[gmx-users] protein topology file with some substitutions by other founction groups
Hello gmx-users, I want to run a system which contains about 200 amino acids. But i met some problems with the topology file of this protein. Beacuse groups of some residues are expected to be substituted by some other groups. For example, the hydrogen atome of SH group in Cys is expected to be substituted by -SH group to form a disulphur bond. So, Is there any one who can teach me how to get a topology file of a protein like this? Thank you in advance. Best Huifang -- Huifang Liu (Ph.D. Student) School of Pharmacy Fudan University No.826 Zhang Heng Rd. Shanghai, China, 200032 Tel: (86-21)51980010 (O)Cell phone: +86-13764669357 E-mail: huifangliu1...@gmail.comFax: (86-21)51980010 ___ 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. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] How to calculate PMF after AFM pulling
Hello, Justin As the mannul said, it is intended to analyze .pdo files generated by mdrun using umbrella sampling tocreate a potential of mean force (PMF). But i were using AFM method not umbrella sampling. How can i do that? Thanks. Huifang -- Huifang Liu (Ph.D. Student) School of Pharmacy Fudan University 138 Yi Xue Yuan Rd. Tel: (86-21)54237419 (O) Shanghai, China, 200032 Cell phone: +86-13764669357 E-mail: huifangliu1...@gmail.com Fax: (86-21)54237264 ___ gmx-users mailing listgmx-users@gromacs.org http://www.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. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] How to calculate PMF after AFM pulling
Hello everybody, I have recently run a SMD with AFM method, and i got the .pdo file. But i don't know how to use the .pdo file to calculate the PMF profile. Could someone give me some suggestion? Thanks a lot. Huifang -- Huifang Liu (Ph.D. Student) School of Pharmacy Fudan University 138 Yi Xue Yuan Rd. Tel: (86-21)54237419 (O) Shanghai, China, 200032 Cell phone: +86-13764669357 E-mail: huifangliu1...@gmail.com Fax: (86-21)54237264 ___ gmx-users mailing listgmx-users@gromacs.org http://www.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. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re:problem in DMPC lipid bilayer
Hi, You should include the topology file of DMPC in your current directory. The present version of Gromacs seems not include the DMPC in their database. Good luck -- Huifang Liu (Ph.D. Student) School of Pharmacy Fudan University 138 Yi Xue Yuan Rd. Tel: (86-21)54237419 (O) Shanghai, China, 200032 Cell phone: +86-13764669357 E-mail: huifangliu1...@gmail.com Fax: (86-21)54237264 ___ gmx-users mailing listgmx-users@gromacs.org http://www.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. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re:how to get the the force plot after pulling
Date: Thu, 19 Mar 2009 13:52:09 +0800 From: huifang liu huifangliu1...@gmail.com Subject: [gmx-users] how to get the the force plot after pulling dynamic simulation using GMX-3.3 To: gmx-users@gromacs.org Message-ID: e523c6be0903182252i114666bam4bbe591a10a30...@mail.gmail.com Content-Type: text/plain; charset=iso-8859-1 I am recently doing a SMD. I think i did it very well. But i don't know how to get the force plot. Is there some one can give me a suggestion? Thank you very much. At the end of the SMD you should have obtained a .pdo file. In that file the time and the coordinates of the reference- (R), pull-group (P) and of the spring (S) are written. If i remember correctly it was: t, Rx, Ry, Rz, Px, Sx, Py, Sy, Pz, Sz. If you have more pullgroups then you have first the x-coordinates of P and S, then y-coordinates ... (look