when those dedicated FF could be avaible in Gromacs? THX best A. -- gmx-use

Re: [gmx-users] when new FF would be available in Gromacs website?

HI Justin thanks for kind reply. Unfortunately I am didn't go that deep of the FF and probably I am not so qualified for this job. So, I will wait a little for then. best A On 08/21/2012 08:25 PM, Justin Lemkul wrote: On 8/21/12 2:20 PM, Albert wrote: Hello: I found that rec

Re: [gmx-users] any alternative methods?

satisfied ALP for the membrane/lipids system. best Albert -- 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 befo

Re: [gmx-users] any alternative methods?

On 08/22/2012 07:44 AM, Mark Abraham wrote: I don't see how this relates to your claim that you computed a value with GridMAT that doesn't relate to a value computed some other way. Mark HI Mark: thanks for kind reply. here is my parameter for for calculation. The vector values was tak

Re: [gmx-users] any alternative methods?

On 08/22/2012 07:44 AM, Mark Abraham wrote: I don't see how this relates to your claim that you computed a value with GridMAT that doesn't relate to a value computed some other way. Mark And here is the results. As we can see The values is really low. However, when I visulizaed the system i

Re: [gmx-users] any alternative methods?

lations. best Albert Ave APL = 50.4388701869839 sq. Ang protein5.01580.671044407 ResidZ-valueArea (sq. Ang.) 3543.67564.615701 3553.72550.2566296323 3562.9734.4852282957 3574.02852.4928731054 3583.21758.2600273255 3593.8212

Re: [gmx-users] any alternative methods?

y for this since I forgot to change the box size values but the protein/lipids case is with correct box size. best Albert On 08/22/2012 02:02 PM, Justin Lemkul wrote: On 8/22/12 3:16 AM, Albert wrote: On 08/22/2012 08:23 AM, Mark Abraham wrote: The authors use a 200x200 grid in their

Re: [gmx-users] any alternative methods?

1.jpg thanks again for comments Albert On 08/22/2012 03:16 PM, Justin Lemkul wrote: On 8/22/12 9:12 AM, Albert wrote: hello Justin: thanks for reply. I've read both the paper and manual script. As indicated from the output, I found the following line: 3684.2953.88400182

Re: [gmx-users] any alternative methods?

On 08/22/2012 03:58 PM, Justin Lemkul wrote: On 8/22/12 9:54 AM, Albert wrote: hello Justin: thanks for reply. I've checked this residue, it is close to protein but I am still curious for the value with 3.88. Even we also observe something 11, 13 which are the same weired to me.

[gmx-users] what's the difference between gen_seed and ld_seed?

er. when should we turn this option on? thank you very much best Albert -- 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/Sea

Re: [gmx-users] what's the difference between gen_seed and ld_seed?

hello guys I am producing MD production. That's really helpful. thank you very much best Albert On 08/23/2012 08:09 PM, Justin Lemkul wrote: On 8/23/12 2:06 PM, Albert wrote: hello : I am a little bit confused about the difference between gen_seed and ld_seed. I checked the m

[gmx-users] g_tune_pme restart

correct using the following command to append the jobs? mpirun -np 144 mdrun -npme -1 -s tuned.tpr -v -f md.trr -e md.edr -g md.log -o md.trr -cpi -append thank you very much best Albert -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users

[gmx-users] how to optimize performance of IBM Power 775?

same system, Core number and parameters, I can get up to 30 ns/day. Does anybody have any advices for this issue? thank you very much Albert -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please searc

[gmx-users] mismatch atoms?

you very much best Albert -- 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

[gmx-users] job restart error

body have any advices? how can I solve this problem? thank you very much best Albert -- 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! * P

Re: [gmx-users] job restart error

le to continue. Will the results the same as -append does? thank you very much best Albert -- 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! * P

Re: [gmx-users] job restart error

thank you very much. it works now. best Albert On 09/04/2012 11:06 PM, Justin Lemkul wrote: On 9/4/12 5:03 PM, Albert wrote: On 09/04/2012 10:59 PM, Justin Lemkul wrote: If your files have been modified in some way, you can't use -append. -Justin HI Justin: thanks for kind

[gmx-users] how to measure distance between two helix?

hello: I would like to make statistics for the distance between two helix (mass center) and I am wondering which command would be helpful for such kind of purpose? thank you very much best Albert -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo

[gmx-users] strange continued jobs

hello: I've restart my jobs with command: mpiexec -n 160 /opt/gromacs/4.5.5/bin/mdrun -nosum -dlb yes -v -s md.tpr -npme 20 -o md2.trr -g md2.log -e md2.edr -cpi The previous log file is: log---one--- DD step 11346 vol min/aver 0.540! load

Re: [gmx-users] strange continued jobs

HI Justin: thanks for such kind comments. I restart the job and it works fine now. best Albert On 09/11/2012 12:50 PM, Justin Lemkul wrote: On 9/11/12 3:11 AM, Albert wrote: hello: I've restart my jobs with command: mpiexec -n 160 /opt/gromacs/4.5.5/bin/mdrun -nosum -dlb y

[gmx-users] does anybody knows how to use CTMD for gromacs trajectories?

Hello: I am wondering does anybody knows how to use CTMD for gromacs trajectories? In the manual, it only support NAMD but it claimed to support Gromacs. Does anybody knows how to use it for Gromacs output analysis? THX Albert -- gmx-users mailing listgmx-users@gromacs.org http

[gmx-users] why the output of g_saltbr is so large?

