[gmx-users] Is Gromos force field 45a3 out of dated?
Hello, I submitted a paper and get rejected immediately by editor because of the following comment. The simulations described here rely on an outdated force field (Gromos 45a3) and I suspect that the partial unfolding described here is at least in part due to force field artifacts. Our simulation work fit the results from the experimental work quite well but the editor returned his suspicion. Is the force field Gromos 45a3 outdated? Could anyone refer me more details about the force field of Gromos 45a3? Could anyone refer me about any cases of the broken simulation from the force field artifacts? Thank you 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 the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Counting non-bonding interaction
Hi Is there any function counting non-bonding interaction with Gromacs ? Thanks 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 the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Counting number of non-bonded interactions ?
Hi Is there any function to count number of non-bonded interactions with Gromacs ? Thank you 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 the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] How to calculate RMSD per residue with Gromacs ?
Hi How to calculate RMSD per residue with Gromacs ? Thank you 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 the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Domain Motion = How do get the rotational axis from eigenvectors ?
Hi I want to get the rotational axis about the protein domain motion. *From the DynDom website = DynDom* is a program to determine domains, hinge axes and hinge bending residues in proteins where two conformations are available. Questions: 1. Do the hinge axes represent the rotational axis about the protein domain motion ? 2. From its User created database, domains and hinge bending residues, rotation angles and translation are created. = The rotation angles must be defined as the angle of rotation between two domains based on the hinge axes, right ? = The vector of the hinge axes is not given by DynDom website, or I did not find it ??? = Hinge axes could be obtained from hinge bending axes residues, right If so, How = How can I get the vector of the hinge axes with the results from DynDom ??? = I found some papers drawing the hinge axes, can Gromacs help me find and draw the hinge axes = From User created database in the DynDom website, it is showing Sequence. What does sequence represent ??? 3. Should I install the program of DynDom and then g_dyndom can be functioned ??? (we need to install DSSP before using do_dssp) 4. From Gromacs manual = The purpose of this program (g_dyndom) is to interpolate and extrapolate the rotation as found by DynDom. What does it mean to interpolate and extrapolate the rotation as found by DynDom ? Thank you Lin Message: 1 Date: Thu, 26 May 2011 19:54:29 -0700 From: Chih-Ying Lin chihying2...@gmail.com Subject: [gmx-users] Domain Motion = How do get the rotational axis fromeigenvectors ? To: gmx-users@gromacs.org Message-ID: banlktinje0fhg6e1dso8aj66_n16xnc...@mail.gmail.com Content-Type: text/plain; charset=iso-8859-1 Hi I want to protein's domain motion. I use g_covarandg_anaeig to get the eigenvectors. How can i get the rotational axis of which protein do its domain motion from those eigenvectors? I found the papers and the authors plot its rotational axis of domain motion. How did they make it ? Thank you Lin -- next part -- An HTML attachment was scrubbed... URL: http://lists.gromacs.org/pipermail/gmx-users/attachments/20110526/9dde6334/attachment-0001.html -- Message: 2 Date: Fri, 27 May 2011 05:54:07 +0200 From: Tsjerk Wassenaar tsje...@gmail.com Subject: Re: [gmx-users] Domain Motion = How do get the rotational axis from eigenvectors ? To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: BANLkTinKF=-c5+M7op80Dy2VaFM=ml4...@mail.gmail.com Content-Type: text/plain; charset=ISO-8859-1 Hi Lin, You don't get such axes directly from covariance analysis. If you want to know which rotations are associated with a certain eigenvector, you have to run a routine like dyndom (http://fizz.cmp.uea.ac.uk/dyndom/) on the extreme projections of your trajectory onto an eigenvector. Cheers, Tsjerk -- 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 send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Domain Motion = How do get the rotational axis from eigenvectors ?
Hi I want to protein's domain motion. I use g_covarandg_anaeig to get the eigenvectors. How can i get the rotational axis of which protein do its domain motion from those eigenvectors? I found the papers and the authors plot its rotational axis of domain motion. How did they make it ? Thank you 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 the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re-compile Gromacs Program?
Hi I found the Gromacs Program could not do the parallel computing since the staff of the compter center in my school upgraded the intel compiler to v 12, and rebuilt the mpich build with intel. I requested them to recompile the Gromacs Program but they rejected and they answered that the updated intel compiler is not the issue for the failure of running the parallel computing of Gromacs Program. I listed the bounced-back of summited job to the computer center. Warning: no access to tty (Bad file descriptor). Thus no job control in this shell. /usr/bin/xmgrace: No such file or directory. /usr/usc/mpich/default/mx-intel/setup.csh: line 30: syntax error: unexpected end of file /usr/usc/gromacs/default/setup.csh: line 19: syntax error: unexpected end of file /usr/usc/intel/default/setup.csh: line 24: syntax error: unexpected end of file mpiexec_hpc1982: cannot connect to local mpd (/tmp/ 10429754.hpc-pbs.usc.edu/mpd2.console_hpc1982_chihying); possible causes: 1. no mpd is running on this host 2. an mpd is running but was started without a console (-n option) How does the problem happen? Thank you 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 the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Diffusion Coefficient
Hi I calculated the diffusion coefficient for lysozyme and get ~4x1e-6 (cm2/s) But, the experimental data is around 1x1e-6 (cm2/s). How could I explain for this discrepency? Thank you 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 the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] ZN2+ qtot 1.233e-06 ?
Hi I issued pdb2gmx with G45a3 force field on the bovine carbonic anhydrase From the .top value, the ZN+2 is given qtot 1.233e-06 .. 2611 ZN2+257 ZN ZN 1137 2 65.37 ; qtot 1.233e-06 I am confused with the charges. Isn't ZN+2 carrying +2 charges ?? From Mark = It is - look at the column headings higher up. See http://www.gromacs.org/Documentation/Floating_Point_Arithmeticfor why the total charge doesn't look nice. However, qtot 1.233e-06 ~ 0 isn't it away from +2 charges too much? Or, it is the tolerable ? Thank you 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 the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] ZN2+ qtot 1.233e-06 ?
Hi I issued pdb2gmx with G45a3 force field on the bovine carbonic anhydrase From the .top value, the ZN+2 is given qtot 1.233e-06 .. 2611 ZN2+257 ZN ZN 1137 2 65.37 ; qtot 1.233e-06 I am confused with the charges. Isn't ZN+2 carrying +2 charges ?? Thank you 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 the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Standard Procedures to perform MD under High Temperature 498 K, either NVT or NTP ?
Hi I read some papers and many simulations were performed under high temperature to induce the unfolded protein. However, the authors did not mention how they conducted the simulations under high temperature, 498 K. They did not mention which NVT or NPT were adopted for such high temperature. None of any parameters about the temperature coupling and pressure coupling were described on the papers. Are there any standard procedures to perform High temperature - MD simulation? Where can I find the standard procedures? At 498K, protein is cooked. Under NPT, the water evaporated. = so, turn on pressure coupling with a (very) high pressure to keep the water molecules. Under NVT, the pressure increased dramatically. So, to run MD simulations under the high temperature means to run the MD simulation under high pressure at the same time? But, I did read one paper that the authors performed the MD simulation under high temperature and high pressures separately and further discuss the effect the high temperature and the high pressures on protein separately. Thank you 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 the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] High Temperature 498 K, NVT or NTP ?
Hi At high temperature 498 K, the protein is cooked. For NVT, the volume of the system is much expanded. For NPT, the water evaporated. How do people simulate the condition under high temperature, 498K? THank you 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 the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] g_rmsf -res = does Gromacs do average over time for each residue ?
Hi g_rmsf -f abc.xtc -s abc.tpr -res -o abcrmsf.xvg From manual = it saysCalculate averages for each residue = does Gromacs do average over time for each residue ? = however, the results did not show difference with and without -res Thank you 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 the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] g_rmsf -res = what does this function work?
Hi From Manual http://manual.gromacs.org/current/online/g_rmsf.html g_rmsf = optiontypedefaultdescription -[no]res bool noCalculate averages for each residue what does this function work? Thank you 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 the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] g_rmsf -res yes ? = should I type yes to activate the average-function ?
Hi g_rmsf -res yes ? g_rmsf -res no ? should I type yes to activate the average-function? As i tested g_rmsf -res, the average is not over time and not over the atoms in the residue. Anyway, how to activate the average function ? Thank you Lin Chih-Ying Lin wrote: Hi g_rmsf -f abc.xtc -s abc.tpr -res -o abcrmsf.xvg From manual = it saysCalculate averages for each residue = does Gromacs do average over time for each residue ? The average is done over time and over the atoms in the residue. = however, the results did not show difference with and without -res I doubt that. Without -res, you get RMSF per atom. With -res, you get RMSF per residue. The output is inherently (and necessarily) different. -Justin Thank you 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 the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] g_rmsf = average over # of time frames ???
Hi
From source code = gmx_rmsf.c
g_rmsf computes the root mean square fluctuation (RMSF, i.e. standard ,
deviation) of atomic positions ,
if (devfn) {
/* Calculate RMS Deviation */
for(i=0;(iisize);i++) {
aid = index[i];
for(d=0;(dDIM);d++) {
rmsd_x[i][d] += sqr(x[aid][d]-xref[aid][d]);
}
}
}
count += 1.0;
rmsf[i] = (rmsd_x[i][XX]+rmsd_x[i][YY]+rmsd_x[i][ZZ])/count;
Therefore, g_rmsf is the average of structure deviation over the time
frames.
However, I issued the commands ( C-alpha is selected )
g_rmsf -f abc.xtc -b 0 -e 100 -s abc-crystal.tpr -o RMSF-abc-0th-100th.xvg
g_rmsf -f abc.xtc -b 100 -e 200 -s abc-crystal.tpr -o
RMSF-abc-100th-200th.xvg
g_rmsf -f abc.xtc -b 200 -e 300 -s abc-crystal.tpr -o
RMSF-abc-200th-300th.xvg
g_rmsf -f abc.xtc -b 300 -e 400 -s abc-crystal.tpr -o
RMSF-abc-300th-400th.xvg
g_rmsf -f abc.xtc -b 400 -e 500 -s abc-crystal.tpr -o
RMSF-abc-400th-500th.xvg
g_rmsf -f abc.xtc -b 500 -e 600 -s abc-crystal.tpr -o
RMSF-abc-500th-600th.xvg
g_rmsf -f abc.xtc -b 600 -e 700 -s abc-crystal.tpr -o
RMSF-abc-600th-700th.xvg
g_rmsf -f abc.xtc -b 700 -e 800 -s abc-crystal.tpr -o
RMSF-abc-700th-800th.xvg
g_rmsf -f abc.xtc -b 800 -e 900 -s abc-crystal.tpr -o
RMSF-abc-800th-900th.xvg
g_rmsf -f abc.xtc -b 900 -e 1000 -s abc-crystal.tpr -o
RMSF-abc-900th-1000th.xvg
Also, ( C-alpha is selected )
g_rmsf -f abc.xtc -b 0 -e 1000 -s abc-crystal.tpr -o RMSF-abc-0th-1000th.xvg
Then I ploted,
RMSF-abc-0th-100th.xvg
RMSF-abc-100th-200th.xvg
RMSF-abc-200th-300th.xvg
RMSF-abc-300th-400th.xvg
RMSF-abc-400th-500th.xvg
RMSF-abc-500th-600th.xvg
RMSF-abc-600th-700th.xvg
RMSF-abc-700th-800th.xvg
RMSF-abc-800th-900th.xvg
RMSF-abc-900th-1000th.xvg
Also, I ploted
RMSF-abc-0th-1000th.xvg
The PLOT RMSF-abc-0th-1000th.xvg has all RMSF-Values much higher than those
from RMSF-abc-0th-100th.xvg / RMSF-abc-100th-200th.xvg
/ RMSF-abc-200th-300th.xvg / .. / RMSF-abc-900th-1000th.xvg...
It does not make sense... I supposed.
Did I misunderstand something ?
THank you
Lin
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[gmx-users] g_rmsf -res = average over time for each residue?
Hi g_rmsf -f abc.xtc -s abc.tpr -res -o abcrmsf.xvg *-[no]res* bool no Calculate averages for each residue abcrmsf.xvg = average over time for each residue? Thank you 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 the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] g_dipole ? =salt-molecule = Does Gromacs consider counter ions?
Hi Sorry, I ask the same question again because i am not a decent person in this field. If possible, someone can give me a quick answer while i am trying to get understanding the source codes. My basic understanding is that Gromacs has other approach of calculating dipole moment instead of the following equation. dipole moment = 48.0 sum of q_i x_i x_i is the atomic position. When I issued the command g_dipole, the dialog poped out and asked me to select a group. 1. system 2. protein . 11. solvent 12. the rest of the salt-molecule except its counter ion 13. counter ions (CL-) If I select #12, Gromacs will not consider counter ions to calculate the dipole moment ??? Sorry for disturbing people in the Gromacs mailing list. Thank you Lin On 2010-10-22 00.49, Chih-Ying Lin wrote: Hi When I issued the command g_dipole, the dialog poped out and asked me to select a group. 1. system 2. protein . 11. solvent 12. the rest of the salt-molecule except its counter ion 13. counter ions (CL-) If I select #12, Gromacs will not consider counter ions to calculate the dipole moment ??? Thank you Lin you should try to understand what is going on yourself rather than sending many email to the mailing list. Please read the source code of the program. -- -- 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 send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] g_dipole ? = The salt molecule = The discrepancy of dipole moment between my calculation and GROMACS
HI dipole moment = 48.0 sum of q_i x_i x_i is the atomic position. The PBC is considered. I did not include the counter ion of the salt molecule in my calculation. The salt molecule is A-N(CH3)3-Br and it has two structures, cis and trans. Here A are a string of atoms, most of them are carbons. For the cis-structure Dipole moment from GROMACS Average = 33.0312 Std. Dev. = 3.5144 Error = 0.0236 Dipole moment from my calculation = 55.8675 For the trans-structure Dipole moment from GROMACS Average = 36.8470 Std. Dev. = 3.4917 Error = 0.0238 Dipole moment from my calculation = 77.2346 Questions: 1. There is a huge discrepancy between my calculation results and GROMACS. Or, the two results are within acceptable discrepancy ??? 2. In the beginning, I suppose that the trans-structure has smaller dipole moment than cis-structure. However, it seems to be the opposite conclusion based on both GROMACS and my calculation. Is there something possible wrong ??? 3. I get the partial charges from the Journal papers and the partial charges are derived for the similar molecules as mine. Is that wrong? Thank you Lin Hey Lin, Did you consider PBC? Also, I wouldn't include the bromide if I were you, as it just adds noise, because it can move around freely. You seem to be interested in the change in dipole moment in the cation only, anyway. Cheers, Tsjerk On Oct 21, 2010 7:02 AM, Chih-Ying Lin chihying2...@gmail.com wrote: HI dipole moment = 48.0 sum of q_i x_i x_i is the atomic position. I did not include the counter ion of the salt molecule in my calculation. The salt molecule is A-N(CH3)3-Br and it has two structures, cis and trans. Here A are a string of atoms, most of them are carbons. For the cis-structure Dipole moment from GROMACS Average = 33.0312 Std. Dev. = 3.5144 Error = 0.0236 Dipole moment from my calculation = 55.8675 For the trans-structure Dipole moment from GROMACS Average = 36.8470 Std. Dev. = 3.4917 Error = 0.0238 Dipole moment from my calculation = 77.2346 Questions: 1. There is a huge discrepancy between my calculation results and GROMACS. Or, the two results are within acceptable discrepancy ??? 2. In the beginning, I suppose that the trans-structure has smaller dipole moment than cis-structure. However, it seems to be the opposite conclusion based on both GROMACS and my calculation. Is there something possible wrong ??? 3. I get the partial charges from the Journal papers and the partial charges are derived for the similar molecules as mine. Is that wrong? Thank you 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 the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] g_dipole ? = dipole moment = trans-structure is more hydrophobic than the cis-structure ?
Hi In one paper, the salt-molecule has two structures, trans and cis. The sentence in the paper is that trans-structure is more hydrophobic than the cis-structure without providing the value of the dipole moment. I wonder know if the value of dipole moment is the main indicator to decide if trans-structure is more hydrophobic than the cis-structure. Also, is it all true for salt-molecule that trans-structure is more hydrophobic than the cis-structure ? Thank you 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 the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] g_dipole ? =salt-molecule = the relative position of counter ions to the rest of salt-molecule matters ???
