[gmx-users] How to output a single index group
Hello, I am running a simulation of 5 time steps and am trying to avoid setting nstxtcout = 1 or nstxout = 1. The file size becomes unmanageable if I set either of these two parameters to 1. I do not need the coordinates for all atoms in the system, just the alpha carbons, which are grouped in the index file, but I do need coordinates for each time step. Is there any way of specifying in the parameter file to only output the coordinates for the alpha carbons? Thanks! --Venk __ Venkatesh Hariharan The Pennsylvania State University Schreyer Honors College Undergraduate - Bioengineering You must be the change you wish to see in the world. --Mohandas Karamchand Gandhi ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Box Exploding Error
Hello All,
First, for this question I am referring to GROMACS 3.3.3. I have thoroughly
read the archives for errors on why a simulation box might explode. My
simulations require that I bring the N and C terminal ends of a ~20 amino acid
peptide as close together as possible. To do this, I am using the pull code to
freeze the C terminus and pull the N Terminus toward it. I keep getting the
following error during the simulation:
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Back Off! I just
backed up md_traj.xtc to ./#md_traj.xtc.1#
Warning: 1-4 interaction between 5 and 10 at distance 1.480 which is larger
than the 1-4 table size 1.000 nm
These are ignored for the rest of the simulation
This usually means your system is exploding,
if not, you should increase table-extension in your mdp file
My question: Is there any way to completely ignore this error, so that the N
Terminus is pulled as close as possible to the C Terminus? I understand that
the results in the .pdo file of the pull simulation may be unrealistic, but I
simply need to get a peptide structure whose N and C Terminal ends are close
together (within .5 nm). On a side note, are there any suggestions for
respectable molecular modeling software with which I may be able to BUILD a
circular peptide (i.e. - N and C Terminal ends are brought close together)?
Any help is appreciated.
__
Venkatesh Hariharan
The Pennsylvania State University
Schreyer Honors College
Undergraduate - Bioengineering
You must be the change you wish to see in the world.
--Mohandas Karamchand Gandhi
___
gmx-users mailing listgmx-users@gromacs.org
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[gmx-users] Box Exploding Error
I would like to thank everyone for their help. Several individuals responded to my initial post. The consensus seemed to be to use distance restraints. My question is, because distance restraints creates penalties if the distance between two atoms EXCEEDS UPPER BOUNDS, wouldn't that apply more for pulling two terminal atoms apart? In example, as the peptide is being pulled apart, if the distance exceeded a certain value, a penalty would be assessed to the force. In my simulation, with the terminal ends coming together, how UPPER bounds be set? Would I set my upper bounds very low (i.e. - 0.5 nm range)? This way, even the starting structure, with the distance between the terminal ends starting at ~3.5 nm, would be assessed a penalty. Another idea suggested by the GROMACS manual was to incorporate a [bonds] type 6 exclusion in the topology, to create a harmonic potential between the two atoms. Would this serve to help bring the two ends together during simulation? Again, much thanks to those who responded. --Venk VENKATESH HARIHARAN wrote: Hello All, First, for this question I am referring to GROMACS 3.3.3. I have thoroughly read the archives for errors on why a simulation box might explode. My simulations require that I bring the N and C terminal ends of a ~20 amino acid peptide as close together as possible. To do this, I am using the pull code to freeze the C terminus and pull the N Terminus toward it. I would use normal MD with distance restraints between suitable terminal atoms. This is a much simpler approach to this problem. I keep getting the following error during the simulation: Back Off! I just backed up md_traj.xtc to ./#md_traj.xtc.1# Warning: 1-4 interaction between 5 and 10 at distance 1.480 which is larger than the 1-4 table size 1.000 nm These are ignored for the rest of the simulation This usually means your system is exploding, if not, you should increase table-extension in your mdp file See a target=_new href=http://wiki.gromacs.org/index.php/blowing_up;http://wiki.gromacs.org/index.php/blowing_up/a My question: Is there any way to completely ignore this error, so that the N Terminus is pulled as close as possible to the C Terminus? That's not your problem. Atoms 5 and 10 are too close because there's something unphysical about your model, and anyway these atoms are not your terminal pair. I understand that the results in the .pdo file of the pull simulation may be unrealistic, but I simply need to get a peptide structure whose N and C Terminal ends are close together (within .5 nm). On a side note, are there any suggestions for respectable molecular modeling software with which I may be able to BUILD a circular peptide (i.e. - N and C Terminal ends are brought close together)? Any help is appreciated. There are a few links here a target=_new href=http://wiki.gromacs.org/index.php/Coordinate_File;http://wiki.gromacs.org/index.php/Coordinate_File/a that might help. Mark __ Venkatesh Hariharan The Pennsylvania State University Schreyer Honors College Undergraduate - Bioengineering You must be the change you wish to see in the world. --Mohandas Karamchand Gandhi ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Converting Output Files