Dear: I am using command: g_saltbr -f md.trr -s tuned.tpr -dt 16800 to calculate the saltbr and I found the output is really large: ls -lt *.xvg -rw-r--r-- 1 albert users 640869568 Sep 21 09:53 min-min.xvg -rw-r--r-- 1 albert users 2392154038 Sep 21 09:53 plus-min.xvg -rw-r--r-- 1 albert

Re: [gmx-users] why the output of g_saltbr is so large?

Francesco Hello : thank you very much for kind reply. Is it possible simple restrict the calculation to protein sidechain? thank you very much best Albert -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http

[gmx-users] how to assign protonation sate at pH-8?

s so that gromacs can assign the correct protonation state for related residues? Or there are some internal methods in Gromacs for such kind of purpose? thank you very much best Albert -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please

[gmx-users] what is theta in g_helixorient?

hello guys: I am using g_helixorient to analyze the helix property in my system and it generate three theta[1,2,3].xvg file. I am wondering what's that? I didn't find any comments in the help file. thanks Albert -- gmx-users mailing listgmx-users@gromacs.org http://lists.g

Re: [gmx-users] what is theta in g_helixorient?

On 10/02/2012 05:16 PM, Justin Lemkul wrote: On 10/2/12 11:13 AM, Albert wrote: hello guys: I am using g_helixorient to analyze the helix property in my system and it generate three theta[1,2,3].xvg file. I am wondering what's that? I didn't find any comments in the help fil

Re: [gmx-users] what is theta in g_helixorient?

IC. thanks a lot for kind comments. On 10/02/2012 05:38 PM, Justin Lemkul wrote: On 10/2/12 11:35 AM, Albert wrote: On 10/02/2012 05:16 PM, Justin Lemkul wrote: On 10/2/12 11:13 AM, Albert wrote: hello guys: I am using g_helixorient to analyze the helix property in my system and

[gmx-users] can we generate .xtc file directly from mdrun?

md.xtc I also found that the CHARMM36 FF (charmm36.ff_4.5.4_ref.tgz <http://www.gromacs.org/@api/deki/files/184/=charmm36.ff_4.5.4_ref.tgz>) in gromac website seems to be update, I am wondering is it the latest CHARMM37 FF? THX Albert -- gmx-users mailing listgmx-users@gromacs.or

Re: [gmx-users] can we generate .xtc file directly from mdrun?

output file nstvout= 5000; Write velocities to output file nstenergy= 1000; Write energies to output .edr file nstlog= 1000; Write output to .log file nsxtcout = 5000 xtc_precision = 1000 THX Albert -- gmx-users mailing listgmx-users@gromacs.org http

[gmx-users] how to center to molecule in pbc box?

box, otherwise it is messy when we visualize in VMD. I am wondering, is it possible to ask mdrun generate the .xtc file cetering the molecule in PBC box automatically and we no longer need to use trjconv command to convert it. thank you very much best Albert -- gmx-users mailing listgmx

[gmx-users] how to center the protein?

://dl.dropbox.com/u/56271062/position.jpg as we cab see the protein is just in the corner of box and the water molecules (lefft sphere) in the protein was separate from protein and on the otherside of box. THX Albert -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman

[gmx-users] VMD problem?

olve this problem? I try to install the 64bit VMD, but it crashed as soon as it start up. thank you very much Albert -- 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

Re: [gmx-users] VMD problem?

On 10/15/2012 08:46 AM, Peter C. Lai wrote: Depending on the # of atoms, 6000 frames may exceed the amount of ram a 32bit application can address (4GB). If you're having problems with the 64bit version, you should probably ask the vmd-l list. The only workaround other than that is trjconv -skip

[gmx-users] why g_tune_pme generate .trr file?

, I've removed the output for .trr file, but the g_tune_pme still generate a .trr file called : traj.trr I am wondering why it still generate .trr file? is it possible to disable it generate .trr file? I only need the .xtc file. thank you very much best Albert -- gmx-users mailing list

[gmx-users] some question about REMD

generate a random seed thank you very much best Albert -- 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

Re: [gmx-users] some question about REMD

Hi Saber: thanks a lot for such kind reply. How about the second question? I don't find any tutorial for the GBSA solvent simulation in Gromacs website and I am not sure what kind of parameters we should use for GBSA. thank you very much best Albert On 10/17/2012 05:48 PM, saber n

Re: [gmx-users] some question about REMD

neighborlist cutoff (in nm) rcoulomb = 999 ; short-range electrostatic cutoff (in nm) rvdw = 999 ; short-range van der Waals cutoff (in nm) thank you very much Albert On 10/17/2012 06:18 PM, saber naderi wrote: I am no expert in implicit solvent simulations but I think for these simulations it is

Re: [gmx-users] some question about REMD

hello Justin: thanks a lot for kind reply. I've got another question: how to disable PBC? shall I simply delete "pbc=xyz" from .mdp file? I found that sometimes if we delete some parameters from .mdp, gromacs will use the default instead of disable it. thank you very much best

Re: [gmx-users] some question about REMD

07:45 PM, Justin Lemkul wrote: On 10/17/12 1:43 PM, Albert wrote: hello Justin: thanks a lot for kind reply. I've got another question: how to disable PBC? shall I simply delete "pbc=xyz" from .mdp file? I found that sometimes if we delete some parameters from .mdp, groma

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