HI As Timo M.D. Graen described As long as the system is neutral, the reference point will not affect the calculation result of the dipole moment for the system. On the other hand, I also play around the small salt-molecule as Timo M.D. Graen suggested. take two ions for a start, Na+ and Cl-, place them at NA(1,1,0) and CL(2,1,0). Now calculate the dipole moment for this system using different points of reference, i.e. (0,0,0) and (1,2,0) and (3,3,0). What do you observe? Next, add an additional NA+ ion to your system at NA(3,1,0) and repeat your calculation for the same reference points. So, i include the counter ion in my dipole moment-calculation this time. But, the dipole moment of the system depends on where the counter ions are located. For the cis-structure, the dipole moment is range from 45 to 75 as I randomly set the position of the counter ions. For the trans-structure, the dipole is range from 35 to 77 as I randomly set the position of the counter ions. I have used GROMACS to test the dipole moment of the similar systems where GROMACS set the positions of the counter ions and the rest of molecules. For the cis-structure, the dipole moment is around 33. The standard deviation ~ 3 For the trans-structure, the dipole is around 36. The standard deviation ~ 3 How could GROMACS get the much lower standard deviation than what I calculated? Is there any specific rules while GROMACS decides the relative positions of the counter ions to the rest of the molecules? My calculation result is not very close to what GROMACS derived. Am I doing correctly ? For the cis-structure Dipole moment from GROMACS Average = 33.0312 Std. Dev. = 3.5144 Error = 0.0236 Dipole moment from my calculation = 45 to 75 For the trans-structure Dipole moment from GROMACS Average = 36.8470 Std. Dev. = 3.4917 Error = 0.0238 Dipole moment from my calculation = range from 35 to 77 Thank you Lin dipole moment = 48.0 sum of q_i x_i x_i is the atomic position. I did not include the counter ion of the salt molecule in my calculation. The salt molecule is A-N(CH3)3-Br and it has two structures, cis and trans. Here A are a string of atoms, most of them are carbons. For the cis-structure Dipole moment from GROMACS Average = 33.0312 Std. Dev. = 3.5144 Error = 0.0236 Dipole moment from my calculation = 55.8675 For the trans-structure Dipole moment from GROMACS Average = 36.8470 Std. Dev. = 3.4917 Error = 0.0238 Dipole moment from my calculation = 77.2346 Questions: 1. There is a huge discrepancy between my calculation results and GROMACS. Or, the two results are within acceptable discrepancy ??? 2. In the beginning, I suppose that the trans-structure has smaller dipole moment than cis-structure. However, it seems to be the opposite conclusion based on both GROMACS and my calculation. Is there something possible wrong ??? 3. I get the partial charges from the Journal papers and the partial charges are derived for the similar molecules as mine. Is that wrong? Thank you 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 the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] g_dipole ? =salt-molecule = Does Gromacs consider counter ions?
Hi When I issued the command g_dipole, the dialog poped out and asked me to select a group. 1. system 2. protein . 11. solvent 12. the rest of the salt-molecule except its counter ion 13. counter ions (CL-) If I select #12, Gromacs will not consider counter ions to calculate the dipole moment ??? Thank you 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 the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] g_dipole ? = salt molecule in water = what is the the displacement vector pointing from the negative charge to the positive charge?
Hi molecule dipole is 48.0 sum of q_i x_i based on the following two websites, *x_i * is the displacement vectorhttp://en.wikipedia.org/wiki/Displacement_%28vector%29pointing from the negative charge to the positive charge. what about the x_i for the salt-molecule, which dissociates into one counter ion and the rest of the molecule in water? http://en.wikipedia.org/wiki/Bond_dipole_moment http://en.wikipedia.org/wiki/Electric_dipole_moment Thank you Lin On 2010-10-20 06.06, Chih-Ying Lin wrote: Hi molecule dipole is 48.0 sum of q_i x_i x_i the bond length for covalent bond. No. x_i is the atomic position. but what is x_i for salt-molecule? For salt-molecule, the ionic bonds are broken in water solvent and the counter ions are spread among the water. What is the x_i of the ionic bond in the dipole moment calculation? Is x_i equal to the distance of the two parts of the salt-molecules (the counter ion and the rest of the molecule) even though the salt molecule has dissolved in the water? I mean, is x_i equal to the length of simulation box if the counter ion and the rest of the molecule are in the two sides of the simulation box? I mean, if Gromacs takes x_i as the length of simulation box if the counter ion and the rest of the molecule are in the two sides of the simulation box? Thank you Lin Try http://en.wikipedia.org/wiki/Electric_dipole_moment , you might want to read the part about calculating dipole moments for an array of point charges, it is not difficult. 33 point charges are doable using pencil and calculator in about 10min. Do not worry about the reference point as long as your system is neutral, just set it to (0,0,0). Otherwise, take any kind of first year physics book it will contain very similar information. On 10/19/2010 05:39 AM, Chih-Ying Lin wrote: Hi According to the following website, http://en.wikipedia.org/wiki/Bond_dipole_moment \mu = \delta \, d. The bond dipole is modeled as +ä -- ä- with a distance /d/ between the partial charges http://en.wikipedia.org/wiki/Partial_charges +ä and ä-. For a complete molecule the total molecular dipole moment may be approximated as the vector sum of individual bond dipole moments. However, for a molecule of multiple atoms, There may be more than one bond connected on one atom. E | B - A - C partial charge of atom_A = -0.5 partial charge of atom_B = 0.2 partial charge of atom_C = 0.35 partial charge of atom_E = 0.4 Which partial charges should I use when I calculate bond-dipole-moment of A-B ? Which partial charges should I use when I calculate bond-dipole-moment of A-C ? Which partial charges should I use when I calculate bond-dipole-moment of A-E ? Thank you Lin On 2010-10-18 03.30, Chih-Ying Lin wrote: HI I confined one molecule in the center of box and issue the g_dipole command. The average dipole moment is still around 32. It is the molecule with 33 atoms / united atoms of most carbon groups, isn't the dipole moment around 32 too high? How can I test next and know that the dipole moment around 32 is acceptable? By calculating on paper: dipole is 48.0 sum of q_i x_i, therefore if you have large charge separation you will get a large dipole. Thank you Lin On 2010-10-16 21.36, Chih-Ying Lin wrote: Hi I issue the g_dipole command on Gromacs = And, the following information is shown. There are 10 molecules in the selection, Does the Average =32.1611 refer to the average for a single over the simulation time? Or, the Average = 32.1611 summing for all the 10 molecules over the simulation time? If the average = 32.1611 for a single molecule with 33 atoms / united atoms of most carbon groups, isn't the dipole moment too high? I think this is the average per molecule. You may need to run trjconv -pbc whole, because mdrun may break molecules in two parts, meaning that the molecule becomes as big as the box. What does will subtract their charge at their center of mass this mean? Why will subtract their charge at their center of mass ? -- next part -- An HTML attachment was scrubbed... URL: http://lists.gromacs.org/pipermail/gmx-users/attachments/20101019/4cf32833/attachment.html -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- -- gmx-users mailing list gmx-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! End of gmx-users Digest, Vol 78, Issue 142 ** -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx
[gmx-users] g_dipole ? = salt molecule in water = should I include counter ions in my calculation?
HI 48.0 sum of q_i x_i x_i is the atomic position. For the salt molecule in water, should I include counter ions in my calculation ? Or, only the rest of the salt molecule except the counter ions? Thank you 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 the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] g_dipole ? = The salt molecule = The discrepancy of dipole moment between my calculation and GROMACS
HI dipole moment = 48.0 sum of q_i x_i x_i is the atomic position. I did not include the counter ion of the salt molecule in my calculation. The salt molecule is A-N(CH3)3-Br and it has two structures, cis and trans. Here A are a string of atoms, most of them are carbons. For the cis-structure Dipole moment from GROMACS Average = 33.0312 Std. Dev. = 3.5144 Error = 0.0236 Dipole moment from my calculation = 55.8675 For the trans-structure Dipole moment from GROMACS Average = 36.8470 Std. Dev. = 3.4917 Error = 0.0238 Dipole moment from my calculation = 77.2346 Questions: 1. There is a huge discrepancy between my calculation results and GROMACS. Or, the two results are within acceptable discrepancy ??? 2. In the beginning, I suppose that the trans-structure has smaller dipole moment than cis-structure. However, it seems to be the opposite conclusion based on both GROMACS and my calculation. Is there something possible wrong ??? 3. I get the partial charges from the Journal papers and the partial charges are derived for the similar molecules as mine. Is that wrong? Thank you 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 the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] g_dipole ? = ionic bond = how to determine the direction of ionic bond dipole moment ?
Hi molecule dipole is 48.0 sum of q_i x_i For a multiple-atoms molecule, the dipole moment of a covalent bond is a vector, parallel to the bond axis, For a multiple-atoms molecule, which includes a ionic bond, how to determine the direction of ionic bond dipole moment in theory ? How does Gromacs determine the direction of ionic bond dipole moment ? Thank you Lin Try http://en.wikipedia.org/wiki/Electric_dipole_moment , you might want to read the part about calculating dipole moments for an array of point charges, it is not difficult. 33 point charges are doable using pencil and calculator in about 10min. Do not worry about the reference point as long as your system is neutral, just set it to (0,0,0). Otherwise, take any kind of first year physics book it will contain very similar information. On 10/19/2010 05:39 AM, Chih-Ying Lin wrote: Hi According to the following website, http://en.wikipedia.org/wiki/Bond_dipole_moment \mu = \delta \, d. The bond dipole is modeled as +δ -- δ- with a distance /d/ between the partial charges http://en.wikipedia.org/wiki/Partial_charges +δ and δ-. For a complete molecule the total molecular dipole moment may be approximated as the vector sum of individual bond dipole moments. However, for a molecule of multiple atoms, There may be more than one bond connected on one atom. E | B - A - C partial charge of atom_A = -0.5 partial charge of atom_B = 0.2 partial charge of atom_C = 0.35 partial charge of atom_E = 0.4 Which partial charges should I use when I calculate bond-dipole-moment of A-B ? Which partial charges should I use when I calculate bond-dipole-moment of A-C ? Which partial charges should I use when I calculate bond-dipole-moment of A-E ? Thank you Lin On 2010-10-18 03.30, Chih-Ying Lin wrote: HI I confined one molecule in the center of box and issue the g_dipole command. The average dipole moment is still around 32. It is the molecule with 33 atoms / united atoms of most carbon groups, isn't the dipole moment around 32 too high? How can I test next and know that the dipole moment around 32 is acceptable? By calculating on paper: dipole is 48.0 sum of q_i x_i, therefore if you have large charge separation you will get a large dipole. Thank you Lin On 2010-10-16 21.36, Chih-Ying Lin wrote: Hi I issue the g_dipole command on Gromacs = And, the following information is shown. There are 10 molecules in the selection, Does the Average =32.1611 refer to the average for a single over the simulation time? Or, the Average = 32.1611 summing for all the 10 molecules over the simulation time? If the average = 32.1611 for a single molecule with 33 atoms / united atoms of most carbon groups, isn't the dipole moment too high? I think this is the average per molecule. You may need to run trjconv -pbc whole, because mdrun may break molecules in two parts, meaning that the molecule becomes as big as the box. What does will subtract their charge at their center of mass this mean? Why will subtract their charge at their center of mass ? -- 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 send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] g_dipole ? = what is the bond length of the ionic bond in the dipole moment calculation?
Hi molecule dipole is 48.0 sum of q_i x_i x_i the bond length for covalent bond. but what is x_i for salt-molecule? For salt-molecule, the ionic bonds are broken in water solvent and the counter ions are spread among the water. What is the x_i of the ionic bond in the dipole moment calculation? Is x_i equal to the distance of the two parts of the salt-molecules (the counter ion and the rest of the molecule) even though the salt molecule has dissolved in the water? I mean, is x_i equal to the length of simulation box if the counter ion and the rest of the molecule are in the two sides of the simulation box? I mean, if Gromacs takes x_i as the length of simulation box if the counter ion and the rest of the molecule are in the two sides of the simulation box? Thank you Lin Try http://en.wikipedia.org/wiki/Electric_dipole_moment , you might want to read the part about calculating dipole moments for an array of point charges, it is not difficult. 33 point charges are doable using pencil and calculator in about 10min. Do not worry about the reference point as long as your system is neutral, just set it to (0,0,0). Otherwise, take any kind of first year physics book it will contain very similar information. On 10/19/2010 05:39 AM, Chih-Ying Lin wrote: Hi According to the following website, http://en.wikipedia.org/wiki/Bond_dipole_moment \mu = \delta \, d. The bond dipole is modeled as +ä -- ä- with a distance /d/ between the partial charges http://en.wikipedia.org/wiki/Partial_charges +ä and ä-. For a complete molecule the total molecular dipole moment may be approximated as the vector sum of individual bond dipole moments. However, for a molecule of multiple atoms, There may be more than one bond connected on one atom. E | B - A - C partial charge of atom_A = -0.5 partial charge of atom_B = 0.2 partial charge of atom_C = 0.35 partial charge of atom_E = 0.4 Which partial charges should I use when I calculate bond-dipole-moment of A-B ? Which partial charges should I use when I calculate bond-dipole-moment of A-C ? Which partial charges should I use when I calculate bond-dipole-moment of A-E ? Thank you Lin On 2010-10-18 03.30, Chih-Ying Lin wrote: HI I confined one molecule in the center of box and issue the g_dipole command. The average dipole moment is still around 32. It is the molecule with 33 atoms / united atoms of most carbon groups, isn't the dipole moment around 32 too high? How can I test next and know that the dipole moment around 32 is acceptable? By calculating on paper: dipole is 48.0 sum of q_i x_i, therefore if you have large charge separation you will get a large dipole. Thank you Lin On 2010-10-16 21.36, Chih-Ying Lin wrote: Hi I issue the g_dipole command on Gromacs = And, the following information is shown. There are 10 molecules in the selection, Does the Average =32.1611 refer to the average for a single over the simulation time? Or, the Average = 32.1611 summing for all the 10 molecules over the simulation time? If the average = 32.1611 for a single molecule with 33 atoms / united atoms of most carbon groups, isn't the dipole moment too high? I think this is the average per molecule. You may need to run trjconv -pbc whole, because mdrun may break molecules in two parts, meaning that the molecule becomes as big as the box. What does will subtract their charge at their center of mass this mean? Why will subtract their charge at their center of mass ? -- next part -- An HTML attachment was scrubbed... URL: http://lists.gromacs.org/pipermail/gmx-users/attachments/20101019/4cf32833/attachment.html -- 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 send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] g_dipole ? = Calculate bond dipole moment for a molecule of multiple atoms by hand?
Hi According to the following website, http://en.wikipedia.org/wiki/Bond_dipole_moment [image: \mu = \delta \, d]. The bond dipole is modeled as +δ -- δ- with a distance *d* between the partial charges http://en.wikipedia.org/wiki/Partial_charges +δ and δ-. For a complete molecule the total molecular dipole moment may be approximated as the vector sum of individual bond dipole moments. However, for a molecule of multiple atoms, There may be more than one bond connected on one atom. E | B - A - C partial charge of atom_A = -0.5 partial charge of atom_B = 0.2 partial charge of atom_C = 0.35 partial charge of atom_E = 0.4 Which partial charges should I use when I calculate bond-dipole-moment of A-B ? Which partial charges should I use when I calculate bond-dipole-moment of A-C ? Which partial charges should I use when I calculate bond-dipole-moment of A-E ? Thank you Lin On 2010-10-18 03.30, Chih-Ying Lin wrote: HI I confined one molecule in the center of box and issue the g_dipole command. The average dipole moment is still around 32. It is the molecule with 33 atoms / united atoms of most carbon groups, isn't the dipole moment around 32 too high? How can I test next and know that the dipole moment around 32 is acceptable? By calculating on paper: dipole is 48.0 sum of q_i x_i, therefore if you have large charge separation you will get a large dipole. Thank you Lin On 2010-10-16 21.36, Chih-Ying Lin wrote: Hi I issue the g_dipole command on Gromacs = And, the following information is shown. There are 10 molecules in the selection, Does the Average =32.1611 refer to the average for a single over the simulation time? Or, the Average = 32.1611 summing for all the 10 molecules over the simulation time? If the average = 32.1611 for a single molecule with 33 atoms / united atoms of most carbon groups, isn't the dipole moment too high? I think this is the average per molecule. You may need to run trjconv -pbc whole, because mdrun may break molecules in two parts, meaning that the molecule becomes as big as the box. What does will subtract their charge at their center of mass this mean? Why will subtract their charge at their center of mass ? -- 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 send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] g_dipole ? = dipole moment ?
HI I confined one molecule in the center of box and issue the g_dipole command. The average dipole moment is still around 32. It is the molecule with 33 atoms / united atoms of most carbon groups, isn't the dipole moment around 32 too high? How can I test next and know that the dipole moment around 32 is acceptable? Thank you Lin On 2010-10-16 21.36, Chih-Ying Lin wrote: Hi I issue the g_dipole command on Gromacs = And, the following information is shown. There are 10 molecules in the selection, Does the Average =32.1611 refer to the average for a single over the simulation time? Or, the Average = 32.1611 summing for all the 10 molecules over the simulation time? If the average = 32.1611 for a single molecule with 33 atoms / united atoms of most carbon groups, isn't the dipole moment too high? I think this is the average per molecule. You may need to run trjconv -pbc whole, because mdrun may break molecules in two parts, meaning that the molecule becomes as big as the box. What does will subtract their charge at their center of mass this mean? Why will subtract their charge at their center of mass ? == There are 10 molecules in the selection There are 10 charged molecules in the selection, will subtract their charge at their center of mass Using Volume from topology: 220.317 nm^3 Back Off! I just backed up epsilon.xvg to ./#epsilon.xvg.1# Back Off! I just backed up aver.xvg to ./#aver.xvg.1# Last frame 1 time 2.000 Average volume over run is 221.043 Dipole moment (Debye) - Average = 32.1161 Std. Dev. = 2.9926 Error = 0.0095 -- 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 send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] g_dipole ? = dipole moment ?