in the manual or the header of the .pdo; or for t=0 you should know the position of all particals and springs and can calculate a little bit to see which entry corresponds to which group). Hi, Thomas, Thank you very much for your reply. It is really helpful to me. But there are two things that still confuse me. My .pdo file is like this: # AFM 3.0 # Component selection: 1 1 1 # nSkip 1 # Ref. Group 'USK' # Nr. of pull groups 1 # Group 1 'UNK' afmVec -0.179258 0.695867 -0.695439 AfmRate 0.005000 AfmK 500.00 # 0.002.7391006.9843082.668408 4.0162774.0162802.0263862.026388 7.6232777.623278 0.0020002.7391006.9843082.668408 4.0162774.0162782.0263862.026394 7.6232777.623271 0.0040002.7391006.9843082.668408 4.0162774.0162762.0263862.026401 7.6232777.623264 0.0060002.7391006.9843082.668408 4.0162774.0162752.0263862.026408 7.6232777.623257 0.0080002.7391006.9843082.668408 4.0162774.0162732.0263862.026415 7.6232777.623250 0.012.7391006.9843082.668408 4.0162774.0162712.0263862.026422 7.6232777.623243 0.0120002.7391006.9843082.668408 4.0162774.0162692.0263862.026429 7.6232777.623236 0.0140002.7391006.9843082.668408 4.0162774.0162672.0263862.026436 7.6232777.623229 0.0160002.7391006.9843082.668408 4.0162774.0162662.0263862.026443 7.6232777.623222 0.0180002.7391006.9843082.668408 4.0162774.0162642.0263862.026450 7.6232777.623215 0.022.7391006.9843082.668408 4.0162774.0162622.0263862.026457 7.6232777.623208 0.0220002.7391006.9843082.668408 4.0162774.0162602.0263862.026464 7.6232777.623201 Since the column 5, 7, 9 only changed after every picosecond and column 6, 8,10 changed per 0.002 ps (i set the dt=0.002 in .mdp file). I am wondering whether the column 5,7,9 stand for Sx, Sy, Sz or Px, Py, Pz as you said. If you are right, why the Px, Py, Pz keep the same every picosecond? Is this beacuse that i set the nstxout=500 in the .mdp file (1ps=dt*nstxout). For the force-calculation: The force is the deflection of the spring times the force-constant of the spring - Fx = k(Sx-Px) ... for the other directions it's analog. Then you can calculate the magnitude of F and plot it against the time (if you are only interested in the magnitude of force). Or you can calculate the force in the pulling direction and plot it against time. If i want to calcutate the force in the pulling direction, F=sqrt(Fx*Fx+Fy*Fy+Fz*Fz) ? Thank you so much. Huifang Hope this helps. Thomas Huifang -- Huifang Liu (Ph.D. Student) School of Pharmacy Fudan University 138 Yi Xue Yuan Rd. Tel: (86-21)54237419 (O) Shanghai, China, 200032 Cell phone: +86-13764669357 E-mail: huifangliu1...@gmail.com Fax: (86-21)54237264 -- next part -- An HTML attachment was scrubbed... URL: http://www.gromacs.org/pipermail/gmx-users/attachments/20090319/2f249dff/attachment-0001.html -- Huifang Liu (Ph.D. Student) School of Pharmacy Fudan University 138 Yi Xue Yuan Rd. Tel: (86-21)54237419 (O) Shanghai, China, 200032 Cell phone: +86-13764669357 E-mail: huifangliu1...@gmail.com Fax: (86-21)54237264 ___ gmx-users mailing listgmx-users@gromacs.org http://www.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. Use the www interface or send it to gmx-users-requ...@gromacs.org
[gmx-users] how to get the the force plot after pulling dynamic simulation using GMX-3.3
I am recently doing a SMD. I think i did it very well. But i don't know how to get the force plot. Is there some one can give me a suggestion? Thank you very much. Huifang -- Huifang Liu (Ph.D. Student) School of Pharmacy Fudan University 138 Yi Xue Yuan Rd. Tel: (86-21)54237419 (O) Shanghai, China, 200032 Cell phone: +86-13764669357 E-mail: huifangliu1...@gmail.com Fax: (86-21)54237264 ___ gmx-users mailing listgmx-users@gromacs.org http://www.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. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] problem with pull direction