Hello, After generating a .pdb video using the trjconv command, how can I convert that .pdb video to .avi or .mpeg format? Is that a feature in GROMACS or do I need to use an outside program. If so, any suggestions on which programs to use? Thanks! --Venk __ Venkatesh Hariharan The Pennsylvania State University Schreyer Honors College Undergraduate - Bioengineering You must be the change you wish to see in the world. --Mohandas Karamchand Gandhi ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Pull.pdo Columns
Hello, I understand this topic has been dealt with previously, and I have read all the relative material from the archives, but I am still having trouble deciphering what each column corresponds to in the pull.pdo file for an AFM pull, with one pull group and one reference group, and pulling in only the X direction. From what I've read, the columns are as follows: Time RefX RefY RefZ PullX PullY PullZ SpringX SpringY SpringZ ...for a total of 10 columns. The problem is that when I use the values of for the reference group and pull group at time zero to calculate end to end distance, they do not correspond to my starting pdb file after solvation. Any thoughts? __ Venkatesh Hariharan Pennsylvania State University Schreyer Honors College Undergraduate - Bioengineering You must be the change you wish to see in the world. --Mohandas Karamchand Gandhi ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] (no subject)
Hello all, I am using the pull code and was wondering if there was a way to permanently fix the position of only a single atom of a polypeptide throughout the simulation? Thank you. __ Venkatesh Hariharan Pennsylvania State University Schreyer Honors College Undergraduate - Bioengineering You must be the change you wish to see in the world. --Mohandas Karamchand Gandhi ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] PBS Script - trjconv Options
Hello, Simple question. I am running constraint pulling and getting the .xtc and .tpr output files in order to create a pdb video using trjconv. I am running simulations on a cluster, and so a pbs script must be submitted with the necessary commands. When using trjconv command, the group must subsequently be specified. Is there any way to modify the below command to also select a specific group (i.e. - 1 for 'Protein'). For example, when using mdrun, the -ff option can be used to specify which forcefield to use. Is there something similar to this with regards to the group selection when using trjconv? Thanks. trjconv -s peptide.tpr -f trajectory.xtc -o pullvideo.pdb __ Venkatesh Hariharan Pennsylvania State University Schreyer Honors College Undergraduate - Bioengineering You must be the change you wish to see in the world. --Mohandas Karamchand Gandhi ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Force Distance Curve from .trr .xtc
Hello, After running an AFM or Constraint pull simulation, I am looking to generate a force distance curve between the pulled group and the reference group. Any suggestions on how to do this? Currently I am doing it manually by generating a .pdb movie of the entire pulling, and extracting the distance between the two groups via coordinates in the .pdb at specified time points. I then compare the distance at that time point with the force for that time point in the .pdo file. As you might imagine, this is very time consuming. Does Gromacs have a command to do this for you? Thanks. __ Venkatesh Hariharan Pennsylvania State University Schreyer Honors College Undergraduate - Bioengineering You must be the change you wish to see in the world. --Mohandas Karamchand Gandhi ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] g_wham.c
Hello, I've read the threads but could not find the file itself, or the needed corrections for the existing g_wham.c. Is anyone able to send me a copy of the corrected g_wham.c by David Bostick of Scripps. Thank you. __ Venkatesh Hariharan Pennsylvania State University Schreyer Honors College Undergraduate - Bioengineering You must be the change you wish to see in the world. --Mohandas Karamchand Gandhi ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Constraint Pulling - Oscillating Forces
Hello, I am running constraint pulling on a peptide chain. After the run, the pull.pdo file outputs the time, along with the force (in kJ/(mol nm)). The problem is that the forces are oscillating between almost 1000 pN. I tried to reduce the constraint tolerance, but it does not help that much. Any suggestions on reducing hte oscillations of force? Thanks. __ Venkatesh Hariharan Pennsylvania State University Schreyer Honors College Undergraduate - Bioengineering You must be the change you wish to see in the world. --Mohandas Karamchand Gandhi ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Force Extension Curve