Hi I issue the g_dipole command on Gromacs = And, the following information is shown. There are 10 molecules in the selection, Does the Average =32.1611 refer to the average for a single over the simulation time? Or, the Average = 32.1611 summing for all the 10 molecules over the simulation time? If the average = 32.1611 for a single molecule with 33 atoms / united atoms of most carbon groups, isn't the dipole moment too high? What does will subtract their charge at their center of mass this mean? Why will subtract their charge at their center of mass ? == There are 10 molecules in the selection There are 10 charged molecules in the selection, will subtract their charge at their center of mass Using Volume from topology: 220.317 nm^3 Back Off! I just backed up epsilon.xvg to ./#epsilon.xvg.1# Back Off! I just backed up aver.xvg to ./#aver.xvg.1# Last frame 1 time 2.000 Average volume over run is 221.043 Dipole moment (Debye) - Average = 32.1161 Std. Dev. = 2.9926 Error = 0.0095 -- 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 send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Force Field = Residues PHE, TRP, TYR, HIS ?
HI Residues PHE, TRP, TYR, and HIS are carrying Rings, or say pi bonds. How does the Gromacs deal with polarity for all this four residues? Is a single charge assigned for each atom on the center of atoms of the four residues ? Is pi bond given for the four residues in the force field? Thank you 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. 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] g_sas = protein interface = HALF of ( A+B-AB) ?
Hi Execute g_sas to get protein interface From David = If you have protein A and B in complex you do three g_sas: AB AB A A B B the interface is now A + B - AB WHy not HALF of (A+B-AB) ? Thank you 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. 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] dipole moment of molecule of trans and cis azobenzene ?
Hi The partial charges of the trans and cis azobenzene are given as point charges lied on each atom center in my MD simulation. It is supposed that the real molecule of trans-azobenzene has a lower dipole moment than the cis one. So, the real molecule of trans-azobenzene is supposed to be more hydrophobic than the cis one. However, in my MD simulation = The partial charges of the trans and cis azobenzene are given as point charges lied on each atom center. = Is my trans-azobenzene molecule structure more hydrophobic than the cis-one? = how can I calculate the dipole moment from the given partial charges for each atom? Thank you 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. 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] dipole moment of molecule of trans and cis azobenzene ?
HI The charges of azobenzene from the authors, who made the QM/MM simulations and fit some experimental data about the azobenzene. Thank you Lin On 2010-08-26 18.59, Chih-Ying Lin wrote: Hi The partial charges of the trans and cis azobenzene are given as point charges lied on each atom center in my MD simulation. and where do you get the charges from? It is supposed that the real molecule of trans-azobenzene has a lower dipole moment than the cis one. So, the real molecule of trans-azobenzene is supposed to be more hydrophobic than the cis one. However, in my MD simulation = The partial charges of the trans and cis azobenzene are given as point charges lied on each atom center. = Is my trans-azobenzene molecule structure more hydrophobic than the cis-one? = how can I calculate the dipole moment from the given partial charges for each atom? mu = sum_i q r Or g_dipoles. Thank you 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. 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] g_sas = protein interface = HALF of ( A+B-AB) ?
Hi Execute g_sas to get protein interface From David = If you have protein A and B in complex you do three g_sas: AB AB A A B B the interface is now A + B - AB WHy not HALF of (A+B-AB) ? Thank you 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. 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] dipole moment of molecule of trans and cis azobenzene ?
HI From David = dipole moment = mu = sum_i q r. is that sum of partial charges * r ? what is the r ? Thank you Lin On 2010-08-26 18.59, Chih-Ying Lin wrote: Hi The partial charges of the trans and cis azobenzene are given as point charges lied on each atom center in my MD simulation. and where do you get the charges from? It is supposed that the real molecule of trans-azobenzene has a lower dipole moment than the cis one. So, the real molecule of trans-azobenzene is supposed to be more hydrophobic than the cis one. However, in my MD simulation = The partial charges of the trans and cis azobenzene are given as point charges lied on each atom center. = Is my trans-azobenzene molecule structure more hydrophobic than the cis-one? = how can I calculate the dipole moment from the given partial charges for each atom? mu = sum_i q r Or g_dipoles. Thank you 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. 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] g_sas = calculate the SASA for each residues ?
Hi How can I calculate the SASA for each residue ? From Manual = The program will ask for a group for the surface calculation and a group for the output. When I issue the command = g_sas -f abc.gro -s abc.tpr -n Residue1.ndx -o SASA.xvg = Gromacs will pick Residue1.ndx as both a group for the surface calculation and a group for the output. When I issue the command = g_sas -f abc.gro -s abc.tpr -n Residue1.ndx -n protein.ndx -o SASA.xvg = Gromacs will show = Fatal error:Double command line argument -n I want protein.ndx as a group for the surface calculation and Residue1.ndx as a group for the output. How to do fix the problem ? Thank you Lin Group 0 ( System) has 20659 elements Group 1 ( Protein) has 1321 elements Group 2 ( Protein-H) has 1001 elements Group 3 ( C-alpha) has 129 elements Group 4 (Backbone) has 387 elements Group 5 ( MainChain) has 517 elements Group 6 (MainChain+Cb) has 634 elements Group 7 ( MainChain+H) has 646 elements Group 8 ( SideChain) has 675 elements Group 9 ( SideChain-H) has 484 elements Group10 ( Prot-Masses) has 1321 elements Group11 ( Non-Protein) has 19338 elements Group12 ( azo) has 330 elements Group13 ( SOL) has 19008 elements Group14 ( Other) has 19338 elements -- 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
[gmx-users] g_gyrate -p = the radii of gyration about the principal axes ?
HI What is the math definition of the radii of gyration about the principal axes in Gromacs? I use the command g_gyrate -p For lysozyme , I got = 0.922754 1.22249 1.25603 but in some paper, the authors got = 0.660 0.833 0.991 It is a quite difference. From David = The difference seems to be a constant factor. Gromacs computes sqrt (sum m (r-r_com)^2 / sum m) I'm pretty sure it says so in the manual. 1. so the different factor is sum m , not sum_N, right ? (N= number of atoms) 2. the choice of the principal axes of the protein molecule is a standard process ? = I mean the principal axes of the protein molecule is fixed, right ? = I mean the math of the principal axes of the protein molecule is defined all over the world , right ? Thank you Lin On 2010-08-14 23.49, Chih-Ying Lin wrote: Hi To Calculate the radii of gyration about the principal axes I use the command g_gyrate -p For lysozyme , I got = 0.922754 1.22249 1.25603 but in some paper, the authors got = 0.660 0.833 0.991 It is a quite difference. what is the definition of the radii of gyration about the principal axes ? i have checked the Gromacs manual but see nothing there. The difference seems to be a constant factor. Gromacs computes sqrt (sum m (r-r_com)^2 / sum m) I'm pretty sure it says so in the manual. Thank you 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. 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] g_gyrate -p = the radii of gyration about the principal axes ?
Hi To Calculate the radii of gyration about the principal axes I use the command g_gyrate -p For lysozyme , I got = 0.922754 1.22249 1.25603 but in some paper, the authors got = 0.660 0.833 0.991 It is a quite difference. what is the definition of the radii of gyration about the principal axes ? i have checked the Gromacs manual but see nothing there. Thank you 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. 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] g_gyrate -p = Calculate the radii of gyration about the principal axes
Hi To Calculate the radii of gyration about the principal axes I use the command g_gyrate -p For lysozyme , I got = 0.922754 1.22249 1.25603 but in some paper, the authors got = 0.660 0.833 0.991 It is a quite difference. what is the definition of the radii of gyration about the principal axes ? i have checked the Gromacs manual but see nothing there. Thank you 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. 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] trjconv = -[no]vel = print out the velocity ?
Hi Trjconv = with option - [no] vel what does the bracket no mean ? with the following command, trjconv -f MD.trr -s MD.tpr -vel -o MD-test.gro the velocity is not print out on MD-test.gro. How to print out both the velocity and trajectory at the same time from .trr file? THank you 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. 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] g_sas = micelle ?
HI how to calculate SASA of micelle using g_sas? i put -n -micelle-index.ndx , where micelle-index.ndx includes all of the atom numbers of micelle. if micelle is not compact enough but there are no water molecules inside the micelle, will g_sas calculate the vacancy part inside the micelle? Or, if there exists water molecules inside the micelle, will g_sas calculate the water/micelle interface part inside the micelle? Thank you 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. 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] g_sas = protein and ligand aggregate interface area ?
HI As David said, = How to compute protein-protein interface area? If you have protein A and B in complex you do three g_sas: AB AB A A B B the interface is now A + B - AB I want to calculate protein and ligand aggregate (small micelle of ligand) interface area. Is it the same step as calculation of protein A and B interface, which David mentioned above? But replacing protein B to Ligand aggregate (small micelle of ligand) ? g_sas -n ligand-micelle-index.ndx ? where ligand-micelle-index.ndx includes all the atom numbers of ligand micelle, which attached on the protein . Is my idea correct? Thank you 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. 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] g_sas -pbc ???
Hi g_sas By default, periodic boundary conditions are taken into account. How does g_sas deal with periodic boundary conditions effects? ? ? Take trjconv an example, I have tried trjconv -pbc ( nojump , whole, atom... ) or, trjconv -center . I could not get what i wanted. Thank you 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. 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] DSSP= how to edit .eps file
Hi With the following two commands, do_dssp -f 6LYZ-MD.xtc -s 6LYZ-MD.tpr -o secondary-structure.xpm -sc secondary-structure.xvg xpm2ps -f secondary-structure.xpm -o secondary-structure.eps With GIMP, i can see the secondary structure plot. The legend indicates the color of different second structure is shown under the secondary-structure plot. One legend is half-shown. The picture of legend is cut. How can I get that legend full-shown. Thank you 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. 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] g_sas
Hi g_sas computes hydrophobic, hydrophilic and total solvent accessible surface area. I chose = protein for calculation group = protein for output group what does it define hydrophobic solvent accessible surface area? = does that, the surface area, enclose the hydrophobic atoms/residues? what does it define hydrophilic solvent accessible surface area? = does that, the surface area, enclose the hydrophilic atoms/residues? what does it define total solvent accessible surface area? = does that, the surface area, enclose the total surface of the protein? I got hydrophobic SAS is greater than hydrophilic SAS. Isn't correct ? I am supposing that hydrophobic atoms/residues are within the protein. And, hydrophilic atoms/residues are on the surface of the protein. Then, how can hydrophobic SAS is greater than hydrophilic SAS ? Thank you 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. 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] g_sas
Hi From David, If you select a group consisting of a single residue in a protein the SAS will be computed as if the rest of the protein is not there. Very useful when you want to compute protein-protein interface areas. = therefore, if i select a group consisting of a single residue, which is in the core of a protein, it is impossible that water penetrates into the core of the protein so SAS is supposed to be zero. = However, after calculation with g_sas, the SAS_calculation of the single residue residing in the core of the protein is NOT ZERO. = My understanding is that g_sas returns the surface area of the single residue and it does not matter where the single residue locates. right? = The single residue can locate in the core of the protein or on the surface of the protein. The g_sas calculation for the single residue will not make a huge difference unless the single residue deforms/ twists . on the surface or in the core of the protein,right ? = How to compute protein-protein interface area? = In the protein + ligands + water system, I want to compute protein-ligand interface, protein-water interface, and ligand-water interface separately. = How? = in the protein + water system, g_sas computes the total SAS fluctuating between 88 and 144 (angstrom_squares) = does it make sense ? = I don't think that protein will swell 50 % plus in the pure water. = But why ?? = How to calculate the surface area of a micelle ? Thank you Lin Hi The command g_sas = Select a group for calculation of surface and a group for output What is the difference between a group for calculation of surface and a group for output? Please consult the documentation. From g_sas -h: The program will ask for a group for the surface calculation and a group for the output. The calculation group should always consists of all the non-solvent atoms in the system. The output group can be the whole or part of the calculation group. Actually this documentation is not correct. The calculation group are those atoms taken into account in the computation, whether or not they are solvent accessible. If you select a group consisting of a single residue in a protein the SAS will be computed as if the rest of the protein is not there. Very useful when you want to compute protein-protein interface areas. -Justin Thank you Lin -- David. -- 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
[gmx-users] DSSP= how to edit .eps file
HI How to pass an .m2p file to xpm2ps to change the dimensions of the plot, data point size, etc. ??? Thank you Lin Chih-Ying Lin wrote: Hi With the following two commands, do_dssp -f 6LYZ-MD.xtc -s 6LYZ-MD.tpr -o secondary-structure.xpm -sc secondary-structure.xvg xpm2ps -f secondary-structure.xpm -o secondary-structure.eps With GIMP, i can see the secondary structure plot. The legend indicates the color of different second structure is shown under the secondary-structure plot. One legend is half-shown. The picture of legend is cut. How can I get that legend full-shown. The dimensions of the plot area are likely too small to accommodate the full legend. As I said before, pass an .m2p file to xpm2ps to change the dimensions of the plot, data point size, etc. -Justin Thank you 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. 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] g_sas
Hi The command g_sas = Select a group for calculation of surface and a group for output What is the difference between a group for calculation of surface and a group for output? Thank you 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. 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] DSSP= how to edit .eps file
HI 1. dssp -n index.ndx = only atom numbers of one residue in the index.ndx = can dssp decide the exact second structure for the only one residue without considering other residues of protein? = can i get the same second structure for the residue with [ dssp -n one-residue.ndx ] and [dssp -n protein-main chain + H .ndx ] ? 2. The legend indicates the color of different second structure is shown under the secondary-structure plot. I don't want to change the colors assigned, but one legend is half-shown. The picture of legend is cut. How can I get that legend full-shown. 3. With the option -sss string HE HE = helix ? Thanks 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. 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] g_sas
HI THe command = g_sas_mpi -f 6LYZ-MD566500.xtc -s 6LYZ-MD566500.tpr -o solvent-accessible-surface.xvg -oa atomic-sas.xvg -or residue-sas.xvg In the solvent-accessible-surface.xvg = @ s0 legend Hydrophobic @ s1 legend Hydrophilic @ s2 legend Total @ s3 legend D Gsolv What does Hydrophobic mean here? What does Hydrophilic mean here? Does Total = Hydrophobic+Hydrophilic ? What does D Gsolv mean here? How can Gromacs define Hydrophobic atoms and Hydrophilic atoms ? What does the Area unit mean ? = Area (nm\S2\N) Thank you 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. 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] trjcat and trjconv
Hi file1.xtc and file2.xtc are two consecutive MD trajectory files of the same simulation system. file1.xtc = 238 frames (t= 0.0 to t= 476.0) file2.xtc = 366 frames (t= 0.0 to t= 732.0) trjcat -f file1.xtc file2.xtc -cat -o file3.xtc file3.xtc = 604 frames =238+366 I did not get file3.xtc (t= 0.0 to t= 1208.0=476+732) Instead, file3.xtc (t= 0.0 to t= 476.0 and then t= 0.0 to t= 732.0) trjconv -s file1.tpr -f file3.xtc -o file4.xtc -dt 100 file4.xtc = file3 (t=0) + file3 (t=100) + file3 (t=200) + file3 (t=300) +file3 (t=400) +file3 (t=0) +file3 (t=100) + file3 (t=200) + file3 (t=300) + file3 (t=400) +file3 (t=500) +file3(t=600) +file3(t=700) How can I get a combined file3 (t= 0.0 to t= 1208.0) ? THEN, file4.xtc = file3 (t=0) + file3 (t=100) + file3 (t=200) + file3 (t=300) +file3 (t=400) +file3 (t=500) +file3 (t=600) + file3 (t=700) + file3 (t=800) + file3 (t=900) +file3 (t=1000) +file3(t=1100) +file3(t=1200) Thank you 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. 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] Backbone and MainChain
Hi From Gromacs Manual: - Backbone: all protein backbone atoms (C-alpha, N, C) - MainChain: backbone atoms, plus the carbonyl oxygens The following is part of .gro file. I listed the atom number, are those all correct ? C-alpha: 161,170,179 N:158,163, 172 C: ??? what does this C represent ? carbonyl oxygens: 162,171,180 Thank you Lin 16GLY N 158 4.365 -0.145 3.067 -0.6971 -0.0210 0.0556 16GLY H 159 4.280 -0.127 3.017 0.4468 0.2941 -1.8808 16GLY CA 160 4.377 -0.037 3.166 -0.3605 0.4870 -0.5237 16GLY C 161 4.250 -0.037 3.252 0.0432 -0.0265 0.0901 16GLY O 162 4.180 -0.137 3.266 0.2570 -0.1341 0.3963 17LEU N 163 4.216 0.087 3.287 0.7572 0.0242 0.6305 17LEU H 164 4.276 0.160 3.254 0.7410 -0.8313 -1.4811 17LEU CA 165 4.102 0.123 3.372 -0.0401 -0.2644 -0.2910 17LEU CB 166 4.156 0.220 3.477 0.1016 -0.1889 -0.4337 17LEU CG 167 4.275 0.181 3.566 -0.0012 -0.5604 -0.4598 17LEUCD1 168 4.338 0.303 3.632 1.2085 -0.9864 -0.7919 17LEUCD2 169 4.233 0.084 3.676 0.8349 -0.3795 0.0241 17LEU C 170 3.980 0.184 3.303 -0.0634 0.2558 0.2056 17LEU O 171 3.993 0.297 3.258 -0.2180 0.0717 -0.3035 18ASP N 172 3.867 0.113 3.302 0.0759 0.0338 -0.0172 18ASP H 173 3.855 0.036 3.364 -0.9960 1.0931 1.1466 18ASP CA 174 3.744 0.153 3.233 -0.1100 -0.0437 0.2680 18ASP CB 175 3.638 0.047 3.201 -0.1316 0.1250 -0.2304 18ASP CG 176 3.612 -0.052 3.315 -0.1959 0.1668 -0.2089 18ASPOD1 177 3.588 -0.170 3.282 0.1094 0.1194 -0.2643 18ASPOD2 178 3.643 -0.033 3.435 -0.2608 -0.1375 -0.1441 18ASP C 179 3.665 0.270 3.294 0.1485 0.2274 0.0883 18ASP O 180 3.660 0.382 3.245 -0.2873 0.2105 0.0864 -- 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
[gmx-users] grompp - commands
Hi Here are four commands. PART I grompp_mpi -np 16 -v -f md.mdp -c 6LYZ-MD.gro -p 6LYZ.top -o 6LYZ-MD55.tpr mpiexec -np 16 mdrun_mpi -deffnm 6LYZ-MD55 PART II grompp_mpi -np 16 -v -f md.mdp -c 6LYZ-MD55.gro -p 6LYZ.top -o 6LYZ-MD155.tpr mpiexec -np 16 mdrun_mpi -deffnm 6LYZ-MD155 Will the last snapshot of trajectory of the simulation PART I be save as 6LYZ-MD55.gro? Will the commands in PART II intrigue the simulation starting from the last snapshot of trajectory of PART I , 6LYZ-MD55.gro ? Thank you 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. 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] PH 5.0 ?