Hello gmx-users, I find the pulling direction in PULL INFO section of the log file is not coincident with the afm_dir1 parameter i defined in the pull.ppa. could some one tell me which direction is actually used in the pulling process? Thank you very much. Huifang Liu -- Huifang Liu (Ph.D. Student) School of Pharmacy Fudan University 138 Yi Xue Yuan Rd. Tel: (86-21)54237419 (O) Shanghai, China, 200032 Cell phone: +86-13764669357 E-mail: huifangliu1...@gmail.com Fax: (86-21)54237264 ___ gmx-users mailing listgmx-users@gromacs.org http://www.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. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] problems with pulling direction and the initial spring position
Hello GMX user, I want to pull a compound named UNK (whose initial center of mass is X1, Y1, Z1) through a nanotube named STACK(whose center of mass is X2, Y2, Z2). The final position of UNK is supposed to be around X3, Y3, Z3. I used the pull.ppa file as follows: ngroups = 1 group_1 = UNK reference_group = STACK reftype = com reflag = 1 pulldim = Y Y Y afm_rate1= 0.002 afm_k1 = 1673 afm_dir1 = X3-X1, Y3-Y1, Z3-Z1 afm_init1= 0.0, 0.0 ,0.0 What make me confused is that when the UNK is pulled to the center of mass of the channel (nanotube), it begins to fluctuate around the center and doesn't go through the channel. Why could the UNK not be pulled forwards? How can i solve this problem? In addtion, do i use the correct options of afm_dir1 and afm_init1? Thank you very much! Huifang -- Huifang Liu (Ph.D. Student) School of Pharmacy Fudan University 138 Yi Xue Yuan Rd. Tel: (86-21)54237419 (O) Shanghai, China, 200032 Cell phone: +86-13764669357 E-mail: huifangliu1...@gmail.com Fax: (86-21)54237264 ___ gmx-users mailing listgmx-users@gromacs.org http://www.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. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Problems with SMD using gromacs
Hello, gmx users I've been doing SMD with gromacs program. being a new user, i have some questions. I want to pull a small oragnic compound throught a cyclic peptide nanotube which was inserted in the bilayer. 1. As some papers mentioned that the velocity is very important, what velocity should i use in the afm_rate1 option? i am also not sure about the afm_k1 option. 2. The nanotube is not parallel to any axis, what value should i use in the pulldim and afm_dir options? 3. should the reference group in my system be the nanotube and the group_1 be the small compound? Thank you for you attention. Hope for your reply Huifang -- Huifang Liu (Ph.D. Student) School of Pharmacy Fudan University 138 Yi Xue Yuan Rd. Tel: (86-21)54237419 (O) Shanghai, China, 200032 Cell phone: +86-13764669357 E-mail: huifangliu1...@gmail.com Fax: (86-21)54237264 ___ gmx-users mailing listgmx-users@gromacs.org http://www.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. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re:problem with mdrun in parallel
Hello, Mark I configured MPI using the following command: ./configure --prefix=/home/program/mpich-1.2.7 Then, i added the following line in .bashrc file: export PATH=/home/program/mpich-1.2.7/bin:$PATH I don't think it is the problem with MPI. I can run other parallel MD software normally? By the way, I am sorry that i made a mistake. My workstation has two 4-cords CPU, not two 8-cords CPU. Huifang. -- Huifang Liu (Ph.D. Student) School of Pharmacy Fudan University 138 Yi Xue Yuan Rd. Tel: (86-21)54237419 (O) Shanghai, China, 200032 Cell phone: +86-13764669357 E-mail: huifangliu1...@gmail.com Fax: (86-21)54237264 ___ gmx-users mailing listgmx-users@gromacs.org http://www.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. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] problem with mdrun in parallel