Hello, Two questions. First, what parameters are to be modified if I want to reduce the output data in the .trr output file in a constraint pull. I am reaching the 4GB allowable maximum and the simulation is shutting down. Second, what command should be used in order to generate a Force Extension curve from the output .xtc, .trr, and/or .pdo files. Any help is appreciated. __ Venkatesh Hariharan Pennsylvania State University Schreyer Honors College Undergraduate - Bioengineering You must be the change you wish to see in the world. --Mohandas Karamchand Gandhi ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] g_wham command issues
Hello, I am having trouble analyzing the XXX.pdo file output from my mdrun simulation using the g_wham command. Specifically, my command entered is: g_wham pull.pdo -o pull1.xvg The error given is: Opening file pull.pdo _ Program g_wham, VERSION 3.3.3 Source code file: gmx_wham.c, line 89 Fatal error: This does not appear to be a valid pdo file _ Motherhood Means Mental Freeze (The Breeders) I've looked into the gmx_wham.c file and found that line 89 corresponds to: if(strcmp(Buffer1,UMBRELLA)) fatal_error( 704 ,This does not appear to be a valid pdo file); I'm not sure of what this means. I've noticed that others have had this issue in the past, and am hoping someone has found my mistake. Formatting of my .pdo file maybe? If this is the case, can anyone provide sample .pdo file to compare with my own? Any help is appreciated. __ Venkatesh Hariharan Pennsylvania State University Schreyer Honors College Undergraduate - Bioengineering You must be the change you wish to see in the world. --Mohandas Karamchand Gandhi ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] g_wham command issues
I've also tried to gzip the files, and subsequently use the same command line as below with the zipped file. Same problem. Any other ideas? On Tue, Jul 1, 2008 12:12 PM, LuLanyuan [EMAIL PROTECTED] wrote: I remember that at least for the old version of g_wham, you need to gzip the pdo files first. Lanyuan Lu Date: Tue, 1 Jul 2008 11:38:18 -0400 To: gmx-users@gromacs.org From: [EMAIL PROTECTED] Subject: [gmx-users] g_wham command issues Hello, I am having trouble analyzing the XXX.pdo file output from my mdrun simulation using the g_wham command. Specifically, my command entered is: g_wham pull.pdo -o pull1.xvg The error given is: Opening file pull.pdo _ Program g_wham, VERSION 3.3.3 Source code file: gmx_wham.c, line 89 Fatal error: This does not appear to be a valid pdo file _ Motherhood Means Mental Freeze (The Breeders) I've looked into the gmx_wham.c file and found that line 89 corresponds to: if(strcmp(Buffer1,UMBRELLA) fatal_error( 704 ,This does not appear to be a valid pdo file); I'm not sure of what this means. I've noticed that others have had this issue in the past, and am hoping someone has found my mistake. Formatting of my .pdo file maybe? If this is the case, can anyone provide sample .pdo file to compare with my own? Any help is appreciated. __ Venkatesh Hariharan Pennsylvania State University Schreyer Honors College Undergraduate - Bioengineering You must be the change you wish to see in the world. --Mohandas Karamchand Gandhi _ ���껻���գױ���Լ���MSN�ǵ�TAһ��ϲ�� http://im.live.cn/emoticons/?ID=18 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php __ Venkatesh Hariharan Pennsylvania State University Schreyer Honors College Undergraduate - Bioengineering You must be the change you wish to see in the world. --Mohandas Karamchand Gandhi ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] AFM Pulling index.ndx pull.ppa
Hello, I am attempting to use AFM pulling on a 17 amino acid peptide, but am having trouble with the 'group' concept. I've read the manual and searched sample XXX.ndx files, but have had no luck. How would I define the first amino acid as the reference group (i.e. - fixed in space) and the last amino acid in the peptide as group 1 (i.e. - amino acid at which the spring acts). The first amino acid is Alanine and the last is Leucine. Is a sample .ndx file available? The second issue is with the afm_init value in the pull.ppa file. If I understand correctly it is the center of mass vector of the peptide, and should go from the reference group to the pulled group ( from first amino acid A to last amino acid L). How is this vector calculated and what is the syntax used to enter this vector in the pull.ppa file. Any help is appreciated. __ Venkatesh Hariharan Pennsylvania State University Schreyer Honors College Undergraduate - Bioengineering You must be the change you wish to see in the world. --Mohandas Karamchand Gandhi ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] (no subject)
Hello, I am new to GROMACS, and so my questions my seem relatively simple. I'm attempting to use the AFM Pulling facet of the program to generate force extension curves of ~20 amino acid polypeptide chains. After cutting down my .pdb file to the desired amino acids, i used the command: pdb2gmx -f 3B6U.pdb -p protein.top -o protein.gro The command generated the required gromacs files. Now, I am unsure of the next step. Would it be to create a .mdp file with my specified parameters? If so, what command should I use after creating the .mdp to start the simulation? Is there an AFM Pulling / Force Extension Curve tutorial available? Thanks. __ Venkatesh Hariharan Schreyer Honors College Undergraduate - Bioengineering You must be the change you wish to see in the world. --Mohandas Karamchand Gandhi ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