HI How to assign charge for the residue of protein at PH 5.0 ? I have Ka values of each residue of protein then i can calculate the overall charge for each residue at PH 5.0 solution. However, how to calculate the partial charges of atoms within the residue of protein at PH 5.0? Thank you 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. 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] 6LYZ.pdb + Gromacs version 4.0.5 = Simulation Broke
Hi From Tsjerk, Previously you had an issue with the addition of ions to your .top file. In your protocol, it's not mentioned. Have you made sure that issue is cleared? = Yes, I did. I encountered two cases that my simulation broke. Case I = 6LYZ + ligands + water molecules + CL- = Gromacs 3.3.3 = error from the addition of ions to my .top file = The problem is solved and the simulation runs successfully. Case II = 6LYZ + water molecules + CL- = Gromacs 4.0.5 = Have tried the correct addition of ions to my .top file = The potential energy goes very negative after EM = the PR step broke. Thank you Lin Hi Lin, First of all, I would suggest sticking to a single processor until you have a protocol that works. Previously you had an issue with the addition of ions to your .top file. In your protocol, it's not mentioned. Have you made sure that issue is cleared? Cheers, Tsjerk On Sun, Jan 10, 2010 at 5:25 AM, Justin A. Lemkul jalem...@vt.edu wrote: On 1/9/10 10:42 PM, Chih-Ying Lin wrote: Hi I did the EM and the potential energy went to the very negative number. But the simulaiton broke in the PR step. Thank you Lin Saying the system broke is useless. There will certainly be some information in the .log file (LINCS warnings, etc). If that is the case, then you need to follow the standard advice that is always given in such cases: http://www.gromacs.org/Documentation/Errors#LINCS.2fSETTLE.2fSHAKE_warnings http://www.gromacs.org/Documentation/Terminology/Blowing_Up If you want more detailed advice, provide real output - information from how well the EM converged, messages in the .log file (unless it's just LINCS stuff, see the above links). Also realize that EM does not always remove all potentially problematic contacts. Your system may require a bit more finesse. -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/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] 6LYZ.pdb + Gromacs version 4.0.5 = Simulation Broken
Today's Topics: 1. 6LYZ.pdb + Gromacs version 4.0.5 = Simulation Broken (Chih-Ying Lin) 2. 6LYZ.pdb + Gromacs version 4.0.5 = Simulation Broken (output file) (Chih-Ying Lin) -- Message: 1 Date: Sun, 10 Jan 2010 10:11:17 +0800 From: Chih-Ying Lin chihying2...@gmail.com Subject: [gmx-users] 6LYZ.pdb + Gromacs version 4.0.5 = Simulation Broken To: gmx-users@gromacs.org Message-ID: 5777f3841001091811l41fbe079ida9822609fc8e...@mail.gmail.com Content-Type: text/plain; charset=iso-8859-1 Hi 6LYZ.pdb is simply a lysozyme structure and I merely solvated it running the simulation on Gromacs. System = 6LYZ.pdb + CL- + water molecules Before I put the 6LYZ.pdb on Gromacs 3.3.3, there is no problem at all. Recently, I tried the Gromacs 4.0.5, the simulation is broken at the step Position restrained MD. The commands are as follows. minim.mdp and pr.mdp are as follows. And outputs are as follows. Any thing wrong? Thank you Lin 1. Energy minimization of the structure (vacuum) pbc=no grompp_mpi -v -f minim.mdp -c 6LYZ.gro -p 6LYZ.top -o 6LYZ-EM-vacuum.tpr mpiexec -np 16 mdrun_mpi -pd -v -deffnm 6LYZ-EM-vacuum 2. Periodic boundary conditions editconf_mpi -f 6LYZ-EM-vacuum.gro -o 6LYZ-PBC.gro -bt cubic -box 6.0 6.0 6.0 3. Solvent addition genbox_mpi -cp 6LYZ-PBC.gro -cs spc216.gro -p 6LYZ.top -o 6LYZ-water.gro 4. Addition of ions: counter charge and concentration grompp_mpi -v -f minim.mdp -c 6LYZ-water.gro -p 6LYZ.top -o 6LYZ-water.tpr genion_mpi -s 6LYZ-water.tpr -o 6LYZ-solvated.gro -nn 8 -nname CL- 5 Energy minimization of the solvated system = Potential Energy went to the very negative number pbc =xyz (minim.mdp) grompp_mpi -v -f minim.mdp -c 6LYZ-solvated.gro -p 6LYZ.top -o 6LYZ-EM-solvated mpiexec -np 16 mdrun_mpi -pd -v -deffnm 6LYZ-EM-solvated 6 Relaxation of solvent and hydrogen atom positions: Position restrained MD = Simulation Broke grompp_mpi -v -f pr.mdp -c 6LYZ-EM-solvated.gro -p 6LYZ.top -o 6LYZ-PR.tpr mpiexec -np 16 mdrun_mpi -deffnm 6LYZ-PR = minim.mdp ; LINES STARTING WITH ';' ARE COMMENTS title = Minimization of Lysozyme (1LW9.pdb) ; Title of run ; The following lines tell the program the standard locations where to find certain files cpp = /lib/cpp ; Preprocessor ; Definea can be used to control processes define = -DFLEXIBLE ; Parameters describing what to do, when to stop and what to save integrator = steep ; Algorithm (steep = steepest descent minimization) emtol = 1.0 ; Stop minimization when the maximum force 1.0 kJ/mol nsteps = 5 ; Maximum number of (minimization) steps to perform nstenergy = 1 ; Write energies to disk every nstenergy steps energygrps = System; Which energy group(s) to write to disk ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions nstlist = 5 ; Frequency to update the neighbor list and long range forces ns_type = simple; Method to determine neighbor list (simple, grid) rlist = 1.0 ; Cut-off for making neighbor list (short range forces) coulombtype = cut-off ; Treatment of long range electrostatic interactions rcoulomb= 1.0 ; long range electrostatic cut-off rvdw= 1.0 ; long range Van der Waals cut-off constraints = none ; Bond types to replace by constraints pbc = xyz ; Periodic Boundary Conditions (yes/no) = pr.mdp ; VARIOUS PREPROCESSING OPTIONS title= cpp = /lib/cpp include = define = -DPOSRES ; RUN CONTROL PARAMETERS integrator = md tinit= 0 dt = 0.001 nsteps = 5000 nstcomm = 0 ; OUTPUT CONTROL OPTIONS nstxout = 0 nstvout = 0 nstfout = 0 nstlog = 10 nstenergy= 1 nstxtcout= 0 xtc_precision= 1000 xtc-grps = System energygrps = Protein Non-Protein ; NEIGHBORSEARCHING PARAMETERS nstlist = 5 ns-type = Grid pbc = xyz rlist= 0.9 ; OPTIONS FOR ELECTROSTATICS AND VDW coulombtype = Reaction-Field rcoulomb = 1.4 epsilon_rf = 78 epsilon_r= 1 vdw-type = Cut-off rvdw = 1.4 ; Temperature coupling Tcoupl = Berendsen tc-grps = Protein Non-Protein tau_t
[gmx-users] 6LYZ.pdb + Gromacs version 4.0.5 = Simulation Broken
Hi 6LYZ.pdb is simply a lysozyme structure and I merely solvated it running the simulation on Gromacs. System = 6LYZ.pdb + CL- + water molecules Before I put the 6LYZ.pdb on Gromacs 3.3.3, there is no problem at all. Recently, I tried the Gromacs 4.0.5, the simulation is broken at the step Position restrained MD. The commands are as follows. minim.mdp and pr.mdp are as follows. And outputs are as follows. Any thing wrong? Thank you Lin 1. Energy minimization of the structure (vacuum) pbc=no grompp_mpi -v -f minim.mdp -c 6LYZ.gro -p 6LYZ.top -o 6LYZ-EM-vacuum.tpr mpiexec -np 16 mdrun_mpi -pd -v -deffnm 6LYZ-EM-vacuum 2. Periodic boundary conditions editconf_mpi -f 6LYZ-EM-vacuum.gro -o 6LYZ-PBC.gro -bt cubic -box 6.0 6.0 6.0 3. Solvent addition genbox_mpi -cp 6LYZ-PBC.gro -cs spc216.gro -p 6LYZ.top -o 6LYZ-water.gro 4. Addition of ions: counter charge and concentration grompp_mpi -v -f minim.mdp -c 6LYZ-water.gro -p 6LYZ.top -o 6LYZ-water.tpr genion_mpi -s 6LYZ-water.tpr -o 6LYZ-solvated.gro -nn 8 -nname CL- 5 Energy minimization of the solvated system = Potential Energy went to the very negative number pbc =xyz (minim.mdp) grompp_mpi -v -f minim.mdp -c 6LYZ-solvated.gro -p 6LYZ.top -o 6LYZ-EM-solvated mpiexec -np 16 mdrun_mpi -pd -v -deffnm 6LYZ-EM-solvated 6 Relaxation of solvent and hydrogen atom positions: Position restrained MD = Simulation Broke grompp_mpi -v -f pr.mdp -c 6LYZ-EM-solvated.gro -p 6LYZ.top -o 6LYZ-PR.tpr mpiexec -np 16 mdrun_mpi -deffnm 6LYZ-PR = minim.mdp ; LINES STARTING WITH ';' ARE COMMENTS title = Minimization of Lysozyme (1LW9.pdb) ; Title of run ; The following lines tell the program the standard locations where to find certain files cpp = /lib/cpp ; Preprocessor ; Definea can be used to control processes define = -DFLEXIBLE ; Parameters describing what to do, when to stop and what to save integrator = steep ; Algorithm (steep = steepest descent minimization) emtol = 1.0 ; Stop minimization when the maximum force 1.0 kJ/mol nsteps = 5 ; Maximum number of (minimization) steps to perform nstenergy = 1 ; Write energies to disk every nstenergy steps energygrps = System; Which energy group(s) to write to disk ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions nstlist = 5 ; Frequency to update the neighbor list and long range forces ns_type = simple; Method to determine neighbor list (simple, grid) rlist = 1.0 ; Cut-off for making neighbor list (short range forces) coulombtype = cut-off ; Treatment of long range electrostatic interactions rcoulomb= 1.0 ; long range electrostatic cut-off rvdw= 1.0 ; long range Van der Waals cut-off constraints = none ; Bond types to replace by constraints pbc = xyz ; Periodic Boundary Conditions (yes/no) = pr.mdp ; VARIOUS PREPROCESSING OPTIONS title= cpp = /lib/cpp include = define = -DPOSRES ; RUN CONTROL PARAMETERS integrator = md tinit= 0 dt = 0.001 nsteps = 5000 nstcomm = 0 ; OUTPUT CONTROL OPTIONS nstxout = 0 nstvout = 0 nstfout = 0 nstlog = 10 nstenergy= 1 nstxtcout= 0 xtc_precision= 1000 xtc-grps = System energygrps = Protein Non-Protein ; NEIGHBORSEARCHING PARAMETERS nstlist = 5 ns-type = Grid pbc = xyz rlist= 0.9 ; OPTIONS FOR ELECTROSTATICS AND VDW coulombtype = Reaction-Field rcoulomb = 1.4 epsilon_rf = 78 epsilon_r= 1 vdw-type = Cut-off rvdw = 1.4 ; Temperature coupling Tcoupl = Berendsen tc-grps = Protein Non-Protein tau_t= 0.1 0.1 ref_t= 200 200 ; Pressure coupling Pcoupl = No ; GENERATE VELOCITIES FOR STARTUP RUN gen_vel = yes gen_temp = 200.0 gen_seed = 1735 ; OPTIONS FOR BONDS constraints = all-bonds constraint-algorithm = Lincs unconstrained-start = no lincs-order = 4 lincs-iter = 1 lincs-warnangle = 30 === -- gmx-users
[gmx-users] 6LYZ.pdb + Gromacs version 4.0.5 = Simulation Broken (output file)
Hi 6LYZ.pdb is simply a lysozyme structure and I merely solvated it running the simulation on Gromacs. System = 6LYZ.pdb + CL- + water molecules Before I put the 6LYZ.pdb on Gromacs 3.3.3, there is no problem at all. Recently, I tried the Gromacs 4.0.5, the simulation is broken at the step Position restrained MD. The commands are as follows. minim.mdp and pr.mdp are as follows. And outputs are as follows. Any thing wrong? Thank you Lin === - Hide quoted text - grompp_mpi -v -f minim.mdp -c 6LYZ-solvated.gro -p 6LYZ.top -o 6LYZ-EM-solvated :-) G R O M A C S (-: Good gRace! Old Maple Actually Chews Slate :-) VERSION 4.0.5 (-: Written by David van der Spoel, Erik Lindahl, Berk Hess, and others. Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2008, The GROMACS development team, check out http://www.gromacs.org for more information. This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. :-) grompp_mpi (-: Option Filename Type Description -f minim.mdp Input, Opt! grompp input file with MD parameters -po mdout.mdp Output grompp input file with MD parameters -c 6LYZ-solvated.gro InputStructure file: gro g96 pdb tpr tpb tpa -r conf.gro Input, Opt. Structure file: gro g96 pdb tpr tpb tpa -rb conf.gro Input, Opt. Structure file: gro g96 pdb tpr tpb tpa -n index.ndx Input, Opt. Index file -p 6LYZ.top InputTopology file -pp processed.top Output, Opt. Topology file -o 6LYZ-EM-solvated.tpr Output Run input file: tpr tpb tpa -t traj.trr Input, Opt. Full precision trajectory: trr trj cpt -e ener.edr Input, Opt. Energy file: edr ene Option Type Value Description -- -[no]h bool no Print help info and quit -niceint0 Set the nicelevel -[no]v bool yes Be loud and noisy -timereal -1 Take frame at or first after this time. -[no]rmvsbds bool yes Remove constant bonded interactions with virtual sites -maxwarn int0 Number of allowed warnings during input processing -[no]zerobool no Set parameters for bonded interactions without defaults to zero instead of generating an error -[no]renum bool yes Renumber atomtypes and minimize number of atomtypes Ignoring obsolete mdp entry 'title' Ignoring obsolete mdp entry 'cpp' Back Off! I just backed up mdout.mdp to ./#mdout.mdp.1# checking input for internal consistency... processing topology... Opening library file /usr/usc/gromacs/4.0.5/share/gromacs/top/ffG43a2.itp Opening library file /usr/usc/gromacs/4.0.5/share/gromacs/top/ffG43a2nb.itp Opening library file /usr/usc/gromacs/4.0.5/share/gromacs/top/ffG43a2bon.itp Opening library file /usr/usc/gromacs/4.0.5/share/gromacs/top/ff_dum.itp Generated 380 of the 1326 non-bonded parameter combinations Opening library file /usr/usc/gromacs/4.0.5/share/gromacs/top/ions.itp Excluding 3 bonded neighbours molecule type 'Protein_A' Excluding 2 bonded neighbours molecule type 'SOL' Excluding 1 bonded neighbours molecule type 'CL-' processing coordinates... double-checking input for internal consistency... renumbering atomtypes... converting bonded parameters... initialising group options... processing index file... Analysing residue names: Opening library file /usr/usc/gromacs/4.0.5/share/gromacs/top/aminoacids.dat There are: 6512 OTHER residues There are: 129PROTEIN residues There are: 0DNA residues Analysing Protein... Analysing Other... Making dummy/rest group for T-Coupling containing 20841 elements Making dummy/rest group for Acceleration containing 20841 elements Making dummy/rest group for Freeze containing 20841 elements Making dummy/rest group for VCM containing 20841 elements Number of degrees of freedom in T-Coupling group rest is 62520.00 Making dummy/rest group for User1 containing 20841 elements Making dummy/rest group for User2 containing 20841 elements Making dummy/rest group for XTC containing 20841 elements Making dummy/rest group for Or. Res. Fit containing 20841 elements Making dummy/rest group for QMMM containing 20841 elements T-Coupling has 1 element(s): rest Energy Mon. has 1 element(s): System Acceleration has 1 element(s): rest Freeze has 1
[gmx-users] 6LYZ.pdb + Gromacs version 4.0.5 = Simulation Broken
Hi I did the EM and the potential energy went to the very negative number. But the simulaiton broke in the PR step. Thank you 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. 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] simulation broke at 4.0.5 version
Hi I am using Gromacs version 4.0.5. I put one protein in a simulation box with water molecules and CL- only. My simulation broke at the step, Relaxation of solvent and hydrogen atom position. Here are the .top file, command, output of the grommp, pr.mdp. anything wrong here? Thank you Lin *[6YZ.top]* [ molecules ] ; Compound#mols Protein_A 1 SOL 6504 CL- 8 *Relaxation of solvent and hydrogen atom positions: Position restrained MD* *[command]* grompp_mpi -v -f pr.mdp -c 6LYZ-EM-solvated.gro -p 6LYZ.top -o 6LYZ-PR.tpr mpiexec -np 16 mdrun_mpi -deffnm 6LYZ-PR *[output of the grompp comand]* grompp_mpi -v -f pr.mdp -c 6LYZ-EM-solvated.gro -p 6LYZ.top -o 6LYZ-PR.tpr :-) G R O M A C S (-: Gyas ROwers Mature At Cryogenic Speed :-) VERSION 4.0.5 (-: Written by David van der Spoel, Erik Lindahl, Berk Hess, and others. Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2008, The GROMACS development team, check out http://www.gromacs.org for more information. This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. :-) grompp_mpi (-: Option Filename Type Description -f pr.mdp Input, Opt! grompp input file with MD parameters -po mdout.mdp Output grompp input file with MD parameters -c 6LYZ-EM-solvated.gro InputStructure file: gro g96 pdb tpr tpb tpa -r conf.gro Input, Opt. Structure file: gro g96 pdb tpr tpb tpa -rb conf.gro Input, Opt. Structure file: gro g96 pdb tpr tpb tpa -n index.ndx Input, Opt. Index file -p 6LYZ.top InputTopology file -pp processed.top Output, Opt. Topology file -o6LYZ-PR.tpr Output Run input file: tpr tpb tpa -t traj.trr Input, Opt. Full precision trajectory: trr trj cpt -e ener.edr Input, Opt. Energy file: edr ene Option Type Value Description -- -[no]h bool no Print help info and quit -niceint0 Set the nicelevel -[no]v bool yes Be loud and noisy -timereal -1 Take frame at or first after this time. -[no]rmvsbds bool yes Remove constant bonded interactions with virtual sites -maxwarn int0 Number of allowed warnings during input processing -[no]zerobool no Set parameters for bonded interactions without defaults to zero instead of generating an error -[no]renum bool yes Renumber atomtypes and minimize number of atomtypes Ignoring obsolete mdp entry 'cpp' Replacing old mdp entry 'unconstrained-start' by 'continuation' Back Off! I just backed up mdout.mdp to ./#mdout.mdp.1# checking input for internal consistency... NOTE 1 [file pr.mdp, line unknown]: The Berendsen thermostat does not generate the correct kinetic energy distribution. You might want to consider using the V-rescale thermostat. processing topology... Opening library file /usr/usc/gromacs/4.0.5/share/gromacs/top/ffG45a3.itp Opening library file /usr/usc/gromacs/4.0.5/share/gromacs/top/ffG45a3nb.itp Opening library file /usr/usc/gromacs/4.0.5/share/gromacs/top/ffG45a3bon.itp Opening library file /usr/usc/gromacs/4.0.5/share/gromacs/top/ff_dum.itp Generated 141 of the 1176 non-bonded parameter combinations Opening library file /usr/usc/gromacs/4.0.5/share/gromacs/top/ions.itp Excluding 3 bonded neighbours molecule type 'Protein_A' turning all bonds into constraints... Excluding 2 bonded neighbours molecule type 'SOL' turning all bonds into constraints... Excluding 1 bonded neighbours molecule type 'CL-' turning all bonds into constraints... processing coordinates... double-checking input for internal consistency... Velocities were taken from a Maxwell distribution at 200 K Reading position restraint coords from 6LYZ-EM-solvated.gro renumbering atomtypes... converting bonded parameters... initialising group options... processing index file... Analysing residue names: Opening library file /usr/usc/gromacs/4.0.5/share/gromacs/top/aminoacids.dat There are: 6512 OTHER residues There are: 129PROTEIN residues There are: 0DNA residues Analysing Protein... Analysing Other... Making dummy/rest group for Acceleration containing 20841 elements Making dummy/rest group for Freeze containing 20841 elements Making dummy/rest group for VCM containing 20841 elements Number of degrees of
[gmx-users] low concentration simulation ?