Hello, everybody, I recently installed FFTW-3.0.1, mpich-1.2.7 and Gromacs 3.3.3 on my workstation with two 8-cords CPUs. I think i installed them correctly, beause it runs normally with other parellel MD software. It also went nomorally when i run mdrun command in gromacs with 4 nodes. The problem is it doesn't run with when it is up to 8 nodes. In fact, i only change the '-np 4' to '-np 8' in both grompp and mdrun commmand. When i typed the 'top' command, it shows there are only two node are running. And after a little while, it stopped run with the follow error: p7_19858: p4_error: Timeout in establishing connection to remote process: 0 p5_19808: p4_error: Timeout in establishing connection to remote process: 0 p6_19832: p4_error: Timeout in establishing connection to remote process: 0 p0_19710: (324.359375) net_recv failed for fd = 9 p0_19710: p4_error: net_recv read, errno = : 104 In addition, it runs very well, when i use '-np 5' Hope for your help. Thanks Huifang -- Huifang Liu (Ph.D. Student) School of Pharmacy Fudan University 138 Yi Xue Yuan Rd. Tel: (86-21)54237419 (O) Shanghai, China, 200032 Cell phone: +86-13764669357 E-mail: huifangliu1...@gmail.com Fax: (86-21)54237264 ___ gmx-users mailing listgmx-users@gromacs.org http://www.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. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] how to use gromacs for steered molecular dynamics(SMD)
Hi, gmx-users i want to use gromacs to pull a small ligand through a protein channel and study the interaction between the ligand and the protein during this process. However, i have not found out any useful information about steered molecular dynamics(SMD) using Gromacs software. What are the differences between SMD and general MD in using Gromacs and how to set up the related parameters? Thanks a lot. Dove. ___ gmx-users mailing listgmx-users@gromacs.org http://www.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. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] problem with mpirun
Hi, Gromacs users, This command grompp_ompi -np 6 -f pr_10_200.mdp -c after_em_newton_1000.gro -p all.top -o pr_10_100.tpr -po mdrun_pr_10_100.mdp run normally. But when i run the next command mpirun -np 6 mdrun_ompi -s pr_10_100.tpr -c after_pr_10_100.gro -o after_pr_10_100.trr -e after_pr_10_100.edr -g after_pr_10_100.log -v. It gave out as follows: Wrote pdb files with previous and current coordinates step 0 [node1:13598] *** Process received signal *** [node1:13598] Signal: Segmentation fault (11) [node1:13598] Signal code: Address not mapped (1) [node1:13598] Failing at address: 0x2cc3f38 [node1:13600] *** Process received signal *** [node1:13600] Signal: Segmentation fault (11) [node1:13600] Signal code: Address not mapped (1) [node1:13600] Failing at address: 0x6063518 [node1:13602] *** Process received signal *** [node1:13602] Signal: Segmentation fault (11) [node1:13602] Signal code: Address not mapped (1) [node1:13602] Failing at address: 0xc6519968 [node1:13599] *** Process received signal *** [node1:13599] Signal: Segmentation fault (11) [node1:13599] Signal code: Address not mapped (1) [node1:13599] Failing at address: 0x55dabc8 [node1:13601] *** Process received signal *** [node1:13601] Signal: Segmentation fault (11) [node1:13601] Signal code: Address not mapped (1) [node1:13601] Failing at address: 0x21ae2148 [node1:13598] [ 0] /lib64/tls/libpthread.so.0 [0x3078e0c5b0] [node1:13598] [ 1] mdrun_ompi(inl3100+0x248) [0x524b58] [node1:13598] [ 2] mdrun_ompi(do_fnbf+0xfe7) [0x4a3d97] [node1:13598] [ 3] mdrun_ompi(force+0x120) [0x4432f0] [node1:13598] [ 4] mdrun_ompi(do_force+0xb8b) [0x471afb] [node1:13598] [ 5] mdrun_ompi(do_md+0x139f) [0x426fdf] [node1:13598] [ 6] mdrun_ompi(mdrunner+0xb9c) [0x42a6dc] [node1:13598] [ 7] mdrun_ompi(main+0x1dd) [0x42aabd] [node1:13598] [ 8] /lib64/tls/libc.so.6(__libc_start_main+0xdb) [0x307851c3fb] [node1:13598] [ 9] mdrun_ompi [0x412e8a] [node1:13598] *** End of error message *** [node1:13600] [ 0] /lib64/tls/libpthread.so.0 [0x3078e0c5b0] [node1:13600] [ 1] mdrun_ompi(inl3120+0x4a7) [0x525bb7] [node1:13600] [ 2] mdrun_ompi(do_fnbf+0xe96) [0x4a3c46] [node1:13600] [ 3] mdrun_ompi(force+0x120) [0x4432f0] [node1:13600] [ 4] mdrun_ompi(do_force+0xb8b) [0x471afb] [node1:13600] [ 5] mdrun_ompi(do_md+0x139f) [0x426fdf] [node1:13600] [ 6] mdrun_ompi(mdrunner+0xb9c) [0x42a6dc] [node1:13600] [ 7] mdrun_ompi(main+0x1dd) [0x42aabd] [node1:13600] [ 8] /lib64/tls/libc.so.6(__libc_start_main+0xdb) [0x307851c3fb] [node1:13600] [ 9] mdrun_ompi [0x412e8a] [node1:13600] *** End of error message *** [node1:13602] [ 0] /lib64/tls/libpthread.so.0 [0x3078e0c5b0] [node1:13602] [ 1] mdrun_ompi(inl3120+0x4a7) [0x525bb7] [node1:13602] [ 2] mdrun_ompi(do_fnbf+0xe96) [0x4a3c46] [node1:13602] [ 3] mdrun_ompi(force+0x120) [0x4432f0] [node1:13602] [ 4] mdrun_ompi(do_force+0xb8b) [0x471afb] [node1:13602] [ 5] mdrun_ompi(do_md+0x139f) [0x426fdf] [node1:13602] [ 6] mdrun_ompi(mdrunner+0xb9c) [0x42a6dc] [node1:13602] [ 7] mdrun_ompi(main+0x1dd) [0x42aabd] [node1:13602] [ 8] /lib64/tls/libc.so.6(__libc_start_main+0xdb) [0x307851c3fb] [node1:13602] [ 9] mdrun_ompi [0x412e8a] [node1:13602] *** End of error message *** [node1:13599] [ 0] /lib64/tls/libpthread.so.0 [0x3078e0c5b0] [node1:13599] [ 1] mdrun_ompi(inl3100+0x248) [0x524b58] [node1:13599] [ 2] mdrun_ompi(do_fnbf+0xfe7) [0x4a3d97] [node1:13599] [ 3] mdrun_ompi(force+0x120) [0x4432f0] [node1:13599] [ 4] mdrun_ompi(do_force+0xb8b) [0x471afb] [node1:13599] [ 5] mdrun_ompi(do_md+0x139f) [0x426fdf] [node1:13599] [ 6] mdrun_ompi(mdrunner+0xb9c) [0x42a6dc] [node1:13599] [ 7] mdrun_ompi(main+0x1dd) [0x42aabd] [node1:13599] [ 8] /lib64/tls/libc.so.6(__libc_start_main+0xdb) [0x307851c3fb] [node1:13599] [ 9] mdrun_ompi [0x412e8a] [node1:13599] *** End of error message *** [node1:13601] [ 0] /lib64/tls/libpthread.so.0 [0x3078e0c5b0] [node1:13601] [ 1] mdrun_ompi(inl3120+0x4a7) [0x525bb7] [node1:13601] [ 2] mdrun_ompi(do_fnbf+0xe96) [0x4a3c46] [node1:13601] [ 3] mdrun_ompi(force+0x120) [0x4432f0] [node1:13601] [ 4] mdrun_ompi(do_force+0xb8b) [0x471afb] [node1:13601] [ 5] mdrun_ompi(do_md+0x139f) [0x426fdf] [node1:13601] [ 6] mdrun_ompi(mdrunner+0xb9c) [0x42a6dc] [node1:13601] [ 7] mdrun_ompi(main+0x1dd) [0x42aabd] [node1:13601] [ 8] /lib64/tls/libc.so.6(__libc_start_main+0xdb) [0x307851c3fb] [node1:13601] [ 9] mdrun_ompi [0x412e8a] [node1:13601] *** End of error message *** [node1:13603] *** Process received signal *** [node1:13603] Signal: Segmentation fault (11) [node1:13603] Signal code: Address not mapped (1) [node1:13603] Failing at address: 0x2bb7c08 [node1:13603] [ 0] /lib64/tls/libpthread.so.0 [0x3078e0c5b0] [node1:13603] [ 1] mdrun_ompi(inl3100+0x248) [0x524b58] [node1:13603] [ 2] mdrun_ompi(do_fnbf+0xfe7) [0x4a3d97] [node1:13603] [ 3] mdrun_ompi(force+0x120) [0x4432f0] [node1:13603] [ 4] mdrun_ompi(do_force+0xb8b) [0x471afb] [node1:13603] [ 5] mdrun_ompi(do_md+0x139f) [0x426fdf] [node1:13603] [ 6] mdrun_ompi(mdrunner+0xb9c) [0x42a6dc]
