normal g_fg2cg error

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12 years 10 months ago - 12 years 10 months ago #659 by Jessie Guo
g_fg2cg error was created by Jessie Guo
Hello all,

I was trying to tranverse my structure obtaied from cg simulations to a fg one by g_fg2cg. But in my output all-atom gro file, atoms with atom id larger than 12237 all have coornidates (0,0,0).

My system contains 1194 amino acids(4776 beads) and 7461 water beads.

I used g_fg2cg -pfg fg.top -pcg cg.top -c cg.gro -n 0 -wat 1

any suggestions?

Thanks in advance!

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12 years 10 months ago #660 by xavier
Replied by xavier on topic g_fg2cg error
Dear Jessie,

I suppose this is the result of the number of water molecules defined in your topology. If I remember correctly the number of water molecules to be defined in the atomistic topology is the same as the number in the CG topology.

Could you try that?

XAvier.

Jessie Guo wrote: Hello all,

I was trying to tranverse my structure obtaied from cg simulations to a fg one by g_fg2cg. But in my output all-atom gro file, atoms with atom id larger than 12237 all have coornidates (0,0,0).

My system contains 1194 amino acids(4776 beads) and 7461 water beads.

I used g_fg2cg -pfg fg.top -pcg cg.top -c cg.gro -n 0 -wat 1

any suggestions?

Thanks in advance!

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12 years 10 months ago #664 by Jessie Guo
Replied by Jessie Guo on topic g_fg2cg error
Dear XAvier,

Thanks for your quick reply. I have solved my problem. The number of water molecule in fg toplogy was the same as that in the cg toplogy. But I made a stupid mistake that I included spc.itp but fg_w.itp. I was confused how can g_fg2cg works as there's no mapping in spc.itp. Now I find the answers.

sorry to ask another question: what dose the option -wat mean?

Best regards,

Jessie

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12 years 10 months ago #665 by xavier
Replied by xavier on topic g_fg2cg error
I do not actualyl know what the -wat option stands for. Is it indicated in the g_fg2cg when -h option is on?

Jessie Guo wrote: Dear XAvier,

Thanks for your quick reply. I have solved my problem. The number of water molecule in fg toplogy was the same as that in the cg toplogy. But I made a stupid mistake that I included spc.itp but fg_w.itp. I was confused how can g_fg2cg works as there's no mapping in spc.itp. Now I find the answers.

sorry to ask another question: what dose the option -wat mean?

Best regards,

Jessie

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12 years 10 months ago #667 by Jessie Guo
Replied by Jessie Guo on topic g_fg2cg error
I found the answer. Thanks all the same.

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