HI I am simulating the protein + ligand + water molecules system. In the experimental work, the concentration of ligand is pretty low, say under 20 mM (avearge 18 ligands attached on one protein) It will be a huge system to create a system with 20 mM and it will take lot of simulation time. Instead, I create a 6nm x 6nm x 6nm simulation box and put one protein molecule with 10 ligands. After 100 nano seconds, 10 ligands are attached on the protein. Then, for this one protein with 10 ligands attached + water molecules I will do the following steps = 1. remove the water molecules 2. center the protein with 10 ligands attached in the 6nm x 6nm x 6nm simulation box 3. put another 10 ligands around the protein with 10 ligand attached 4. solvate the system 5. add ions Are the above steps make sense to create a low concentration simulation? Thank you 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. 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] low concentration simulation ?
Hi From Justin, If you say that you have 20 mM of ligand, which corresponds to 18 ligands attached to one protein, why not just put 18 molecules in your unit cell with one protein? = I want to save the simulaiton time since i will run the simulation up to 1 micro-sencond. = 18 ligand + one protein ( 7nm x 7nm x 7nm) = 10 ligand + one protein ( 6nm x 6 nm x 6nm) = ( 7nm x 7nm x 7nm) is twice size of ( 6nm x 6nm x 6nm) = increase four times simulation time From Justin, can you guarantee that the ligands will interact the same way as if you add ten at a time? Will they aggregate? Will they inherently bind the protein in the same way, or will it be different? = I don't know, but I assume that will make little difference. Thank you Lin Chih-Ying Lin wrote: HI I am simulating the protein + ligand + water molecules system. In the experimental work, the concentration of ligand is pretty low, say under 20 mM (avearge 18 ligands attached on one protein) It will be a huge system to create a system with 20 mM and it will take lot of simulation time. Instead, I create a 6nm x 6nm x 6nm simulation box and put one protein molecule with 10 ligands. After 100 nano seconds, 10 ligands are attached on the protein. Then, for this one protein with 10 ligands attached + water molecules I will do the following steps = 1. remove the water molecules 2. center the protein with 10 ligands attached in the 6nm x 6nm x 6nm simulation box 3. put another 10 ligands around the protein with 10 ligand attached 4. solvate the system 5. add ions Are the above steps make sense to create a low concentration simulation? Your procedure sounds more like a titration with increasing concentration, rather than modeling a low concentration system. If you say that you have 20 mM of ligand, which corresponds to 18 ligands attached to one protein, why not just put 18 molecules in your unit cell with one protein? You may never be able to achieve the actual concentration, but you can certainly model the mole ratio. The other concern would be - if a system initially had 20 ligands (or 18, whatever), can you guarantee that the ligands will interact the same way as if you add ten at a time? Will they aggregate? Will they inherently bind the protein in the same way, or will it be different? -Justin Thank you 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. 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] Simulation Box break into 16 domains = .tpr file is wrong (Gromacs 3.3.3)
Hi, Thanks a lot, Tsjerk ! My simulation is running. I never knew that a discrepancy between the the .top file and .gro, grompp uses the topology information in stead of the coordinate file information. What does issue a set of warnings by grompp ? How do you know the discrepancy between the the .top file and .gro will make simulation wrong? Thank you Lin Hi, Tsjerk gave me suggestion to check the .tpr file created by the command grompp. I also suggested to try and find out why the water molecules got garbled. Between adding solvent and energy minimization, you also added chloride to counter the net positive charge. I assume you used genion for that, which is the most sensible way to do so. Genion typically adds the ions at the end of the topology. I further assume that you manually updated the topology by adding a line 'CL- 26' under [ system ]. But if you inserted that line _before_ the line specifying the number of solvent molecules, whereas in your .gro the chloride ions were at the end of it, then you had a discrepancy between the two. In such cases, grompp uses the topology information in stead of the coordinate file information, but does issue a set of warnings. If my assumptions are correct, then if you had sent the grompp output at first instance, we would have been immediately able to pinpoint your error. Besides, if you had looked at the output from grompp yourself, you would (should) have noticed that something was wrong there. Cheers, Tsjerk -- Tsjerk A. Wassenaar, Ph.D. Computational Chemist Medicinal Chemist Neuropharmacologist -- 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
[gmx-users] Simulation Box break into 16 domains = .tpr file is wrong (Gromacs 3.3.3)
Hi Tsjerk gave me suggestion to check the .tpr file created by the command grompp. *Energy minimization of the solvated system* pbc = xyz (minim.mdp) grompp_mpi -np 16 -v -f minim.mdp -c 6LYZ-solvated.gro -p 6LYZ.top -o 6LYZ-EM-solvated mpiexec -np 16 mdrun_mpi -v -deffnm 6LYZ-EM-solvated I early prepared for *6LYZ-solvated.gro* and then run the command grompp to create 6LYZ-EM-solvated.tpr. Next, run the command *editconf -f **6LYZ-EM-solvated.tpr -o 6LYZ-EM-solvated-after-grompp.gro* ** Use, VMD to visualize both *6LYZ-solvated.gro* and * 6LYZ-EM-solvated-after-grompp.gro* *6LYZ-solvated.gro = all molecules are intact * and protein is centered. *6LYZ-EM-solvated-after-grompp.gro = protein and water molecules are broken.* ** ** This is the main problem that my simulation box into 16 domains. Thank you Lin ** ** ** Chih-Ying Lin wrote: Hi From the Gromacs Manual, http://manual.gromacs.org/current/online/editconf.html editconf = The box can be modified with options -box, -d and -angles. Both -box and -d will center the system in the box. so, without -c option, the protein is already centered in the box. and, there is no description in the manual that people cannot use -d and -box simultaneously. The manual cannot possibly warn against everything that people may try to do. Consider the function of these two options. By using -d, editconf will determine a suitable box size based on the dimensions of the solute. By using -box, you are specifying the box vectors, which completely negates the purpose of using -d. Perhaps the language in the manual is not clear. Both -d and -box may center the solute, but *not* by simultaneously using -box and -d, because they can counteract each other. In the absence of a warning, something odd might be going on; we must eliminate this possibility in order to help you better. I would still suggest using a properly-formed command, with or without -c, to make sure that nothing is breaking down there. The workflow you posted before seems reasonable enough, so something early on is probably breaking down. Is there any reason you minimized your protein without PBC? What was the box size used in this EM step? Usually an in vacuo EM is simply accomplished by using a huge box and plain cutoffs. Solution EM would use a suitable box (with editconf -d *or* editconf -box) and better electrostatics methods. -Justin I visualized the .gro file created by the editconf, the protein is centered in the box as I can see. Thank you Lin Chih-Ying Lin wrote: Hi As I posted the command list earlier, to create the box editconf_mpi -f 6LYZ-EM-vacuum.gro -o 6LYZ-PBC.gro -bt cubic -d 0.75 -box 6.0 6.0 6.0 So, I think Justin's case is not the same as mine. Mark already pointed out that your command line is malformed. You cannot use -d and -box simultaneously. They are mutually exclusive. You are also not centering the protein in the box (you are not using the -c option). So, in fact, what you're doing was exactly what my problem was - not centering and potentially defining the box incorrectly. I would suggest that you at least try rebuilding your system, because the above command is certainly wrong. -Justin Thank you 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. 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] Simulation Box break into 16 domains = Gromacs 3.3.3
Hi As I posted the command list earlier, to create the box editconf_mpi -f 6LYZ-EM-vacuum.gro -o 6LYZ-PBC.gro -bt cubic -d 0.75 -box 6.0 6.0 6.0 So, I think Justin's case is not the same as mine. Thank you Lin Message: 1 Date: Fri, 01 Jan 2010 18:53:53 -0500 From: Justin A. Lemkul jalem...@vt.edu Subject: Re: [gmx-users] Simulation Box break into 16 domains = Gromacs 3.3.3 To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 4b3e8b11.7040...@vt.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed Mark Abraham wrote: Chih-Ying Lin wrote: Hi Sorry that i have posted the same message for several times. I used Gromacs version 3.3.3. My simulation system = one protein + 20 ligand + water molecules ( 7x 7x 7 ) MPI setting = #PBS -l nodes=4:ppn=4,arch=x86_64 = 16 nodes in total After doing the energy minimization, = the potential energy is extremely high ( say, ten to the 9th order ) I visualized the Simulation-System-EM-solvated.gro after the energy minimization. Then, I found that the Simulation Sysmtem is devided into 16 domains very clearly and the molecules (protein, ligand, and water) break into atoms in the boundaries. I have checked that the 20 ligands are not overlapped each other and are not overlapped with protein from the beginning. Chih-Ying sent me before and after .gro files off-list, and the structure really has done something like this (pic attached). After EM, the cubic simulation cell has partitioned four times along each side, and within each small cube, the waters have contracted as if to minimize surface area. The result is as if each small cube did an EM in isolation of any other such cube. Are you sure you are using a 3.3.3 mdrun? Consult the top part of the log file. I'd guess the most likely problem is that you're seeing some bizarre artefact of your MPI or installation. How was GROMACS configured? Did you use shared libraries? Try a version without. Try single-processor grompp+mdrun. If there's no light shed by the above, please send me your input protein and ligand structure files, and your pre-EM .tpr and I'll see if I can reproduce your workflow or result. Mark I have a strong suspicion that this all derives from the incorrect editconf command posted earlier. I saw something like this once, long ago, before I knew what I was doing :) The problem I had stemmed from incorrectly assigning the center of the system. I would suggest re-building the system, starting from the editconf step, and centering the protein with -c in a box defined *either* by -d or -box, to see if that fixes things. -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/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] Simulation Box break into 16 domains = Gromacs 3.3.3
Hi From the Gromacs Manual, http://manual.gromacs.org/current/online/editconf.html editconf = The box can be modified with options -box, -d and -angles. Both -box and -dwill center the system in the box. so, without -c option, the protein is already centered in the box. and, there is no description in the manual that people cannot use -d and -box simultaneously. I visualized the .gro file created by the editconf, the protein is centered in the box as I can see. Thank you Lin Chih-Ying Lin wrote: Hi As I posted the command list earlier, to create the box editconf_mpi -f 6LYZ-EM-vacuum.gro -o 6LYZ-PBC.gro -bt cubic -d 0.75 -box 6.0 6.0 6.0 So, I think Justin's case is not the same as mine. Mark already pointed out that your command line is malformed. You cannot use -d and -box simultaneously. They are mutually exclusive. You are also not centering the protein in the box (you are not using the -c option). So, in fact, what you're doing was exactly what my problem was - not centering and potentially defining the box incorrectly. I would suggest that you at least try rebuilding your system, because the above command is certainly wrong. -Justin Thank you 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. 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] Simulation Break = Due to bad domain decomposition ? (MPI) = Gromacs Version 3.3.3
Hi I used Gromacs version 3.3.3. My simulation system = one protein + 20 ligand + water molecules ( 7x 7x 7 ) MPI setting = #PBS -l nodes=4:ppn=4,arch=x86_64 = 16 nodes in total After doing the energy minimization, = the potential energy is extremely high ( say, ten to the 9th order ) I visualized the Simulation-System-EM-solvated.gro after the energy minimization. Then, I found that the Simulation Sysmtem is devided into 16 domains very clearly and the molecules (protein, ligand, and water) break into atoms in the boundaries. I have checked that the 20 ligands are not overlapped each other and are not overlapped with protein from the beginning. More, i have created 10 alike system and each is with one protein + 20 ligand + water molecules Two of them get the minus potential energy after energy minimization and I can continue running the MD simulation successfully. Others of them get the extreme high positive potential energy and the system is devided into 16 domains after energy minimization and the simulation broke afterall. With one protein + 10 ligand + water molecules, ( 6 x 6 x 6 ) There is no problems like that. Please give me your ideas to solve the problem. Thank you 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. 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] Simulation Box break into 16 domains = Gromacs 3.3.3
Hi
I used Gromacs version 3.3.3.
My simulation system = one protein + 20 ligand + water molecules ( 7x 7x 7
)
MPI setting = #PBS -l nodes=4:ppn=4,arch=x86_64 = 16 nodes in total
After doing the energy minimization, = the potential energy is extremely
high ( say, ten to the 9th order )
I visualized the Simulation-System-EM-solvated.gro after the energy
minimization.