[gmx-users] Problems with molecular dynamic investigation of an cyclic peptide nanotube
Hi, Gromacs users, I was caught by a big problem with molecular dynamic investigation of an cyclic peptide nanotube. When i do energy minimization with em.mdp parameter file as follows, it gave out a warning: Warning: 1-4 interaction between 135 and 144 at distance larger than 1 nm. I ignored it and went on the next step with pr.mdp as follows, but it crashed with the following information: Wrote pdb files with previous and current coordinates [node1:15777] *** Process received signal *** [node1:15777] Signal: Segmentation fault (11) [node1:15777] Signal code: Address not mapped (1) [node1:15777] Failing at address: 0xba8e28 [node1:15777] [ 0] /lib64/tls/libpthread.so.0 [0x3078e0c5b0] [node1:15777] [ 1] mdrun_ompi(inl3100+0x248) [0x524b58] [node1:15777] [ 2] mdrun_ompi(do_fnbf+0xfe7) [0x4a3d97] [node1:15777] [ 3] mdrun_ompi(force+0x120) [0x4432f0] [node1:15777] [ 4] mdrun_ompi(do_force+0xb8b) [0x471afb] [node1:15777] [ 5] mdrun_ompi(do_md+0x139f) [0x426fdf] [node1:15777] [ 6] mdrun_ompi(mdrunner+0xb9c) [0x42a6dc] [node1:15777] [ 7] mdrun_ompi(main+0x1dd) [0x42aabd] [node1:15777] [ 8] /lib64/tls/libc.so.6(__libc_start_main+0xdb) [0x307851c3fb] [node1:15777] [ 9] mdrun_ompi [0x412e8a] [node1:15777] *** End of error message *** Segmentation fault I am extremely puzzed and don't know how to solve this problem. In additon, my previous system runs normally with the same parameter file. ##em.mdp file cpp = /lib/cpp define = -DPOSRES constraints = none integrator = steep nsteps = 100 ; ; Energy minimizing stuff ; emtol = 2000 emstep = 0.01 nstcomm = 1 ns_type = grid rlist = 1 rcoulomb= 1.0 rvdw= 1.0 Tcoupl = no Pcoupl = no gen_vel = no #pr.mdp title = Yo cpp = /lib/cpp define = -DPOSRES constraints = all-bonds integrator = md dt = 0.002; ps ! nsteps = 2500 ; total 5 ps. nstcomm = 1 nstxout = 500 nstvout = 1000 nstfout = 0 nstlog = 500 nstenergy = 500 nstlist = 5 ns_type = grid coulombtype = PME rlist = 0.9 rcoulomb= 0.9 rvdw= 0.9 fourierspacing = 0.12 pme_order = 4 optimize_fft= yes ; Berendsen temperature coupling is on in two groups Tcoupl = berendsen tc-grps = Protein tau_t = 0.1 ref_t =10 ; Energy monitoring energygrps = Protein ; Pressure coupling is not on Pcoupl = berendsen pcoupltype = anisotropic tau_p = 1 compressibility = 4.5e-5 4.5e-5 4.5e-5 0 0 0 ref_p = 1 1 1 1 1 1 ; Generate velocites is on at 300 K. gen_vel = no gen_temp= 300.0 gen_seed= 173529 Look forward to your help. Thanks in advance. Huifang ___ gmx-users mailing listgmx-users@gromacs.org http://www.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. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] grompp -f em.mdp -c speptide.pdb -p \#spetide.top.1#\ -o speptide_empdb.tpr
I typed this command: grompp -f em.mdp -c speptide.pdb -p \#spetide.top.1#\ -o speptide_em.tpr It responded to me like this:Invalid command line argument: speptide_empdb.tpr I am a new -learner.Can you tell me where the problem is. Thanks. ___ gmx-users mailing listgmx-users@gromacs.org http://www.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. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Relationship between the spetide.gro file and the #spetide.gro.1#?
Hi, I am a new learner of Gromacs.I want to kown what relationship between the spetide.gro file and the #spetide.gro.1# file is and how to see the content of the #spetide.gro.1# file. Hope to get your help! ___ gmx-users mailing listgmx-users@gromacs.org http://www.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. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
