[gmx-users] RMSF: Different results for same residue

the same residues. Why is it so ?? Or am I making a mistake at some place ?? Thanks in advance. Alok -- 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

[gmx-users] Diffusion by g_msd

molecules. my input command was g_msd -f XXX.xtc -s XXX.tpr -n index.ndx -o msd.xvg -type z -trestart 20 -b 5001 -e 5500 My question it is the correct way to calculate the diffusion for my desired water molecule within desired time? Regards, Alok -- gmx-users mailing listgmx-users@gromacs.org

[gmx-users] Restraining molecular symmetry

correctly when prompted. But at least with some of the snap shots which I saw, I can find water mediated hydrogen bonds...Is there any other way to calculate solvent mediated hydrogen bonds.. Thanks in advance for your suggestions Alok -- This message has been scanned for viruses and

Re: [gmx-users] angle and dihedral as a function of time

Try g_angle -h more specific g_angle -ov Alok - Original Message - From: "SWAPNA" <[EMAIL PROTECTED]> To: "Discussion list for GROMACS users" Sent: Monday, February 18, 2008 4:48 PM Subject: [gmx-users] angle and dihedral as a function of time Hi, Is ther

Re: [gmx-users] Weird structure after minimization (membrane protein simulation)

+08 . Without flexible water molecules there is no such huge deviation from the original value.Also during the equilibration run I have not observed any LINCS warnings. I am hoping my problem is solved now :-) Thanks again to your valuable suggestions. Best regards, Alok Jain - O

Re: [gmx-users] Weird structure after minimization (membrane proteinsimulation

t in minimization. about " comm_grps = Protein_POP SOL " that was suggested by Dr. Xavier some time ago. http://www.gromacs.org/component/option,com_wrapper/Itemid,165/ I will also try " comm_grps = system" and come back to you. Thanks again for your preci

[gmx-users] Weird structure after minimization (membrane protein simulation)

requesting expert comments from you people. Is it normal to Membrane simulation or there is some problem in my system? Till now I have not encountered any problems/warning. Eagerly waiting for your reply, Best regards, Alok Jain @Mark: Thanks a lot for your reply/comments and time. I am using TIP4P

Re: [gmx-users] [Fwd: Semiisotropic pressure coupling &comm_grps (VCM)]

Dear Xavier, Thanks a lot for your reply. I will follow your suggestions. Best Regards, Alok - Original Message - From: "Xavier Periole" <[EMAIL PROTECTED]> To: "Discussion list for GROMACS users" Sent: Monday, November 26, 2007 5:23 PM Subject: Re: [gmx-

[gmx-users] Semiisotropic pressure coupling & comm_grps (VCM)

Dear All, I have two basic questions regarding membrane protein simulation. First regarding Semiisotropic pressure coupling (NPAT) and second regarding comm_grpp (VCM). 1) If I want to use NPAT ensemble (x/y dimensions of bilayer to be fixed) then is following the correct way to define? Pcoup

Re: [gmx-users] make hole question

3.1.4 or previous - Original Message - From: "Andrei Neamtu" <[EMAIL PROTECTED]> To: Sent: Saturday, November 17, 2007 11:29 PM Subject: [gmx-users] make hole question Hello gmx, I have a quick question: with what distribution of gromacs the mdrun make hole works? Cu bine, Andrei

[gmx-users] Removal of unwanted water from lipid bilayer after solvating the structure from genbox: problem and solution

your suggestion), till now after 1ns run, my structure looks fine to me. Thanks a lot your and mark valuable suggestions and time. PS: If moderator permit me then I will post the picture (size 381 kb only) which will help to explain my problems and solution more clearly. Best Regards, Alok - Ori

Re: [gmx-users] solvate using genbox results in water in thecenterofthe bilayer. How to edit pdb file contents in gromacs ?

. Thanks a lot for your valuable comments/suggetions. Best Regards, Alok - Original Message - From: <[EMAIL PROTECTED]> To: Sent: Friday, October 26, 2007 2:33 AM Subject: [gmx-users] solvate using genbox results in water in thecenterofthe bilayer. How to edit pdb file contents in g

Re: [gmx-users] solvate using genbox results in water in the >centerofthe bilayer. How to edit pdb file contents in gromacs ?

Dear Chris, Thanks a lot your suggestions. I have started the MD based on your suggestions. I will tell you as soon I will get the results. PS: Is this is already reported that Gromacs have some problem with ZERO? Regards, Alok - Original Message - From: <[EMAIL PROTECTED]&g

Re: [gmx-users] solvate using genbox results in water in the centerofthe bilayer. How to edit pdb file contents in gromacs ?