Then, I found that the Simulation Sysmtem is devided into 16 domains very
clearly and the molecules (protein, ligand, and water) break into atoms in
the boundaries.
I have checked that the 20 ligands are not overlapped each other and are
not
overlapped with protein from the beginning.
More, i have created 10 alike system and each is with one protein + 20
ligand + water molecules
Two of them get the minus potential energy after energy minimization and
I
can continue running the MD simulation successfully.
Others of them get the extreme high positive potential energy and the
system is devided into 16 domains after energy minimization and the
simulation broke afterall.
With one protein + 10 ligand + water molecules, ( 6 x 6 x 6 )
There is no problems like that.
Please give me your ideas to solve the problem.
The commands are listed below and the .tpr file created by grompp is
attached.
Thank you
Lin
**
1. pdb2gmx_mpi -f 6LYZ.pdb -o 6LYZ.gro -p 6LYZ.top = G 45a3
2. Energy minimization of the structure (vacuum)
pbc = no,
grompp_mpi -np 16 -v -f minim.mdp -c 6LYZ.gro -p 6LYZ.top -o
6LYZ-EM-vacuum.tpr
mpiexec -np 16 mdrun_mpi -v -deffnm 6LYZ-EM-vacuum
3. Periodic boundary conditions
editconf_mpi -f 6LYZ-EM-vacuum.gro -o 6LYZ-PBC.gro -bt cubic -d 0.75 -box
7.0 7.0 7.0
*4. Add another 20 ligands randomly into the* *simulation (nm^3) box*
genbox_mpi -seed 201 -cp 6LYZ-PBC.gro -ci ligand.gro -nmol 20 -p 6LYZ.top -o
6LYZ20ligand.gro
*6. Solvent addition*
genbox_mpi -cp 6LYZ20ligand.gro -cs spc216.gro -p 6LYZ.top -o
6LYZ-water.gro
*7. Addition of ions: counter charge and concentration*
grompp_mpi -v -f minim.mdp -c 6LYZ-water.gro -p 6LYZ.top -o 6LYZ-water.tpr
genion_mpi -s 6LYZ-water.tpr -o 6LYZ-solvated.gro -nn 28 -nname CL-
*8. Energy minimization of the solvated system*
pbc = xyz (minim.mdp)
grompp_mpi -np 16 -v -f minim.mdp -c 6LYZ-solvated.gro -p 6LYZ.top -o
6LYZ-EM-solvated
mpiexec -np 16 mdrun_mpi -v -deffnm 6LYZ-EM-solvated
Reading file 6LYZ-EM-solvated.tpr, VERSION 3.3.3 (single precision)
Reading file 6LYZ-EM-solvated.tpr, VERSION 3.3.3 (single precision)
6LYZ-EM-solvated.tpr:
header:
bIr= present
bBox = present
bTop = present
bX = present
bV = present
bF = not present
natoms = 33042
step = 0
t = 0.00e+00
lambda = 0.00e+00
ir:
integrator = steep
nsteps = 5
init_step= 0
ns_type = Simple
nstlist = 5
ndelta = 2
bDomDecomp = FALSE
decomp_dir = 0
nstcomm = 1
comm_mode= Linear
nstcheckpoint= 1000
nstlog = 100
nstxout = 100
nstvout = 100
nstfout = 0
nstenergy= 1
nstxtcout= 0
init_t = 0
delta_t = 0.001
xtcprec = 1000
nkx = 0
nky = 0
nkz = 0
pme_order= 4
ewald_rtol = 1e-05
ewald_geometry = 0
epsilon_surface = 0
optimize_fft = FALSE
ePBC = xyz
bUncStart= FALSE
bShakeSOR= FALSE
etc = No
epc = No
epctype = Isotropic
tau_p= 1
ref_p (3x3):
ref_p[0]={ 0.0e+00, 0.0e+00, 0.0e+00}
ref_p[1]={ 0.0e+00, 0.0e+00, 0.0e+00}
ref_p[2]={ 0.0e+00, 0.0e+00, 0.0e+00}
compress (3x3):
compress[0]={ 0.0e+00, 0.0e+00, 0.0e+00}
compress[1]={ 0.0e+00, 0.0e+00, 0.0e+00}
compress[2]={ 0.0e+00, 0.0e+00, 0.0e+00}
andersen_seed= 815131
rlist= 1
coulombtype = Cut-off
rcoulomb_switch = 0
rcoulomb = 1
vdwtype = Cut-off
rvdw_switch = 0
rvdw = 1
epsilon_r= 1
epsilon_rf = 1
tabext = 1
gb_algorithm = Still
nstgbradii = 1
rgbradii = 2
gb_saltconc
[gmx-users] Simulation Box break into 16 domains = Gromacs 3.3.3
Hi
I used Gromacs version 3.3.3.
My simulation system = one protein + 20 ligand + water molecules ( 7x 7x 7
)
MPI setting = #PBS -l nodes=4:ppn=4,arch=x86_64 = 16 nodes in total
After doing the energy minimization, = the potential energy is extremely
high ( say, ten to the 9th order )
I visualized the Simulation-System-EM-solvated.gro after the energy
minimization.
Then, I found that the Simulation Sysmtem is devided into 16 domains very
clearly and the molecules (protein, ligand, and water) break into atoms in
the boundaries.
I have checked that the 20 ligands are not overlapped each other and are not
overlapped with protein from the beginning.
More, i have created 10 alike system and each is with one protein + 20
ligand + water molecules
Two of them get the minus potential energy after energy minimization and I
can continue running the MD simulation successfully.
Others of them get the extreme high positive potential energy and the
system is devided into 16 domains after energy minimization and the
simulation broke afterall.
With one protein + 10 ligand + water molecules, ( 6 x 6 x 6 )
There is no problems like that.
Please give me your ideas to solve the problem.
The commands are listed below and the .tpr file created by grompp is
attached.
Thank you
Lin
1. pdb2gmx_mpi -f 6LYZ.pdb -o 6LYZ.gro -p 6LYZ.top = G 45a3
2. Energy minimization of the structure (vacuum)
pbc = no,
grompp_mpi -np 16 -v -f minim.mdp -c 6LYZ.gro -p 6LYZ.top -o
6LYZ-EM-vacuum.tpr
mpiexec -np 16 mdrun_mpi -v -deffnm 6LYZ-EM-vacuum
3. Periodic boundary conditions
editconf_mpi -f 6LYZ-EM-vacuum.gro -o 6LYZ-PBC.gro -bt cubic -d 0.75 -box
7.0 7.0 7.0
4. Add another 20 ligands randomly into the simulation (nm^3) box
genbox_mpi -seed 201 -cp 6LYZ-PBC.gro -ci ligand.gro -nmol 20 -p 6LYZ.top -o
6LYZ20ligand.gro
6. Solvent addition
genbox_mpi -cp 6LYZ20ligand.gro -cs spc216.gro -p 6LYZ.top -o 6LYZ-water.gro
7. Addition of ions: counter charge and concentration
grompp_mpi -v -f minim.mdp -c 6LYZ-water.gro -p 6LYZ.top -o 6LYZ-water.tpr
genion_mpi -s 6LYZ-water.tpr -o 6LYZ-solvated.gro -nn 28 -nname CL-
8. Energy minimization of the solvated system
pbc = xyz (minim.mdp)
grompp_mpi -np 16 -v -f minim.mdp -c 6LYZ-solvated.gro -p 6LYZ.top -o
6LYZ-EM-solvated
mpiexec -np 16 mdrun_mpi -v -deffnm 6LYZ-EM-solvated
Reading file 6LYZ-EM-solvated.tpr, VERSION 3.3.3 (single precision)
Reading file 6LYZ-EM-solvated.tpr, VERSION 3.3.3 (single precision)
6LYZ-EM-solvated.tpr:
header:
bIr= present
bBox = present
bTop = present
bX = present
bV = present
bF = not present
natoms = 33042
step = 0
t = 0.00e+00
lambda = 0.00e+00
ir:
integrator = steep
nsteps = 5
init_step= 0
ns_type = Simple
nstlist = 5
ndelta = 2
bDomDecomp = FALSE
decomp_dir = 0
nstcomm = 1
comm_mode= Linear
nstcheckpoint= 1000
nstlog = 100
nstxout = 100
nstvout = 100
nstfout = 0
nstenergy= 1
nstxtcout= 0
init_t = 0
delta_t = 0.001
xtcprec = 1000
nkx = 0
nky = 0
nkz = 0
pme_order= 4
ewald_rtol = 1e-05
ewald_geometry = 0
epsilon_surface = 0
optimize_fft = FALSE
ePBC = xyz
bUncStart= FALSE
bShakeSOR= FALSE
etc = No
epc = No
epctype = Isotropic
tau_p= 1
ref_p (3x3):
ref_p[0]={ 0.0e+00, 0.0e+00, 0.0e+00}
ref_p[1]={ 0.0e+00, 0.0e+00, 0.0e+00}
ref_p[2]={ 0.0e+00, 0.0e+00, 0.0e+00}
compress (3x3):
compress[0]={ 0.0e+00, 0.0e+00, 0.0e+00}
compress[1]={ 0.0e+00, 0.0e+00, 0.0e+00}
compress[2]={ 0.0e+00, 0.0e+00, 0.0e+00}
andersen_seed= 815131
rlist= 1
coulombtype = Cut-off
rcoulomb_switch = 0
rcoulomb = 1
vdwtype = Cut-off
rvdw_switch = 0
rvdw = 1
epsilon_r= 1
epsilon_rf = 1
tabext = 1
gb_algorithm = Still
nstgbradii = 1
rgbradii = 2
gb_saltconc = 0
implicit_solvent = No
DispCorr = No
fudgeQQ = 1
free_energy = no
init_lambda = 0
sc_alpha
[gmx-users] Simulation Box break into 16 domains = Gromacs 3.3.3
Hi
Sorry that i have posted the same message for several times.
I used Gromacs version 3.3.3.
My simulation system = one protein + 20 ligand + water molecules ( 7x 7x 7
)
MPI setting = #PBS -l nodes=4:ppn=4,arch=x86_64 = 16 nodes in total
After doing the energy minimization, = the potential energy is extremely
high ( say, ten to the 9th order )
I visualized the Simulation-System-EM-solvated.gro after the energy
minimization.
Then, I found that the Simulation Sysmtem is devided into 16 domains very
clearly and the molecules (protein, ligand, and water) break into atoms in
the boundaries.
I have checked that the 20 ligands are not overlapped each other and are not
overlapped with protein from the beginning.
More, i have created 10 alike system and each is with one protein + 20
ligand + water molecules
Two of them get the minus potential energy after energy minimization and I
can continue running the MD simulation successfully.
Others of them get the extreme high positive potential energy and the
system is devided into 16 domains after energy minimization and the
simulation broke afterall.
With one protein + 10 ligand + water molecules, ( 6 x 6 x 6 )
There is no problems like that.
Please give me your ideas to solve the problem.
The commands are listed below and the .tpr file created by grompp is
attached.
Thank you
Lin
1. pdb2gmx_mpi -f 6LYZ.pdb -o 6LYZ.gro -p 6LYZ.top = G 45a3
2. Energy minimization of the structure (vacuum)
pbc = no,
grompp_mpi -np 16 -v -f minim.mdp -c 6LYZ.gro -p 6LYZ.top -o
6LYZ-EM-vacuum.tpr
mpiexec -np 16 mdrun_mpi -v -deffnm 6LYZ-EM-vacuum
3. Periodic boundary conditions
editconf_mpi -f 6LYZ-EM-vacuum.gro -o 6LYZ-PBC.gro -bt cubic -d 0.75 -box
7.0 7.0 7.0
4. Add another 20 ligands randomly into the simulation (nm^3) box
genbox_mpi -seed 201 -cp 6LYZ-PBC.gro -ci ligand.gro -nmol 20 -p 6LYZ.top -o
6LYZ20ligand.gro
6. Solvent addition
genbox_mpi -cp 6LYZ20ligand.gro -cs spc216.gro -p 6LYZ.top -o 6LYZ-water.gro
7. Addition of ions: counter charge and concentration
grompp_mpi -v -f minim.mdp -c 6LYZ-water.gro -p 6LYZ.top -o 6LYZ-water.tpr
genion_mpi -s 6LYZ-water.tpr -o 6LYZ-solvated.gro -nn 28 -nname CL-
8. Energy minimization of the solvated system
pbc = xyz (minim.mdp)
grompp_mpi -np 16 -v -f minim.mdp -c 6LYZ-solvated.gro -p 6LYZ.top -o
6LYZ-EM-solvated
mpiexec -np 16 mdrun_mpi -v -deffnm 6LYZ-EM-solvated
Reading file 6LYZ-EM-solvated.tpr, VERSION 3.3.3 (single precision)
Reading file 6LYZ-EM-solvated.tpr, VERSION 3.3.3 (single precision)
6LYZ-EM-solvated.tpr:
header:
bIr= present
bBox = present
bTop = present
bX = present
bV = present
bF = not present
natoms = 33042
step = 0
t = 0.00e+00
lambda = 0.00e+00
ir:
integrator = steep
nsteps = 5
init_step= 0
ns_type = Simple
nstlist = 5
ndelta = 2
bDomDecomp = FALSE
decomp_dir = 0
nstcomm = 1
comm_mode= Linear
nstcheckpoint= 1000
nstlog = 100
nstxout = 100
nstvout = 100
nstfout = 0
nstenergy= 1
nstxtcout= 0
init_t = 0
delta_t = 0.001
xtcprec = 1000
nkx = 0
nky = 0
nkz = 0
pme_order= 4
ewald_rtol = 1e-05
ewald_geometry = 0
epsilon_surface = 0
optimize_fft = FALSE
ePBC = xyz
bUncStart= FALSE
bShakeSOR= FALSE
etc = No
epc = No
epctype = Isotropic
tau_p= 1
ref_p (3x3):
ref_p[0]={ 0.0e+00, 0.0e+00, 0.0e+00}
ref_p[1]={ 0.0e+00, 0.0e+00, 0.0e+00}
ref_p[2]={ 0.0e+00, 0.0e+00, 0.0e+00}
compress (3x3):
compress[0]={ 0.0e+00, 0.0e+00, 0.0e+00}
compress[1]={ 0.0e+00, 0.0e+00, 0.0e+00}
compress[2]={ 0.0e+00, 0.0e+00, 0.0e+00}
andersen_seed= 815131
rlist= 1
coulombtype = Cut-off
rcoulomb_switch = 0
rcoulomb = 1
vdwtype = Cut-off
rvdw_switch = 0
rvdw = 1
epsilon_r= 1
epsilon_rf = 1
tabext = 1
gb_algorithm = Still
nstgbradii = 1
rgbradii = 2
gb_saltconc = 0
implicit_solvent = No
DispCorr = No
fudgeQQ = 1
free_energy
[gmx-users] Gromacs 3.3.3 = what MPI based on ?
Hi There is no domain decomposition with Gromacs 3.3.3. What MPI based on with Gromacs 3.3.3? Thank you 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. 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] some molecule clashing with another ?
Hi My simulation broke down and the simulation procedues are as follows. 1. center a protein molecule in the simulation box 2. put 20 ligands around the protein with genbox command 3. make sure that any atom of the ligands does not overlap on any atom of the protein with Visulization-software. 4. solvent addition , with the command genbox *-vdwd* 0.2 5. Addition of ions, with the command genion 6. Energy minimization of the solvated system 7. Position restrained MD = simulation broke down. = It is very probable that some molecule clashing with another. = since i have made sured that any atom of the ligands does not overlap on any atom of the protein with Visulization-software, the clashed pair of the molecules are possible solvent vs solvent or solvent vs protein or solvent vs ligand = however, from the Gromacs manual , command genbox Solvent molecules are removed from the box where the distance between any atom of the solute molecule(s) and any atom of the solvent molecule is less than the sum of the VanderWaals radii of both atoms. A database ( vdwradii.dat http://manual.gromacs.org/current/online/dat.html) of VanderWaals radii is read by the program, atoms not in the database are assigned a default distance -vdw. = here isvdwradii.dat (the ligand is simply made of C, N, O, H) ; Very approximate VanderWaals radii ; only used for drawing atoms as balls or for calculating atomic overlap. ; longest matches are used ; '???' or '*' matches any residue name ; 'AAA' matches any protein residue name ??? C 0.15 ??? F 0.12 ??? H 0.04 ??? N 0.110 ??? O 0.105 ??? S 0.16 My questions are 1. anything wrong of my simulation procedures ? 2. how to find the clashed molecules ? Thank you 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. 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] some molecule clashing with another ?
step-1.pdb to ./#step-1.pdb.3# Back Off! I just backed up step-1.pdb to ./#step-1.pdb.3# Back Off! I just backed up step-1.pdb to ./#step-1.pdb.4# Back Off! I just backed up step-1.pdb to ./#step-1.pdb.3# Back Off! I just backed up step0.pdb to ./#step0.pdb.1# Back Off! I just backed up step0.pdb to ./#step0.pdb.2# Wrote pdb files with previous and current coordinates Back Off! I just backed up step0.pdb to ./#step0.pdb.3# Wrote pdb files with previous and current coordinates Back Off! I just backed up step0.pdb to ./#step0.pdb.1# Sorry couldn't backup step0.pdb to ./#step0.pdb.1# Wrote pdb files with previous and current coordinates Wrote pdb files with previous and current coordinates Back Off! I just backed up step0.pdb to ./#step0.pdb.1# Back Off! I just backed up step0.pdb to ./#step0.pdb.4# Wrote pdb files with previous and current coordinates Back Off! I just backed up step0.pdb to ./#step0.pdb.5# Wrote pdb files with previous and current coordinates Wrote pdb files with previous and current coordinates Wrote pdb files with previous and current coordinates Back Off! I just backed up step0.pdb to ./#step0.pdb.6# Wrote pdb files with previous and current coordinates Terminated Chih-Ying Lin wrote: Hi My simulation broke down and the simulation procedues are as follows. 1. center a protein molecule in the simulation box 2. put 20 ligands around the protein with genbox command 3. make sure that any atom of the ligands does not overlap on any atom of the protein with Visulization-software. 4. solvent addition , with the command genbox *-vdwd* 0.2 5. Addition of ions, with the command genion 6. Energy minimization of the solvated system 7. Position restrained MD = simulation broke down. = It is very probable that some molecule clashing with another. You can change probable to an actual answer if you analyze whatever LINCS warnings are occurring (the atoms are listed) and by watching the resulting trajectory. = since i have made sured that any atom of the ligands does not overlap on any atom of the protein with Visulization-software, the clashed pair of the molecules are possible solvent vs solvent or solvent vs protein or solvent vs ligand Then you should follow up #4 above with another visual inspection, as you did with protein-ligand interactions, in addition to any information printed to the log file (as above). = however, from the Gromacs manual , command genbox Solvent molecules are removed from the box where the distance between any atom of the solute molecule(s) and any atom of the solvent molecule is less than the sum of the VanderWaals radii of both atoms. A database (vdwradii.dat http://manual.gromacs.org/current/online/dat.html) of VanderWaals radii is read by the program, atoms not in the database are assigned a default distance -vdw. So solvent-solvent overlap shouldn't be a problem. = here isvdwradii.dat (the ligand is simply made of C, N, O, H) Yes, this is standard. ; Very approximate VanderWaals radii ; only used for drawing atoms as balls or for calculating atomic overlap. ; longest matches are used ; '???' or '*' matches any residue name ; 'AAA' matches any protein residue name ??? C 0.15 ??? F 0.12 ??? H 0.04 ??? N 0.110 ??? O 0.105 ??? S 0.16 My questions are 1. anything wrong of my simulation procedures ? In theory, not really. What values of potential energy and maximum force did the energy minimization converge to? 2. how to find the clashed molecules ? Read the information printed to the log file (again, I'm assuming you're seeing LINCS warnings, but you haven't told us what broke means!) and watch the trajectory to see where things start to fall apart. As I suggested to someone earlier, if the crash is happening reasonably early, setting nstxout = 1 is a useful diagnostic to capture all frames prior to the crash. -Justin Thank you 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. 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 modify or avoid some molecule clashing with another ?
Hi After reading the log file and watching the trajectory movies(nstxout = 1), some molecule clashes with another in my simulation system. How can i avoid the situation happening again? How to modify the broken simulation? Thank you Lin Message: 4 Date: Wed, 30 Dec 2009 19:00:51 -0500 From: Justin A. Lemkul jalem...@vt.edu Subject: Re: [gmx-users] some molecule clashing with another ? To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 4b3be9b3.8020...@vt.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed Chih-Ying Lin wrote: Hi My simulation broke down and the simulation procedues are as follows. 1. center a protein molecule in the simulation box 2. put 20 ligands around the protein with genbox command 3. make sure that any atom of the ligands does not overlap on any atom of the protein with Visulization-software. 4. solvent addition , with the command genbox *-vdwd* 0.2 5. Addition of ions, with the command genion 6. Energy minimization of the solvated system 7. Position restrained MD = simulation broke down. = It is very probable that some molecule clashing with another. You can change probable to an actual answer if you analyze whatever LINCS warnings are occurring (the atoms are listed) and by watching the resulting trajectory. = since i have made sured that any atom of the ligands does not overlap on any atom of the protein with Visulization-software, the clashed pair of the molecules are possible solvent vs solvent or solvent vs protein or solvent vs ligand Then you should follow up #4 above with another visual inspection, as you did with protein-ligand interactions, in addition to any information printed to the log file (as above). = however, from the Gromacs manual , command genbox Solvent molecules are removed from the box where the distance between any atom of the solute molecule(s) and any atom of the solvent molecule is less than the sum of the VanderWaals radii of both atoms. A database (vdwradii.dat http://manual.gromacs.org/current/online/dat.html) of VanderWaals radii is read by the program, atoms not in the database are assigned a default distance -vdw. So solvent-solvent overlap shouldn't be a problem. = here isvdwradii.dat (the ligand is simply made of C, N, O, H) Yes, this is standard. ; Very approximate VanderWaals radii ; only used for drawing atoms as balls or for calculating atomic overlap. ; longest matches are used ; '???' or '*' matches any residue name ; 'AAA' matches any protein residue name ??? C 0.15 ??? F 0.12 ??? H 0.04 ??? N 0.110 ??? O 0.105 ??? S 0.16 My questions are 1. anything wrong of my simulation procedures ? In theory, not really. What values of potential energy and maximum force did the energy minimization converge to? 2. how to find the clashed molecules ? Read the information printed to the log file (again, I'm assuming you're seeing LINCS warnings, but you haven't told us what broke means!) and watch the trajectory to see where things start to fall apart. As I suggested to someone earlier, if the crash is happening reasonably early, setting nstxout = 1 is a useful diagnostic to capture all frames prior to the crash. -Justin Thank you Lin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/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/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] some molecule clashing with another ?
Hi I print out the energy EM-solvated.edr file here. Since the average is high, is it caused by the molecule clashing? I selected potential, kinetic, total energy. What else energy should I print out to learn the broken simulation system? Thank you Lin Select the terms you want from the following list by selecting either the name or the number or a combination. End your selection with an empty line or a zero. - 1 Bond 2 G96Bond3 Angle 4 G96Angle 5 Proper-Dih.6 Improper-Dih. 7 LJ-14 8 Coulomb-14 9 LJ-(SR)10 Coulomb-(SR) 11 Potential 12 Kinetic-En. 13 Total-Energy 14 Temperature15 Pressure-(bar) 16 Vir-XX 17 Vir-XY 18 Vir-XZ 19 Vir-YX 20 Vir-YY 21 Vir-YZ 22 Vir-ZX 23 Vir-ZY 24 Vir-ZZ 25 Pres-XX-(bar) 26 Pres-XY-(bar) 27 Pres-XZ-(bar) 28 Pres-YX-(bar) 29 Pres-YY-(bar) 30 Pres-YZ-(bar) 31 Pres-ZX-(bar) 32 Pres-ZY-(bar) 33 Pres-ZZ-(bar) 34 #Surf*SurfTen 35 Mu-X 36 Mu-Y 37 Mu-Z 38 T-rest 11 12 13 0 Back Off! I just backed up 6LYZ-EM-solvated.xvg to ./#6LYZ-EM-solvated.xvg.2# Last frame read 41 time 65.000 Statistics over 65 steps [ 1. thru 65. ps ], 3 data sets Energy Average RMSD Fluct. Drift Tot-Drift --- Potential8.98118e+08 4.53312e+08 0 -3.03617e+07 -1.97304e+09 Kinetic En. 0 0 0 0 0 Total Energy 8.98118e+08 4.53312e+08 0 -3.03617e+07 -1.97304e+09 gcq#119: Bring Out the Gimp (Pulp Fiction) Chih-Ying Lin wrote: Hi The follwing is my .out file. From it, can I conclude that some molecule clashing with another ? No, you can conclude that your system is unstable. One possible reason is atomic clashing, but you cannot say for sure. General advice on your problem (which is encountered frequently, and as such, appears thousands of times in the list archive) can be found on the Gromacs wiki site: http://www.gromacs.org/Documentation/Errors#LINCS.2fSETTLE.2fSHAKE_warnings http://www.gromacs.org/Documentation/Terminology/Blowing_Up If you want further help, take the advice that I gave you before - look at the trajectory, focusing specifically on the problematic atoms (looks like 366 and 367 are having problems first, suggesting that either they, or atoms nearby, are unstable). I also asked about the success of your energy minimization, but you haven't provided that information. From the output, it seems that your simulation is crashing immediately, suggesting that EM did not work properly, and there *may* be unresolved clashes. You will have to do visual inspection to determine if this is the case. -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/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] LINCS WARNING max 597108032.000000 (between atoms 366 and 368) ?
Hi what does the max max 597108032.00 (between atoms 366 and 368) mean? is it the max force or max length of the system? where is the max force listed? max 597108032.00 (between atoms 366 and 368) rms 26394490.00 bonds that rotated more than 30 degrees: what does previous, current mean? is it previous length and current length? Thank you Lin Step 0, time 0 (ps) LINCS WARNING relative constraint deviation after LINCS: max 597108032.00 (between atoms 366 and 368) rms 26394490.00 bonds that rotated more than 30 degrees: *atom 1 atom 2 angle previous, current, constraint length * 26 39 52.00.1530 0.1699 0.1530 39 40 69.40.1230 0.1423 0.1230 39 41 40.70.1330 0.1502 0.1330 75 76 36.00.1250 0.1252 0.1250 133134 69.50.1530 0.1937 0.1530 134135 89.80.1470 0.2036 0.1470 344346 42.40.1470 0.2090 0.1470 346347 42.20.1530 0.2141 0.1530 346359 63.90.1530 26006.0332 0.1530 359360 56.90.1230 26006.0469 0.1230 359361 83.20.1330 82898.5859 0.1330 361362 77.50.1000 82845.7109 0.1000 361363 83.80.1470 398710.1875 0.1470 363364 89.30.1530 1909291.8750 0.1530 363369 85.20.1530 393002.8125 0.1530 364365 90.00.1508 31146174. 0.1530 365366 90.20.1544 66925512. 0.1530 366367 92.70.1301 73689816. 0.1250 366368 87.00.1305 74638504. 0.1250 369370 72.10.1230 65978.3203 0.1230 369371 72.60.1330 66864.2812 0.1330 371372 85.70.1000 10685.0596 0.1000 371373 61.00.1470 10685.1035 0.1470 373374 33.30.1530 0.1896 0.1530 373377 33.50.1530 0.1933 0.1530 547548 90.10.1089 0.1358 0.1090 898900 89.90.1530 0.4741 0.1530 -- 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
[gmx-users] clashing happened inside the protein molecule?
Hi Here is my .out file. atoms 366 and 368 are two atoms inside the protein. What is other possible way to solve it ? Thank you Lin relative constraint deviation after LINCS: max 597108032.00 (between atoms 366 and 368) rms 26394490.00 bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 26 39 52.00.1530 0.1699 0.1530 39 40 69.40.1230 0.1423 0.1230 39 41 40.70.1330 0.1502 0.1330 75 76 36.00.1250 0.1252 0.1250 133134 69.50.1530 0.1937 0.1530 134135 89.80.1470 0.2036 0.1470 344346 42.40.1470 0.2090 0.1470 346347 42.20.1530 0.2141 0.1530 346359 63.90.1530 26006.0332 0.1530 359360 56.90.1230 26006.0469 0.1230 359361 83.20.1330 82898.5859 0.1330 361362 77.50.1000 82845.7109 0.1000 361363 83.80.1470 398710.1875 0.1470 363364 89.30.1530 1909291.8750 0.1530 363369 85.20.1530 393002.8125 0.1530 364365 90.00.1508 31146174. 0.1530 365366 90.20.1544 66925512. 0.1530 366367 92.70.1301 73689816. 0.1250 366368 87.00.1305 74638504. 0.1250 369370 72.10.1230 65978.3203 0.1230 369371 72.60.1330 66864.2812 0.1330 371372 85.70.1000 10685.0596 0.1000 371373 61.00.1470 10685.1035 0.1470 373374 33.30.1530 0.1896 0.1530 -- 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
[gmx-users] Break ? = Position restrained MD
Hi In the position restrain MD, only solvent molecules and hydrogen atoms are allowed to move. I checked the .out file. The max is happened on the atoms inside protein. Why? Thank you 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. 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 put more solutes into the system ?
Hi The system = one protein molecule + 10 ligands + water molecules in 6 x 6 x 6 box. after 100 ns simulatin, 10 ligands have attached on the protein. Now, I tried to put another 10 ligands into the system. The steps are as follows. 1. Take one coordinate file and remove all the coordinates of the water molecules. 2. Center the protein with the attached 10 ligands 3. With genbox command, to put another 10 ligands into the simulation box. 4. Solvate the system, with genbox command 5. Add ions, with genion command 6. Energy minimization of the solvated system pbc = xyz (minim.mdp) = the system is crystallized with visualization 7. Relaxation of solvent and hydrogen atom positions Run = Position restrained MD = simulation break What is wrong here? How to put another 10 ligands into the simulation box correctly? Thank you Lin Chih-Ying Lin wrote: Hi I have a system - solutes with water. The system has been under MD simulation for 100 ns. Now, I want to put more solutes in it. Would you please tell me which command can make it ? Go back to the start, take a coordinate file with a suitable periodic box defined (editconf), and replicate it suitably (genconf), then solvate that (genbox), then equilibrate. You could replicate the solvated box, but it's more trouble than it is worth. Mark -- 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
[gmx-users] How to put more solutes into the system ?
Hi The system = one protein molecule + 10 ligands + water molecules in 6 x 6 x 6 box. after 100 ns simulatin, 10 ligands have attached on the protein. Now, I tried to put another 10 ligands into the system. The steps are as follows. 1. Take one coordinate file and remove all the coordinates of the water molecules. 2. Center the protein with the attached 10 ligands 3. With genbox command, to put another 10 ligands into the simulation box. 4. Solvate the system, with genbox command 5. Add ions, with genion command 6. Energy minimization of the solvated system pbc = xyz (minim.mdp) = the system is crystallized with visualization 7. Relaxation of solvent and hydrogen atom positions Run = Position restrained MD = simulation break What is wrong here? How to put another 10 ligands into the simulation box correctly? Thank you Lin Chih-Ying Lin wrote: Hi I have a system - solutes with water. The system has been under MD simulation for 100 ns. Now, I want to put more solutes in it. Would you please tell me which command can make it ? Go back to the start, take a coordinate file with a suitable periodic box defined (editconf), and replicate it suitably (genconf), then solvate that (genbox), then equilibrate. You could replicate the solvated box, but it's more trouble than it is worth. Mark -- 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
[gmx-users] How to put more solutes into the system ?
Hi I have a system - solutes with water. The system has been under MD simulation for 100 ns. Now, I want to put more solutes in it. Would you please tell me which command can make it ? Thank you 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. 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] g_msd = The MSD and periodic boundary condition
Hi With the periodic boundary condition, all the recorded coordinates of the atom are within the simulation box. To calculate the MSD, the movement of the center mass of the molecules between this time step with the next time step is calculated without considering the periodic boundary condition. But all the recorded coordinates of the atom are within the simulation box after considering the periodic boundary condition. Does g_msd remove the effect of the periodic boundary condition ? So, how can I remove the periodic boundary condition to get the truly movement of the atoms between the two time steps ? Thank you 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. 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] Decreasing MSD of ligand ?
Hi The MSD decrease occurs in the long times. The ligand has bounded to a protein. How can the decrease happen? Thank you Lin Chih-Ying Lin wrote: HI MSD = mean square displacement diffusion coefficient = d/dt (MSD) I simulate the protein and ligand system and then calculate the MSD of the ligand. Then, i drew the plot of the time evolution of the MSD. But the the MSD decreases as time for some period. I see nothing about my codings. Would you please tell me about any possible errors i made? MSD can decrease due to insufficient sampling (time of the simulation, number of frames analyzed, etc). Depending on what you define as some period (during the initial part of the simulation? the middle? the end?) the behavior may or may not be normal, but from the few details you provide, there's no way to know. What do you hope to see in this analysis? Will a ligand bound to a protein really diffuse that much anyway? -Justin Thank you 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. 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] Decreasing MSD of ligand ?
HI MSD = mean square displacement diffusion coefficient = d/dt (MSD) I simulate the protein and ligand system and then calculate the MSD of the ligand. Then, i drew the plot of the time evolution of the MSD. But the the MSD decreases as time for some period. I see nothing about my codings. Would you please tell me about any possible errors i made? Thank you 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. 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] Increase temperature to 550K
Hi The system = one lysozyme + TIP3P water I was put the system in NTP simulation. Under 550K, all water molecules should evaporate entirely , I suppose ??? From Justin = There are plenty of other methodological concerns (pressure coupling especially) Would you please direct me about this ? Thank you Lin I agree with Mark's earlier comment; the water model alone is not the most immediate concern. A colleague of mine is currently doing lots of high-temperature (up to 600 K) simulations of proteins in TIP3P using the AMBER force fields. There are plenty of other methodological concerns (pressure coupling especially); a thorough search of the literature will give you some insights into what might be wrong. Plenty of groups have successfully been doing high-temperature MD for a number of years. -Justin Chih-Ying Lin wrote: Hi the water model is TIP3P. Thanks Lin I think the problem is hidden in your water force field model. The simulation system is merely water + one lysozyme. I increase temperate to 550K. Then, the simulation broke. The following message is shown. MX:hpc0011:Remote endpoint is closed, peer=00:60:dd:48:14:5b (hpc0010:0) mpiexec: Warning: task 0 exited with status 1. mpiexec: Warning: tasks 1-2 died with signal 9 (Killed). mpiexec: Warning: task 3 died with signal 11 (Segmentation fault). Anything wrong with the simulation? Thank you -- 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
[gmx-users] Increase temperature to 550K = simulation techniques ?