. Hope I will get any solution for my problem. Best Regards, Alok ## Dear Mark, Thanks a lot for your valuable time, and sorry for inappropriate description, I am describing again, I hope thin time I can make it clear. I took

Re: [gmx-users] solvate using genbox results in water in the center ofthe bilayer. How to edit pdb file contents in gromacs ?

will help Alok - Original Message - From: maria goranovic To: gmx-users@gromacs.org Sent: Sunday, October 21, 2007 3:57 PM Subject: [gmx-users] solvate using genbox results in water in the center ofthe bilayer. How to edit pdb file contents in gromacs ? Hi I am using

Re: [gmx-users] alpha Carbon-Aromatic ring hydrogen bond

ca1 (here ca1 is your CA hydrogen atom no) then you will get new index file containing these two groups. 2) Calculate the distance between these two groups using g_dist (as mark already suggested). Hope it will help. Alok - Original Message - From: sarbani chattopadhyay To

Re: [gmx-users] uneven distribution of water across the bilayer

0 0 0 NVT (Fourth Simulation). I hope I make my problem clear.could some one give some idea what parameters/ensemble I should take to overcome this problem. please suggest me where I am doing mistake. Thanks Regards, Alok - Original Message - From: "Mark Abraham&

[gmx-users] uneven distribution of water across the bilayer

Dear All, I am trying to simulate lipid-water system (340 POPE lipids & 6120 TIP4P Waters), during the solvation by genbox, It also add the the water at the interior of the bilayer. I removed those water molecules by my perl script. But after removing these water molecules I have observed a zon

Re: [gmx-users] Restart

1.5ns Alok - Original Message - From: Mark Zottola To: Discussion list for GROMACS users Sent: Sunday, August 19, 2007 11:17 PM Subject: Re: [gmx-users] Restart Dil, Thanks for the post. However, my original job was set for 750 ps and ran successfully. Now, I would

Re: [gmx-users] 1-4 columb interaction

Thanks Chris for your detail reply. It really help me a lot. Regards, Alok - Original Message - From: <[EMAIL PROTECTED]> To: Sent: Thursday, September 21, 2006 7:08 PM Subject: [gmx-users] 1-4 columb interaction Quoting Alok <[EMAIL PROTECTED]>: Thanks Ch

Re: [gmx-users] 1-4 columb interaction

?     Regards, Alok - Original Message - From: Qiao Baofu To: Discussion list for GROMACS users Sent: Wednesday, September 20, 2006 7:17 PM Subject: Re: [gmx-users] 1-4 columb interaction In the force field file  ff***.itp, there are two terms to scale lj and

[gmx-users] 1-4 columb interaction

was mentioned that there is always scaling for Columb-14 but how I am not able to get?   Regards, Alok     ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe reques

Re: [gmx-users] OPLS + ffgmx

you later as I go about it. Thanking you all again, Regards, Alok. - Original Message - From: "Mark Abraham" <[EMAIL PROTECTED]> To: "Discussion list for GROMACS users" Sent: Wednesday, September 06, 2006 7:47 AM Subject: Re: [gmx-users] OPLS + ffgmx Hi

[gmx-users] OPLS + ffgmx

explicitly. Thanks a lot, Alok ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED]

Re: [gmx-users] mdrun_hole problem again ..SOLVED..THANKS.....

Thanks a lot to all of you, especialy Florian and Chris. My problem has been solved. Best regards, Alok - Original Message - From: <[EMAIL PROTECTED]> To: Sent: Tuesday, September 05, 2006 4:35 AM Subject: Re: [gmx-users] mdrun_hole problem again - you didn't d

Re: [gmx-users] GROMACS with MPICH on Sun Cluster

Thanks again to your help. I will discuss these issues with my system administrator. I am really grateful for being a part of this excellent mailing list. Warm regards, Alok Jain - Original Message - From: "David van der Spoel" <[EMAIL PROTECTED]> To: "Discussion l

Re: [gmx-users] GROMACS with MPICH on Sun Cluster

mdrun_mpi in the SUN CLUSTER) Warm regards, Alok Jain - Original Message - From: "David van der Spoel" <[EMAIL PROTECTED]> To: "Discussion list for GROMACS users" Sent: Thursday, June 08, 2006 11:11 PM Subject: Re: [gmx-users] GROMACS with MPICH on Sun Clust

Re: [gmx-users] GROMACS with MPICH on Sun Cluster

n i will come back to you. Thanks a lot ! best regards, Alok Jain - Original Message - From: "David van der Spoel" <[EMAIL PROTECTED]> To: "Discussion list for GROMACS users" Sent: Thursday, June 08, 2006 8:25 PM Subject: Re: [gmx-users] GROMACS with M

Re: [gmx-users] GROMACS with MPICH on Sun Cluster

I tried mpirun mdrun_mpi -h but I got same error message [0] MPI Abort by user Aborting program ! [0] Aborting program! p0_29243: p4_error: : 0 Thanks for your kind attention. Regards, Alok - Original Message - From: "David van der Spoel" <[EMAIL PROTECTED]> To:

[gmx-users] GROMACS with MPICH on Sun Cluster

in/install/gromacs --program-suffix=_mpi make make install # Any ideas regarding what is going wrong? Please let me know if you need more information... Thank you very much in advance, regards, Alok jain ___ gmx-users mailing