Hi For running simulaion parameters, people normally not write the details in their papers. high-temperature (up to 600 K) simulations of proteins in TIP3P.. any other detailed suggestion about this ? Thank you Lin I agree with Mark's earlier comment; the water model alone is not the most immediate concern. A colleague of mine is currently doing lots of high-temperature (up to 600 K) simulations of proteins in TIP3P using the AMBER force fields. There are plenty of other methodological concerns (pressure coupling especially); a thorough search of the literature will give you some insights into what might be wrong. Plenty of groups have successfully been doing high-temperature MD for a number of years. -Justin Chih-Ying Lin wrote: Hi the water model is TIP3P. Thanks Lin I think the problem is hidden in your water force field model. The simulation system is merely water + one lysozyme. I increase temperate to 550K. Then, the simulation broke. The following message is shown. MX:hpc0011:Remote endpoint is closed, peer=00:60:dd:48:14:5b (hpc0010:0) mpiexec: Warning: task 0 exited with status 1. mpiexec: Warning: tasks 1-2 died with signal 9 (Killed). mpiexec: Warning: task 3 died with signal 11 (Segmentation fault). Anything wrong with the simulation? Thank you -- 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
[gmx-users] Increase temperature to 550K
HI The simulation system is merely water + one lysozyme. I increase temperate to 550K. Then, the simulation broke. The following message is shown. MX:hpc0011:Remote endpoint is closed, peer=00:60:dd:48:14:5b (hpc0010:0) mpiexec: Warning: task 0 exited with status 1. mpiexec: Warning: tasks 1-2 died with signal 9 (Killed). mpiexec: Warning: task 3 died with signal 11 (Segmentation fault). Anything wrong with the simulation? Thank you 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. 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] Increase temperature to 550K
Hi Here is the dt and constraints. Any other suggestion about heating up the system and make the system stable? Thank you Lin dt = 0.001 ; OPTIONS FOR BONDS constraints = all-bonds constraint-algorithm = Lincs unconstrained-start = yes lincs-order = 4 lincs-iter = 1 lincs-warnangle = 30 Chih-Ying Lin wrote: HI The simulation system is merely water + one lysozyme. I increase temperate to 550K. Then, the simulation broke. The following message is shown. MX:hpc0011:Remote endpoint is closed, peer=00:60:dd:48:14:5b (hpc0010:0) mpiexec: Warning: task 0 exited with status 1. mpiexec: Warning: tasks 1-2 died with signal 9 (Killed). mpiexec: Warning: task 3 died with signal 11 (Segmentation fault). Anything wrong with the simulation? I think, pretty clearly, yes. Increasing to a high temperature can make the system unstable. Are you using a suitable dt? Constraints? -Justin Thank you 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. 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] Increase temperature to 550K
Hi the water model is TIP3P. Thanks Lin I think the problem is hidden in your water force field model. The simulation system is merely water + one lysozyme. I increase temperate to 550K. Then, the simulation broke. The following message is shown. MX:hpc0011:Remote endpoint is closed, peer=00:60:dd:48:14:5b (hpc0010:0) mpiexec: Warning: task 0 exited with status 1. mpiexec: Warning: tasks 1-2 died with signal 9 (Killed). mpiexec: Warning: task 3 died with signal 11 (Segmentation fault). Anything wrong with the simulation? Thank you -- 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
[gmx-users] Long Simulation Time
HI i was reading somewhere.. simulation will break / terminate when the simulation is running so so long ... Did anyone read the same information? Please refer me the related information since I have no idea where I read this information. How long is long ? How to avoid this? Thank you 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. 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] Is the time scale of the protein domain motion within nano-second?
Hi Is the time scale of the protein domain motion within nano-second? Thank you 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. 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] trjconv = not get the enough data ?
Hi in my .mdp file, i set up the total 4000 times saving the coordinates of each atom. then, I use the command trjconv -f xx.gro -s xx.tpr -o xx-traj.gro then, i checked the xx-traj.gro file and found there were less than 4000 times of recording coordinates for each atom. say 3600 times of records. what is wrong ? Thank you 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. 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] g_msd ?
Hi # g_msd_mpi is part of G R O M A C S: # # Giant Rising Ordinary Mutants for A Clerical Setup # @title Diffusion Coefficients / Molecule @xaxis label Molecule @yaxis label D @TYPE xy 00.907803 1 3.5355 2 4.34231 3 3.83589 xaxis = Molecule # from .top file yaxis = diffusion coefficient 1. what does the first row represent ? ( Molecule # = 0 ??? ) 2. what is the unit for the diffusion coefficient ?? 3. why are the diffusion coefficients quite different for the same type of molecules ( water ) ?? Thank you 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. 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] Can Gromacs produce the data from NMR?
HI Can Gromacs produce the data from NMR? Thank you 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. 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] template.c
HI To use template.c 1. create a file to put template.c and Makefile.x86_64-unknown-linux-gnu together 2. under C compiler = type the command = make -f Makefile.x86_64-unknown-linux-gnu = type the command = cc -O -o template template.c -lm = type the command = ./template template.in Am I right? Thank you Lin Chih-Ying Lin wrote: Hi Following are 1. template.c 2. README 3. Makefile.x86_64-unknown-linux-gnu In the template.c = it includes several GROMACS headers. #include statutil.h #include typedefs.h #include smalloc.h #include vec.h #include copyrite.h #include statutil.h #include tpxio.h If I put the GROMACS headers with template.c in the same directory, should I still need the Makefile for my architecture, intended to compile template.c and link to the GROMACS libraries correctly ??? The point of the Makefile is that you don't need to move headers around - like it says in the README: A Makefile.arch is created for each architecture you install with the correct paths and libraries. You will have to link (or copy) the correct makefile to Makefile or use the -f option to gmake in order to select a makefile. So do make -f Makefile.x86_64-unknown-linux-gnu like it says :-) Mark ___ 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
[gmx-users] template.c = put the GROMACS headers in the same file ?
Hi
Following are
1. template.c
2. README
3. Makefile.x86_64-unknown-linux-gnu
In the template.c = it includes several GROMACS headers.
#include statutil.h
#include typedefs.h
#include smalloc.h
#include vec.h
#include copyrite.h
#include statutil.h
#include tpxio.h
If I put the GROMACS headers with template.c in the same directory, should I
still need the Makefile for my architecture, intended to compile template.c
and link to the GROMACS libraries correctly ???
Thank you
Lin
= [ TEMPLATE.C ]
===
/*
* $Id: template.c,v 1.5 2008/05/29 08:36:53 hess Exp $
*
*This source code is part of
*
* G R O M A C S
*
* GROningen MAchine for Chemical Simulations
*
*VERSION 3.0
*
* Copyright (c) 1991-2001
* BIOSON Research Institute, Dept. of Biophysical Chemistry
* University of Groningen, The Netherlands
*
* This program is free software; you can redistribute it and/or
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation; either version 2
* of the License, or (at your option) any later version.
*
* If you want to redistribute modifications, please consider that
* scientific software is very special. Version control is crucial -
* bugs must be traceable. We will be happy to consider code for
* inclusion in the official distribution, but derived work must not
* be called official GROMACS. Details are found in the README COPYING
* files - if they are missing, get the official version at www.gromacs.org.
*
* To help us fund GROMACS development, we humbly ask that you cite
* the papers on the package - you can find them in the top README file.
*
* Do check out http://www.gromacs.org , or mail us at grom...@gromacs.org .
*
* And Hey:
* Gyas ROwers Mature At Cryogenic Speed
*/
/* This line is only for CVS version info */
static char *SRCID_template_c = $Id: template.c,v 1.5 2008/05/29 08:36:53
hess
Exp $;
#include statutil.h
#include typedefs.h
#include smalloc.h
#include vec.h
#include copyrite.h
#include statutil.h
#include tpxio.h
int main(int argc,char *argv[])
{
static char *desc[] = {
this is a small test program meant to serve as a template ,
when writing your own analysis tools. The advantage of ,
using gromacs for this is that you have access to all ,
information in the topology, and your program will be ,
able to handle all types of coordinates and trajectory ,
files supported by gromacs. Go ahead and try it! ,
This test version just writes the coordinates of an ,
arbitrary atom to standard out for each frame. You can ,
select which atom you want to examine with the -n argument.
};
static int n=1;
/* Extra arguments - but note how you always get the begin/end
* options when running the program, without mentioning them here!
*/
t_pargs pa[] = {
{ -n, FALSE, etINT, {n},
Plot data for atom number n (starting on 1)
}
};
t_topology top;
intePBC;
char title[STRLEN];
t_trxframe fr;
rvec *xtop;
matrix box;
intstatus;
intflags = TRX_READ_X;
t_filenm fnm[] = {
{ efTPS, NULL, NULL, ffREAD }, /* this is for the topology */
{ efTRX, -f, NULL, ffREAD } /* and this for the trajectory */
};
#define NFILE asize(fnm)
CopyRight(stderr,argv[0]);
/* This is the routine responsible for adding default options,
* calling the X/motif interface, etc. */
parse_common_args(argc,argv,PCA_CAN_TIME | PCA_CAN_VIEW,
NFILE,fnm,asize(pa),pa,asize(desc),desc,0,NULL);
/* We don't need any topology information to write the coordinates,
* but to show how it works we start by writing the name and
* charge of the selected atom. It returns a boolean telling us
* whether the topology was found and could be read
*/
read_tps_conf(ftp2fn(efTPS,NFILE,fnm),title,top,ePBC,xtop,NULL,box,TRUE);
sfree(xtop);
n=n-1; /* Our enumeration started on 1, but C starts from 0 */
/* check that this atom exists */
if(n0 || n(top.atoms.nr))
{
printf(Error: Atom number %d is out of range.\n,n);
exit(1);
}
printf(Atom name: %s\n,*(top.atoms.atomname[n]));
printf(Atom charge: %f\n,top.atoms.atom[n].q);
/* The first time we read data is a little special */
read_first_frame(status,ftp2fn(efTRX,NFILE,fnm),fr,flags);
/* This is the main loop over frames */
do {
/* coordinates are available in the vector fr.x
* you can find this and all other structures in
* the types directory under the gromacs include dir.
* Note how flags determines wheter to read x/v/f!
*/
printf(Coordinates at t=%8.3f : %8.5f %8.5f
%8.5f\n,fr.time,fr.x[n][XX],fr
.x[n][YY],fr.x[n][ZZ]);
} while(read_next_frame(status,fr));
thanx(stderr);
return 0;
}
=== [ README ]
=
[gmx-users] template.c
Hi :
I have difficulties to understand the following three files, which are
in Gromacs Package.
1. template.c
2. README
3. Makefile.x86_64-unknown-linux-gnu
Please tell me if I have to do part 3 to compile template.c.
Thank you
Lin
= [ TEMPLATE.C ]
===
/*
* $Id: template.c,v 1.5 2008/05/29 08:36:53 hess Exp $
*
*This source code is part of
*
* G R O M A C S
*
* GROningen MAchine for Chemical Simulations
*
*VERSION 3.0
*
* Copyright (c) 1991-2001
* BIOSON Research Institute, Dept. of Biophysical Chemistry
* University of Groningen, The Netherlands
*
* This program is free software; you can redistribute it and/or
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation; either version 2
* of the License, or (at your option) any later version.
*
* If you want to redistribute modifications, please consider that
* scientific software is very special. Version control is crucial -
* bugs must be traceable. We will be happy to consider code for
* inclusion in the official distribution, but derived work must not
* be called official GROMACS. Details are found in the README COPYING
* files - if they are missing, get the official version at www.gromacs.org.
*
* To help us fund GROMACS development, we humbly ask that you cite
* the papers on the package - you can find them in the top README file.
*
* Do check out http://www.gromacs.org , or mail us at grom...@gromacs.org .
*
* And Hey:
* Gyas ROwers Mature At Cryogenic Speed
*/
/* This line is only for CVS version info */
static char *SRCID_template_c = $Id: template.c,v 1.5 2008/05/29 08:36:53 hess
Exp $;
#include statutil.h
#include typedefs.h
#include smalloc.h
#include vec.h
#include copyrite.h
#include statutil.h
#include tpxio.h
int main(int argc,char *argv[])
{
static char *desc[] = {
this is a small test program meant to serve as a template ,
when writing your own analysis tools. The advantage of ,
using gromacs for this is that you have access to all ,
information in the topology, and your program will be ,
able to handle all types of coordinates and trajectory ,
files supported by gromacs. Go ahead and try it! ,
This test version just writes the coordinates of an ,
arbitrary atom to standard out for each frame. You can ,
select which atom you want to examine with the -n argument.
};
static int n=1;
/* Extra arguments - but note how you always get the begin/end
* options when running the program, without mentioning them here!
*/
t_pargs pa[] = {
{ -n, FALSE, etINT, {n},
Plot data for atom number n (starting on 1)
}
};
t_topology top;
intePBC;
char title[STRLEN];
t_trxframe fr;
rvec *xtop;
matrix box;
intstatus;
intflags = TRX_READ_X;
t_filenm fnm[] = {
{ efTPS, NULL, NULL, ffREAD }, /* this is for the topology */
{ efTRX, -f, NULL, ffREAD } /* and this for the trajectory */
};
#define NFILE asize(fnm)
CopyRight(stderr,argv[0]);
/* This is the routine responsible for adding default options,
* calling the X/motif interface, etc. */
parse_common_args(argc,argv,PCA_CAN_TIME | PCA_CAN_VIEW,
NFILE,fnm,asize(pa),pa,asize(desc),desc,0,NULL);
/* We don't need any topology information to write the coordinates,
* but to show how it works we start by writing the name and
* charge of the selected atom. It returns a boolean telling us
* whether the topology was found and could be read
*/
read_tps_conf(ftp2fn(efTPS,NFILE,fnm),title,top,ePBC,xtop,NULL,box,TRUE);
sfree(xtop);
n=n-1; /* Our enumeration started on 1, but C starts from 0 */
/* check that this atom exists */
if(n0 || n(top.atoms.nr))
{
printf(Error: Atom number %d is out of range.\n,n);
exit(1);
}
printf(Atom name: %s\n,*(top.atoms.atomname[n]));
printf(Atom charge: %f\n,top.atoms.atom[n].q);
/* The first time we read data is a little special */
read_first_frame(status,ftp2fn(efTRX,NFILE,fnm),fr,flags);
/* This is the main loop over frames */
do {
/* coordinates are available in the vector fr.x
* you can find this and all other structures in
* the types directory under the gromacs include dir.
* Note how flags determines wheter to read x/v/f!
*/
printf(Coordinates at t=%8.3f : %8.5f %8.5f %8.5f\n,fr.time,fr.x[n][XX],fr
.x[n][YY],fr.x[n][ZZ]);
} while(read_next_frame(status,fr));
thanx(stderr);
return 0;
}
=== [ README ]
=
[chihy...@hpc-login2 template]$ more README
Once installed, this directory contains a Makefile and
a small program that you could use as a template when
writing your own analysis software.
[gmx-users] The same lysozyme.pdb file under 3.3.3 and 4.0.5 version
Hi I was testing the same lysozyme.pdb file under 3.3.3 and 4.0.5 version under 16 nodes. Simply, lysozyme.pdb + water. There is no problems (errors) with 3.3.3 version. However, with 4.0.5 version, the same lysozyme pdb file with the same simulation condition. except mdrun -pd with minimisation steps Then, Relaxation of solvent and hydrogen atom positions: Position restrained MDIt shows the following errors. --- Program mdrun_mpi, VERSION 4.0.5 Source code file: domdec.c, line: 3651 Fatal error: A charge group moved too far between two domain decomposition steps This usually means that your system is not well equilibrated --- How does it happen? Why? Thank you 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. 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] Can 3.3.3 and 4.0.5 version exist at the same time?
Hi The 3.3.3 and 4.0.5 version were installed under = * source /usr/gromacs/4.0.5/setup.sh source /usr/gromacs/3.3.3/setup.sh* *The 4.0.5 version is currently the default one.* I want to compare the computation results from 4.0.5 version and 3.3.3 version. So, I write the *source /usr/gromacs/3.3.3/setup.sh* into both my .cshrc file and .pbs file. After this command for 3.3.3 version grompp_mpi -np 16 -v -f minim.mdp -c 6LYZ.gro -p 6LYZ.top -o 6LYZ-EM-vacuum.tpr I obtained the errors shown on the screen. --- Program grompp_mpi, VERSION 4.0.5 Source code file: statutil.c, line: 727 Invalid command line argument: -np --- I Wrapped a Newspaper Round My Head (F. Zappa) What happened? How to solve the problem? Thank you 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. 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
